<p class="jove_content">Nous remercions le Mississippi Department of Wildlife, des Pêches et des parcs (MDWFP) de soutien financier à l’aide de ressources de l’aide fédérale dans Wildlife Restoration Act (W-48-61). Nous remercions les biologistes MDWFP W. McKinley, A. Blaylock, Gary A. et L. Wilf pour leur participation active dans la collecte de données. Nous remercions également S. Tucker comme coordonnateur de l’établissement et plusieurs étudiants des cycles supérieurs et techniciens pour leur aide, collecte de données. Ce manuscrit est la contribution WFA427 du Mississippi State University Forest et Wildlife Research Center.</p>

<p>Ethics Statement: The Mississippi State University Institutional Animal Care and Use Committee approved all capture, handling, and marking techniques under protocols 04-068, 07-036, 10-033 and 13-034.</p>
<p class="jove_title">1. Establish Capture Sites, Immobilize and Transport wild White-tailed Deer</p>
<ol>
	<li><strong>Identify public and private properties that are enrolled in the Deer Management Assistance Program<sup class="xref">22</sup> and establish &#8805;29 capture sites throughout three source regions in Mississippi, USA.</strong>
	<ol>
		<li>Identify several capture locations within each source region to ensure that the range of genetic variation present in the regional population is captured.</li>
		<li>Note: Here, source regions included the Delta, which comprises almost 17% of total land area in Mississippi, USA, and is considered a high-quality soil region with agriculture as the primary land use<sup class="xref">23</sup><sup>,</sup><sup class="xref">24</sup>. All study animals were captured from this region within the distribution of <em>O. v. virginianus</em><sup class="xref">25</sup>. Other regions included the Thin Loess region (upper and lower Thin Loess combined), which comprises almost 14% of total land area in Mississippi, USA and is considered a medium quality soil region. Agriculture is also a primary land use in the Thin Loess region, though not as prevalent as in the Delta<sup class="xref">23</sup><sup>,</sup><sup class="xref">24</sup>. All study animals were captured from this region within the distribution of <em>O. v. virginianus</em><sup class="xref">21</sup>. Lastly, the Lower Coastal Plain (LCP) soil region comprises nearly 22% of Mississippi and is classified as a low quality soil region. Primary land uses in the LCP are pine timber production and livestock grazing<sup class="xref">23</sup><sup>,</sup><sup class="xref">24</sup>. The LCP also overlaps the geographical distribution of <em>O. v. osceola;</em> four of the six source populations were within 21 km of this distribution<sup class="xref">25</sup>. This subspecies was described as smaller than <em>O. v. virginianus</em><sup class="xref">26</sup>.</li>
	</ol>
	</li>
</ol>
<p class="jove_content"><img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56059/56059fig1.jpg" /><br />
<strong class="xfig">Figure 1</strong><strong>: Source Populations.</strong> Physiographic regions where pregnant dams and fawns were caught in Mississippi, USA. This figure has been modified from reference<sup class="xref">31</sup>. <a href="//cloudfront.jove.com/files/ftp_upload/56059/56059fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a></p>
<ol start="2">
	<li><strong>Select potential capture sites that meet the following criteria; habitat characteristics conducive to deer movement, proximity to roads for access, and distribution across the study area.</strong><br />
	NOTE: Capture sites must allow for concealment of the capture technician.
	<ol>
		<li>Bait sites with about 10 kg of shelled corn to entice deer to visit and evaluate use based on bait consumption and deer photographed by motion-sensitive cameras. Relocate to alternate sites if deer do not attend baited sites within 5-7 days.</li>
	</ol>
	</li>
	<li><strong>During capture events, sit in a concealed &#34;stand.&#34;</strong>
	<ol>
		<li>Place stand about 20 m downwind from the bait pile, taking the prevailing wind direction into consideration so that deer approaching the bait are less able to smell the capture technician.<br />
		NOTE: Elevated stands are strongly preferred, and safety harnesses are required. There are several variations of stands with a variety of commercial sources and use varies by personal preference. For example, a lock-on stand would include seating with a ladder for access attached to a tree with straps. Portable climbing stands can be carried in by the capture technician and allow for increased mobility as the technician can choose a specific tree once they arrive at the capture site. Portable climbing stands are limited to use in straight trees without branches up the chosen height.</li>
	</ol>
	</li>
	<li><strong>Use a dart gun coupled with a 3 cc radio-telemetry dart to deliver a mixture of teletamine HCl (4.4 mg/kg) and xylazine HCl (2.2 mg/kg).</strong>
	<ol>
		<li>Schedule capture efforts to coincide with the typical crepuscular activity cycle of deer<sup class="xref">27</sup>. Begin each capture attempt 2-3 h prior to sunset.</li>
		<li>Continue capture events for 2-3 h after sunset using night-vision goggles and a red dot laser for shot placement if deer are not captured during daylight hours.</li>
		<li>Take shots at deer when they are broadside and stationary.<br />
		NOTE: The hind quarter of the deer is the target because it has significant muscle tissue and is located away from the heart and lungs.</li>
		<li>Wait about 15 min for darted target animals (six-month-old fawns of either sex or pregnant adult females) to become fully immobilized before locating it with directional radio-telemetry equipment.</li>
		<li>Confirm individuals are sedated by checking for eye reflexes (blinking). Then apply ophthalmic ointment to the eyes and blindfold deer to reduce stress.<br />
		NOTE: Loss of thermoregulation is a consequence of immobilization.</li>
		<li>Use a rectal thermometer to assess body temperature after recovery. Warm deer with heated blankets if the animal&#39;s temperature is below 37.7 &#176;C. Cool deer with ice packs if the animal&#39;s temperature is above 40.0 &#176;C.</li>
		<li>Place deer in a sternal position on a military style gurney and transport deer from the capture location to an enclosed trailer.</li>
		<li>After placing the deer into the trailer, reverse the effects of xylazine HCl with 0.125 mg/kg yohimbine HCl<sup class="xref">28</sup>.</li>
		<li>Transport all captured deer to the desired captive facility (e.g., Mississippi State University Rusty Dawkins Memorial Deer Unit; MSU Deer Unit) and keep them separated by source region.</li>
	</ol>
	</li>
</ol>
<p class="jove_title">2. Captive Facilities and General Husbandry Practices of Research Animals</p>
<p>NOTE: The MSU Deer Unit is subdivided into five 0.4 to 0.8 ha pens.</p>
<ol>
	<li>Cover every side of each pen with shade cloth to act as a visual and physical barrier between pens. Shade cloth helps reduce injuries and provides shade during summer months.</li>
	<li>Place 1-2 elevated box blinds at one end of each pen to facilitate darting events during data collection.</li>
	<li>Place two trough style feeders at separate ends of each pen to reduce competition for food among deer. Also provide a water trough in each pen.</li>
	<li>Provide deer with a high-quality diet (20% crude protein deer pellets) <em>ad libitum</em>.<br />
	NOTE: Here, additional available forages within pens included (<em>Trifolium spp</em>) and fescue (<em>Festuca spp</em>) along with volunteer grasses and forbs.</li>
	<li>If present, maintain available forages within pens using a mixture of herbicides to control broadleaf weeds and grasses using mixture rates found on respective labels.<br />
	NOTE: Using off-campus facilities to house &#8805;5.5 month old males will likely be needed. These facilities consisted of two 0.7 ha pens on each of three properties with husbandry practices similar to the MSU Deer Unit.</li>
</ol>
<p class="jove_content"><img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/56059/56059fig2.jpg" /><br />
<strong class="xfig">Figure 2</strong><strong>: Captive Facility Locations.</strong> Study area where satellite facilities and the Mississippi State University (MSU) Deer Unit were located. Shaded areas indicate Oktibbeha (<strong>A</strong>), Noxubee (<strong>B</strong>), Attala (<strong>C</strong>), Scott (<strong>D</strong>), and Copiah (<strong>E</strong>), counties, Mississippi, USA.This figure has been modified from reference<sup class="xref">34</sup>. <a href="//cloudfront.jove.com/files/ftp_upload/56059/56059fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a></p>
<p class="jove_title">3. Parasite and Disease Control</p>
<ol>
	<li><strong>Monitor research animals for roundworm parasites (<em>Strongyloides spp</em>) using fecal floatation with parasites measured as eggs per gram (EPG).</strong>
	<ol>
		<li>If present at high levels, provide parasite control by administering a pelleted wormer (active ingredient fenbendazole) at a rate of about 0.77 kg of pelleted wormer per 22.7 kg of feed during the month of May.</li>
		<li>If parasite levels remain high after initial treatment, use an ivermectin pour-on treatment (5 mg/mL)<sup class="xref">29</sup>, mixed at a rate of 2 mL/0.45 kg and administer to animals at a rate of 0.45 kg of treated feed per 45.4 kg of animal mass.<br />
		NOTE: Epizootic hemorrhagic disease is sometimes lethal viral disease spread by a biting midge (<em>Culicoides spp</em>) during summer and fall months. If present, treat the research facility with insecticide (5% ultra-low volume insecticide) 2-3 times per week from July 1 to October 1 to decrease prevalence of the vectors among research animals. Spray this insecticide within each pen and around the perimeter of the facility about 90 min before official sunset via fogger. Preferred methods to control for parasites and diseases are unique to each captive facility. Veterinarians must be consulted during any captive wildlife research to ensure animal health and safety.</li>
	</ol>
	</li>
</ol>
<p class="jove_title">4. Data Collection</p>
<p class="jove_content"><img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/56059/56059fig3.jpg" /><br />
<strong class="xfig">Figure 3</strong><strong>: Data Collection of Newborn Fawns</strong>. Measuring hind foot length from a new born fawn at the Mississippi State University Rusty Dawkins Memorial Deer Unit in Oktibbeha County, Mississippi, USA. <a href="//cloudfront.jove.com/files/ftp_upload/56059/56059fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a></p>
<ol>
	<li><strong>Search the captive facility daily for fawns during the parturition season.</strong>
	<ol>
		<li>Uniquely mark newborn fawns with medium plastic ear tags using an ear tagger with antibiotic applied to the male end of the tag to prevent potential infection. Place ear tag about the center of the fawn&#39;s ear.</li>
		<li>Measure body mass (nearest 0.01 kg) with a digital hanging scale and measure hind foot length and total body length (nearest mm).</li>
		<li>Collect hair samples and send them to a remote site for parentage assignment (see the Table of Materials).<br />
		NOTE: Parentage assignment was made using DNA based on a proprietary, non-statistical custom structured query language database. In the pairwise allele comparison, the remote parentage assignment site assigned parentage when they excluded all but one sire and one dam based upon a shared allele from each parent at all loci tested (B. G. Cassidy, personal communication). This method of parentage assignment was also used in previous research conducted on captive white-tailed deer<sup class="xref">30</sup><sup>,</sup><sup class="xref">31</sup>.</li>
		<li>Administer 2 cc of Clostridium perfringens types C and D toxoid and Clostridium perfringens types C and D antitoxin subcutaneously and administer 0.3 cc/kg of ivermectin in propylene glycol (Mississippi State University Veterinarian School, Mississippi, USA) orally to each fawn.</li>
	</ol>
	</li>
	<li><strong>Chemically immobilize adult males (&#8805;1.5 years-old) during October and November for data collection.</strong>
	<ol>
		<li>Immobilize penned adults using the same combination of teletamine HCl and xylazine HCl used for capture of wild animals (step 1.4).</li>
		<li>During sedation events, walk the technician who will be darting to the end of the pen where the elevated blinds are located. Have a single technician in each of two blinds.</li>
		<li>Have the individual who walked the technician to the blind walk back to the opposite end of the pen.<br />
		NOTE: Deer move away from these technicians and locate themselves in front of the blinds where technicians are in position to take ethical shots on each deer.</li>
		<li>Take shots at deer when they are broadside and stationary (section 1.4).</li>
		<li>Wait about 15 min for darted animals to become fully immobilized before approaching it.</li>
		<li>Confirm individuals are sedated by checking for eye reflexes (blinking). Apply ophthalmic ointment to the eyes and blindfold deer to reduce stress.</li>
		<li>After the darters successfully sedate an individual deer, monitor the deer&#39;s vital rates.
		<ol>
			<li>Use a rectal thermometer to assess body temperature after recovery. Warm deer with heated blankets if the animal&#39;s temperature is below 37.7 &#176;C. Cool deer with ice packs if the animal&#39;s temperature is above 40.0 &#176;C.</li>
		</ol>
		</li>
		<li>Load the deer on a military-style gurney, and transport it via utility task vehicle to a predetermined data collection area.</li>
		<li>Once transported, record the same morphometric measurements recorded at birth (step 4.1).
		<ol>
			<li>Measure body mass (nearest 0.01 kg) with a digital hanging scale and measure hind foot length and total body length (nearest mm).<br />
			NOTE: Individual deer react differently to the combination of drugs used during sedation events so administer about 0.1-0.3 cc of the teletamine HCl and xylazine HCl mixture (depending on body mass of an individual deer) if an individual comes out of sedation before data collection is completed.</li>
		</ol>
		</li>
		<li>Administer size-appropriate amounts of antibiotic, ivermectin, a clostidrial vaccine, and a leptospirosis vaccine to all deer after they are transported to the data collection area (see sections 1 and 3).</li>
	</ol>
	</li>
	<li><strong>Take three antler measurements from adult males using an antler measuring tape while the animal is sedated.</strong>
	<ol>
		<li>Measure the inside spread (widest distance between main beams), basal circumference (smallest diameter located between the burr and G1 tine), and main beam length (distance from antler base to the tip of the main beam) of antlers prior to antler removal.</li>
		<li>Remove antlers about 3 cm above the burr using a reciprocating saw. Do not remove antlers less than 3 cm.</li>
	</ol>
	</li>
</ol>
<p class="jove_content"><img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/56059/56059fig4.jpg" /><br />
<strong class="xfig">Figure 4</strong><strong>: Data Collection of Adult Males.</strong> Antler removal via reciprocating saw from a captive adult male white-tailed deer. <a href="//cloudfront.jove.com/files/ftp_upload/56059/56059fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a></p>
<ol start="4">
	<li>After all data is collected from the sedated individual, place the deer into the appropriate pen and administer either 0.125 mg/kg yohimbine HCl<sup class="xref">28</sup> or 4.0 mg/kg tolazoline HCl<sup class="xref">32</sup> to reverse the effects of xylazine HCl. Monitor individuals to ensure they remain in a sternal position until they come out of sedation and are fully alert.<br />
	NOTE: If complications occur and animals must be euthanized, then euthanasia by cerebral dislocation via bolt stunner and severing of the jugular vein are ethical means to dispatch the animal.</li>
	<li><strong>Bring the antlers to a designated area to finish measuring antler size.</strong>
	<ol>
		<li>Measure each individual tine protruding from the main beam (G1, G2, G3, <em>etc.</em>) and additional abnormal points by aid of wire.<br />
		NOTE: Points that do not have a matching counterpart on the opposite main beam or are not consistent with the definition of a typical antler set are defined by the Boone and Crockett Club<sup class="xref">33</sup>.</li>
		<li>Wrap the wire around where the tine intersects the main beam and mark that point for reference.</li>
		<li>Measure from this reference point to the tip of the tine and repeat for each tine.</li>
		<li>Collect remaining circumference measurements by identifying the smallest point between the G1 and G2 tines (H2 circumference), the G2 and G3 tines (H3 circumference), and the G3 and G4 tine if present (H4 circumference).</li>
		<li>If the G4 tine is not present, measure the distance between the midpoint of the G3 tine and the end of the main beam and measure the H4 circumference at the midway point.</li>
		<li>Measure less than four circumferences when antlers contain less than three tines.<br />
		NOTE: For example, a main beam with two typical points include only three circumference measurements. Individuals may use other guidelines (Safari Club International) for calculating antler size; however, consistent methods must be used for each animal for valid comparison.</li>
		<li>After making all measurements, calculate an antler score similar to the gross nontypical Boone and Crockett score<sup class="xref">33</sup>.</li>
		<li>Weigh antlers to the nearest 0.1 g using a scientific digital scale and assign a minimal critical antler mass of 1 g for first-year animals with antlers shorter than 3 cm.</li>
	</ol>
	</li>
	<li><strong>Chemically immobilize penned juveniles at approximately 5.5 months of age using the same methods for adults (section 4.2) and mark juveniles with a large plastic ear tag (step 4.1.1).</strong>
	<ol>
		<li>Use the same drug mixture rates to immobilize captive adults as used for immobilizing wild deer (section 1).</li>
		<li>Collect the same measurements collected at birth (step 4.1.2) and administer the same prophylactics as adults (section 4.2).<br />
		NOTE: After all data is collected, transport each juvenile male to its randomly assigned satellite facility via trailer.</li>
	</ol>
	</li>
</ol>
<p class="jove_title">5. Producing First- and Second-generation Offspring</p>
<ol>
	<li>Classify six-month-old wild-caught fawns and offspring born at the captive facility from wild-caught mothers as first-generation individuals.</li>
	<li><strong>During the breeding season, place two males with 7-16 females for an average breeding sex ratio of one male to eight females.</strong><br />
	NOTE: Select breeding males from satellite facilities based on physical appearance, because the healthiest males (largest antlers and body size) are most likely to service females for the entirety of the breeding season without suffering from injury due to the aggressive nature of males during the breeding season.
	<ol>
		<li>Only allow deer to breed with other individuals from the same source region (<strong>e.g.</strong>, Delta males breed Delta females, Thin Loess males breed Thin Loess females, and LCP males breed LCP males).</li>
	</ol>
	</li>
	<li>Classify deer conceived by first-generation parents as second-generation offspring. Raise these individuals in captivity from birth and feed the same high-quality diet as their parents.<br />
	NOTE: Females may produce offspring multiple years but typically with different sires each year. Collect the same data on second-generation offspring as collected on first-generation and wild-caught individuals.</li>
</ol>

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A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Variable+breeding+dates+among+populations+of+white-tailed+deer+in+the+southern+United+States:+The+legacy+of+restocking.">Variable breeding dates among populations of white-tailed deer in the southern United States: The legacy of restocking.</a> <em style='font-style: italic'>J Wildl Manage</em>. <b>79</b> (8), 1213-1225 (2015).</li><li>Mech, D. L., Nelson, M. E., McRoberts, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+maternal+and+grandmaternal+nutrition+on+deer+mass+and+vulnerability+to+wolf+predation.">Effects of maternal and grandmaternal nutrition on deer mass and vulnerability to wolf predation.</a> <em style='font-style: italic'>J Mammal</em>. <b>72</b> (1), 146-151 (1991).</li><li>Therrien, J. F., C&#242;t&#234;, S., Festa-Bianchet, D. M., Ouellet, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maternal+care+in+white-tailed+deer:+trade-off+between+maintenance+and+reproduction+under+food+restriction.">Maternal care in white-tailed deer: trade-off between maintenance and reproduction under food restriction.</a> <em style='font-style: italic'>Anim Behav</em>. <b>75</b> (1), 235-243 (2008).</li><li>Parker, K. L., Barboza, P. S., Gillingham, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nutrition+integrates+environmental+responses+of+ungulates.">Nutrition integrates environmental responses of ungulates.</a> <em style='font-style: italic'>Funct Ecol</em>. <b>23</b> (1), 57-69 (2009).</li><li>Monteith, K. L., Schmitz, L. E., Jenks, J. A., Delger, J. A., Bowyer, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+of+male+white-tailed+deer:+consequences+of+maternal+effects.">Growth of male white-tailed deer: consequences of maternal effects.</a> <em style='font-style: italic'>J Mammal</em>. <b>90</b> (3), 651-660 (2009).</li><li>Tollefson, T. N., Shipley, L. A., Myers, W. L., Keisler, D. H., Nairanjana, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+summer+and+autumn+nutrition+on+body+condition+and+reproduction+in+lactating+mule+deer.">Influence of summer and autumn nutrition on body condition and reproduction in lactating mule deer.</a> <em style='font-style: italic'>J Wildl Manage</em>. <b>74</b> (5), 974-986 (2010).</li><li>Guynn, D. C., Mott, S. P., Cotton, W. D., Jacobson, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cooperative+management+of+white-tailed+deer+on+private+lands+in+Mississippi.">Cooperative management of white-tailed deer on private lands in Mississippi.</a> <em style='font-style: italic'>Wildl Soc Bull</em>. <b>11</b> (3), 211-214 (1983).</li><li>Pettry, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soil+resource+areas+of+Mississippi.">Soil resource areas of Mississippi.</a> <em style='font-style: italic'>Mississippi Agricultural and Forestry Experiment Station</em>. , (1977).</li><li>Snipes, C. E., Nichols, S. P., Poston, D. H., Walker, T. W., Evans, L. P., Robinson, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+agricultural+practices+of+the+Mississippi+Delta.">Current agricultural practices of the Mississippi Delta.</a> <em style='font-style: italic'>Office of Agricultural Communications</em>. , (2005).</li><li>Baker, R. H., Halls, L. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Origin,+classification,+and+distribution+of+the+white-tailed+deer.">Origin, classification, and distribution of the white-tailed deer.</a> <em style='font-style: italic'>White-tailed deer: ecology and management</em>. , 1-18 (1984).</li><li>Barbour, T., Allen, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+white-tailed+deer+of+eastern+United+States).">The white-tailed deer of eastern United States).</a> <em style='font-style: italic'>J Mammal</em>. <b>3</b> (2), 65-80 (1922).</li><li>Rouleau, I., Cr&#234;te, M., Ouellet, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Contrasting+the+summer+ecology+of+white-taileddeer+inhabiting+a+forested+and+an+agricultural+landscape.">Contrasting the summer ecology of white-taileddeer inhabiting a forested and an agricultural landscape.</a> <em style='font-style: italic'>Ecoscience</em>. <b>9</b> (4), 459-469 (2002).</li><li>Kreeger, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> <em style='font-style: italic'>Handbook of wildlife chemical immobilization</em>. , (1996).</li><li>Pound, J. M., Miller, J. A., Oethler, D. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Depletion+rates+of+injected+and+ingested+Ivermectin+from+blood+serum+of+penned+white-tailed+deer,+Odocoileus+virginianus+(Zimmermann)+(Artiodactyla:+Cervidae).">Depletion rates of injected and ingested Ivermectin from blood serum of penned white-tailed deer, Odocoileus virginianus (Zimmermann) (Artiodactyla: Cervidae).</a> <em style='font-style: italic'>J Medl Entomol</em>. <b>41</b> (1), 65-68 (2004).</li><li>Jones, P. D., Demarais, S., Strickland, B. K., DeYoung, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inconsistent+relation+of+male+body+mass+with+breeding+success+in+captive+white-tailed+deer.">Inconsistent relation of male body mass with breeding success in captive white-tailed deer.</a> <em style='font-style: italic'>J Mammal</em>. <b>92</b> (3), 527-533 (2011).</li><li>Michel, E. S., Flinn, E. B., Demarais, S., Strickland, B. K., Wang, G., Dacus, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+nutrition+cues+switch+from+efficiency+to+luxury+phenotypes+for+a+long-lived+ungulate.">Improved nutrition cues switch from efficiency to luxury phenotypes for a long-lived ungulate.</a> <em style='font-style: italic'>Ecol Evol</em>. <b>6</b> (20), 7276-7285 (2016).</li><li>Miller, B. F., Muller, L. I., Doherty, T., Osborn, D. A., Miller, K. V., Warren, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effectiveness+of+antagonists+for+tiletamine-zolazepam/xylazine+immobilization+in+female+white-tailed+deer.">Effectiveness of antagonists for tiletamine-zolazepam/xylazine immobilization in female white-tailed deer.</a> <em style='font-style: italic'>J Wildl Dis</em>. <b>40</b> (3), 533-537 (2004).</li><li>Nesbitt, W. H., Wright, P. L., Buckner, E. L., Byers, C. R., Reneau, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> <em style='font-style: italic'>Measuring and scoring North American big game trophies. 3rd edn</em>. , (2009).</li><li>Michel, E. S., Demarais, S., Strickland, B. K., Smith, T., Dacus, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antler+characteristics+are+highly+heritable+but+influenced+by+maternal+factors.">Antler characteristics are highly heritable but influenced by maternal factors.</a> <em style='font-style: italic'>J Wildl Manage</em>. <b>80</b> (8), 1420-1426 (2016).</li><li>Severinghaus, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tooth+development+and+wear+as+criteria+of+age+in+white-tailed+deer.">Tooth development and wear as criteria of age in white-tailed deer.</a> <em style='font-style: italic'>J Wildl Manage</em>. <b>13</b> (2), 195-216 (1949).</li><li>Gee, K. L., Webb, S. L., Holman, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accuracy+and+implications+of+visually+estimating+age+of+male+white-tailed+deer+using+physical+characteristics+from+photographs.">Accuracy and implications of visually estimating age of male white-tailed deer using physical characteristics from photographs.</a> <em style='font-style: italic'>Wild Soc Bull</em>. <b>38</b>, 96-102 (2014).</li><li>Storm, D. J., Samuel, M. D., Rolley, R. E., Beissel, T., Richards, B. J., Van Deelen, T. 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<p class="jove_content">Les auteurs n’ont rien à divulguer.</p>

<p class="jove_content">Il y a plusieurs étapes associées à notre protocole ; Cependant, il y a quatre étapes essentielles qui doivent être prises pour assurer le succès avec ce protocole. Tout d’abord, lors de la capture de cervidés sauvages, il doit y avoir plusieurs lieux de capture dans toute une région source unique (étape 1.1.1). Ayant plusieurs sites de capture s’assure que toute variabilité génétique associée à la région source est représentée parmi les cerfs. Deuxièmement, cerf doit demeurer séparés par région...

<p class="jove_content">Des facteurs environnementaux, qu'une mère éprouve pendant la gestation et de lactation peuvent influencer phénotype de sa progéniture, indépendante du génotype<sup class="xref">1</sup><sup>,</sup><sup class="xref">2</sup><sup>,</sup><sup class="xref">3</sup>. Les mères qui vivent dans des environnements de haute qualité susceptibles produira progéniture qui présentent un phénotype de luxe (grand andouiller et corps taille<sup class="xref">4</sup>), tandis que les mères qui vivent dans un environnement de faible qualité peuvent produire une progéniture qui présentent un phénotype d’efficacité (petit andouiller et corps taille<sup class="xref">4</sup>). Par conséquent, persiste dans un environnement de qualité peut permettre à une mère de produire une descendance mâle avec grands caractères phénotypiques, qui peuvent influer directement sur reproduction possibilités<sup class="xref">5</sup><sup>,</sup><sup class="xref">6</sup><sup>,</sup><sup class="xref">7</sup><sup>,</sup><sup class="xref">8 de la descendance</sup> et influencer indirectement aptitude inclusive de la mère.</p>
<p class="jove_content">Bien que la nutrition influence directement les caractéristiques phénotypiques taxons (<em>Ursus americanus</em>, <em>Ursus arctos</em><sup class="xref">9</sup>; <em>Liasis fuscusI</em> <sup class="xref">10</sup>; <em>Larus michahellis</em> ( <sup class="xref">11</sup>), plusieurs facteurs peuvent affecter les phénotypes de cerfs de Virginie dans le Mississippi, USA. Taille de cartilage de wapiti pur et le corps sont environ un tiers plus grande pour certaines populations par rapport aux autres<sup class="xref">12</sup>. Cette variation est fortement corrélée avec le fourrage qualité<sup class="xref">13</sup><sup>,</sup><sup class="xref">14</sup>; les plus grands mâles sont trouvent dans des zones à la plus grande qualité du fourrage. Toutefois, des efforts de restauration historique du cerf de Virginie dans le Mississippi peuvent ont conduit à des goulets d’étranglement génétiques et/ou fondateur effets<sup class="xref">15</sup><sup>,</sup><sup class="xref">16</sup>, qui peuvent partiellement expliquer une partie de la variation régionale dans le phénotype de cerfs de Virginie.</p>
<p class="jove_content">Nous fournissons le protocole que nous permettant de contrôler la qualité nutritionnelle des sauvages le cerf de Virginie, qui nous a permis de déterminer si le phénotype mâle est limitée par la population au niveau génétique. Ce protocole nous a également permis de déterminer si les effets maternels du retard étaient présents dans nos populations. Notre modèle contrôlé est préférentiel à des études menées sur les populations allant gratuites qui sont limitées à l’utilisation de variables environnementales en tant que proxy pour les restrictions alimentaires<sup class="xref">3</sup><sup>,</sup><sup class="xref">17</sup>. Notre modèle contrôlé permet également pour d’autres variables comme potentiel chronique stress liés à social interactions qui doit se tenir constamment que tous les individus sont soumis à un logement similaire et des pratiques d’élevage. En outre, parce que la nutrition influe directement sur les autres aspects de l’histoire de la vie variant entre reproduction et survie<sup class="xref">18</sup><sup>,</sup><sup class="xref">19</sup>, contrôler la nutrition permet aux chercheurs d’évaluer d’autres variables qui influent sur les aspects de l’histoire de vie chez les mammifères. Des protocoles comparables ont été décrites pour évaluer les questions liées aux aspects d’histoire de vie pour les autres ongulés en Amérique du Nord (<em>p. ex.</em>, <sup class="xref">20</sup><sup>,</sup><sup class="xref">21</sup>).</p>

<table><tbody><tr><td>Shelled Corn</td><td></td><td></td><td></td></tr><tr><td>Elevated Stand</td><td></td><td></td><td></td></tr><tr><td>Safety Harness</td><td></td><td></td><td></td></tr><tr><td>Ground Blind</td><td></td><td></td><td></td></tr><tr><td>Model 196 Projector</td><td>Pneu-Dart, Pennsylvania, USA</td><td></td><td></td></tr><tr><td>3cc Radio-Telemetry Darts</td><td>(Pneu-Dart, Pennsylvania, USA)</td><td></td><td></td></tr><tr><td>Various Sized Darts&amp;nbsp;</td><td>(Pneu-Dart, Pennsylvania, USA)</td><td></td><td></td></tr><tr><td>Teletamine HCl&amp;nbsp;</td><td>(Telazol, Fort Dodge Animal Health, Iowa, USA)</td><td></td><td></td></tr><tr><td>Xylazine HCl&amp;nbsp;</td><td>(West Texas Rx Pharmacy, Amarillo, Texas, USA)</td><td></td><td></td></tr><tr><td>Yhoimbine HCl</td><td></td><td></td><td></td></tr><tr><td>Tolazoline HCl</td><td></td><td></td><td></td></tr><tr><td>Military Style Gurney</td><td></td><td></td><td></td></tr><tr><td>Rectal Thermometer</td><td></td><td></td><td></td></tr><tr><td>Shade Cloth</td><td></td><td></td><td></td></tr><tr><td>20% Crude Protein Deer Pellets&amp;nbsp;</td><td>(Purina AntlerMax Professional High Energy Breeder 59UB, Purina, Missouri, USA)</td><td></td><td></td></tr><tr><td>Trough Style Feeders</td><td></td><td></td><td></td></tr><tr><td>Commercial Clover&amp;nbsp;</td><td>(Durana Clover, Pennington Seed Co., Georgia, USA)</td><td></td><td></td></tr><tr><td>Commercial Fescue&amp;nbsp;</td><td>(Max-Q Fescue, Pennington Seed Co., Georgia, USA)</td><td></td><td></td></tr><tr><td>Blankets</td><td></td><td></td><td></td></tr><tr><td>Ice Packs</td><td></td><td></td><td></td></tr><tr><td>Broadleaf Weed Control (2, 4-DB Herbacide, Butyrac 200)</td><td></td><td></td><td></td></tr><tr><td>Grass Control&amp;nbsp;</td><td>(Poast Herbacide, BASF Co.)</td><td></td><td></td></tr><tr><td>Pelleted Wormer</td><td>Safeguard Co.,&amp;nbsp;</td><td></td><td>active ingredient fenbendazole</td></tr><tr><td>Parasite Pour-on Treatment&amp;nbsp;</td><td>(Ivomec, Merial Co.)</td><td></td><td></td></tr><tr><td>Insecticide</td><td>Riptide, McLaughlin Gormley King Co.)&amp;nbsp;</td><td></td><td></td></tr><tr><td>Medium and Large Plastic Ear Tags&amp;nbsp;</td><td>(Allflex, Texas, USA)</td><td></td><td></td></tr><tr><td>Remote site that assigned parentage</td><td>DNA Solutions Animal Solutions Manager (DNA Solutions, Oklahoma, USA)</td><td></td><td></td></tr><tr><td>Digital Hanging Scale&amp;nbsp;</td><td>(Moultrie, EBSCO Industries, Inc.)&amp;nbsp;</td><td></td><td></td></tr><tr><td>Tape Measure</td><td></td><td></td><td></td></tr><tr><td>Clostridium Perfringens Types C and D Toxoid Essential 3&amp;nbsp;</td><td>(Colorado Serum Co.)</td><td></td><td></td></tr><tr><td>Clostridium Perfringens Types C and D Antitoxin Equine Origin</td><td>(Colorado Serum Co.)</td><td></td><td></td></tr><tr><td>Ivermectin in propylene glycol</td><td></td><td></td><td></td></tr><tr><td>Antibiotic</td><td>(Nuflor, Schuering-Plough Animal Health Corp., New Jersey, USA)</td><td></td><td></td></tr><tr><td>Ivermectin&amp;nbsp;</td><td>(Norbrook Labratories, LTD., Down, Northern Ireland, UK)</td><td></td><td></td></tr><tr><td>Clostidrial vaccine</td><td>(Vision 7 with SPUR, Ivesco LLC, Iowa, USA)</td><td></td><td></td></tr><tr><td>Leptospirosis vaccine&amp;nbsp;</td><td>(Leptoferm-5, Pfizer, Inc., New York, USA)</td><td></td><td></td></tr><tr><td>Trailer for transport</td><td></td><td></td><td></td></tr><tr><td>Reciprocating saw&amp;nbsp;</td><td>(DEWALT, Maryland, USA)</td><td></td><td></td></tr><tr><td>Scientific Digital Scale&amp;nbsp;</td><td>(Global Industrail, Global Equipment Company Inc)</td><td></td><td></td></tr><tr><td>Antler Measuring Tape</td><td></td><td></td><td></td></tr><tr><td>Fogger</td><td></td><td></td><td></td></tr><tr><td>Plastic Ear Tags&amp;nbsp;</td><td>(Allflex, Texas, USA)</td><td></td><td></td></tr><tr><td>Plastic Ear Tagger</td><td>(Allflex, Texas, USA)</td><td></td><td></td></tr></tbody></table>

protocol for assessing the relative effects of environment and genetics on antler and body growth for a long-lived cervid

<p class="jove_content">Cervidés phénotype peut être placé dans l’une des deux catégories : efficacité, ce qui favorise la survie au cours de la croissance extravagante morphométriques et luxe, qui favorise la croissance de la taille de corps et d’armes. Les populations d’une même espèce présentent chaque phénotype selon les conditions environnementales. Bien qu’andouiller et la taille corporelle des mâles le cerf de Virginie (<em>Odocoileus virginianus</em>) varie selon la région physiographique dans le Mississippi, USA et est fortement corrélée avec des variations régionales en qualité nutritionnelle, les effets de la génétique au niveau des populations de stocks indigènes et des efforts antérieurs de re-stockage non négligeable. Ce protocole décrit comment nous avons conçu une étude contrôlée, où les autres facteurs qui influent sur le phénotype, comme l’âge et de la nutrition, sont contrôlés. Nous avons apporté des sauvages les femelles gravides et faons de six mois dans trois régions physiographiques distinctes dans le Mississippi, USA à l’unité de cerf Mississippi State University Rusty Dawkins Memorial. Cerf de la même région ont été élevés pour produire une seconde génération de descendants, nous permettant d’évaluer les réponses générationnelles et effets maternels. Tous les cerfs mangeaient la même qualité (pastille de cerf 20 % protéines brutes) alimentation <em>ad libitum</em>. Unique, nous avons marqué chaque nouveau-né et enregistré corps masse, arrière pied et longueur totale du corps. Chaque chute, nous sous sédation particuliers via injection distante et échantillonné les mêmes morphométrie plus bois d’adultes. Nous avons trouvé que tous morphométrie a augmenté dans la taille de la première à la deuxième génération, avec pleine compensation de la taille (variation régionale n’est plus présente) et une compensation partielle de la masse corporelle (des preuves d’une variation régionale) évidente dans la deuxième génération. Deuxième génération les hommes qui proviennent de notre région la plus pauvre qualité du sol affichée sur une augmentation de 40 % dans la taille et sur une augmentation de 25 % en masse par rapport à leurs homologues sauvages récoltées. Nos résultats indiquent la variation phénotypique de sauvage mâle le cerf de Virginie dans le Mississippi sont plus liés à des différences de qualité nutritionnelle que la génétique au niveau des populations.</p>

<p class="jove_content" fo:keep-together.within-page="1">Âge des individus, qualité nutritionnelle et la génétique influence cerf mâle phénotype. Notre conception de l’étude nous a permis de contrôler la qualité du cerf nutrition consommaient et nous a permis d’identifier l’âge de chaque cerf des comparaisons valables dans les classes d’âge. En contrôlant la nutrition et l’âge avec notre conception de l’étude, nous pouvions mieux comprendre si la génétique au niveau des populations ont été limitant le phénotype de...

Watch this Scientific Journal Video about Protocol for Assessing the Relative Effects of Environment and Genetics on Antler and Body Growth for a Long-lived Cervid at JoVE.com

Protocole d'évaluation des effets relatifs de l'environnement et de la génétique sur la croissance des bois et du corps d'un cervidé à longue durée de vie | Environnement | Vidéo

Protocol for Assessing the Relative Effects of Environment and Genetics on Antler and Body Growth for a Long-lived Cervid

Protocole pour évaluer les effets relatifs de l’environnement et de la génétique sur le cartilage de wapiti pur et la croissance du corps pour une longue durée de vie de cervidés

<p class="jove_content">Différences phénotypiques entre les populations de cervidés peuvent être liés à la génétique au niveau des populations ou de nutrition ; discerner qui est difficile à l’état sauvage. Ce protocole décrit comment nous avons conçu une étude contrôlée où la variation nutritionnelle a été éliminée. Nous avons constaté que la variation phénotypique du cerf mâle était plus limitée par nutrition que génétique.</p>

Cervid phenotype can be placed into one of two categories: efficiency, which promotes survival over extravagant morphometric growth, and luxury, which ...

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Molecular Biology

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Evolution

Unit 2

Population Genetics

Mendelian Genetics

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7.3K vues.  Mississippi State University. Différences phénotypiques entre les populations de cervidés peuvent être liés à la génétique au niveau des populations ou de nutrition ; discerner qui est difficile à l’état sauvage. Ce protocole décrit comment nous avons conçu une étude contrôlée où la variation nutritionnelle a été éliminée. Nous avons constaté que la variation phénotypique du cerf mâle était plus limitée par nutrition que génétique.

Vidéo: Protocol for Assessing the Relative Effects of Environment and Genetics on Antler and Body Growth for a Long-lived Cervid

Natural Selection

<h4>Fitness</h4>
<p>Widespread variation of phenotypes in natural populations provides the raw material for evolution, which is the change in the inherited traits of populations over successive generations. Natural selection is one of the main mechanisms of evolution and requires variable traits to be heritable and associated with differential survival and/or reproductive success. Phenotypes that correlate with greater success will have more offspring that survive to reproduce in the next generation, and will thus be represented at greater levels in each successive generation.</p>
<p>The reproductive success of an organism relative to others is known as its fitness and any heritable trait that contributes to an organism&#39;s fitness is known as an adaptation. Therefore, individuals or phenotypes with higher lifetime reproductive success are considered to be more fit and better adapted to their environment.</p>
<p>An example of differential fitness comes from the snowshoe hare, which is brown in summer but grows a white coat in winter to camouflage in snow. Nonetheless, hares that maintain their brown summer coats throughout the year would be at a fitness disadvantage due to their relatively higher visibility to predators. Therefore, higher predator visibility would decrease the survival rate of the brown coat phenotype relative to the white coat phenotype, consequently reducing its lifetime reproductive success. Climate change, however, threatens organisms that fail to adapt to conditions, thus researchers have been studying how snowshoe hares are coping with warmer temperatures and decreased snow cover in winter. Snowshoe hares that grow a white coat in environments with diminished snow cover become more visible to predators, which reduces their reproductive success. Researchers have found that snowshoe hares did not alter their behavior to adapt to mismatch in their camouflage<sup>1</sup> and mismatched hares experienced significant decreases in their survival rates<sup>2</sup>.</p>
<p>Calculation of fitness relies on the relative survival and reproductive rates of different phenotypes in a population. For a given phenotype, survival rate is the proportion of that phenotype surviving, and reproductive rate is the average offspring produced per individual. The ratio between the products of the survival and reproductive rates for the different phenotypes is known as relative fitness (<em>w</em>). Hence, to calculate <em>w</em> for each phenotype (or trait), first the multiplication product of the survival and reproductive rates are calculated for individual phenotypes, this is then divided by the highest product value amongst them.</p>
<p><em>w</em> = (<em>Survival<sub>A</sub></em> x <em>Reproduction<sub>A</sub></em>) / (<em>Survival<sub>max</sub></em> x <em>Reproduction<sub>max</sub></em>)</p>
<p>This equation can be used in turn to calculate the strength of selection on different phenotypes, or the selection coefficient (<em>s</em>), by subtracting <em>w</em> from 1. Therefore, the value of the selection coefficient ranges between 0 and 1; the lower the value, the higher the selection against the specific trait. Thus, a phenotype that has a maximum fitness of 1.0, will be experiencing no selection.</p>
<p><em>s</em> = 1 &#8211; <em>w</em></p>
<h4>Selection</h4>
<p>There are three main types of selections: directional, stabilizing, and disruptive. Directional selection favors extreme values of a trait in one direction and can be induced by a change in the environment that the population needs to adapt to. One example is the evolution of differential jaw structures of East African cichlid fish in accordance with the diet source<sup>3</sup>. Stabilizing selection holds a trait at an optimum value; it is generally assumed that any deviation from this optimum is disadvantageous. For example, human fetus size is subject to stabilizing selection; babies born too small are less likely to survive and babies that are too big cannot pass through the birth canal during natural birth<sup>4</sup>. Disruptive selection favors two different extremes of a phenotype, creating a bimodal distribution. The evolution of West African seedcracker finch beaks resulted in two common phenotypes, large beaks that easily break hard sedge seeds and small beaks for soft seeds. Finches with medium beaks are not particularly good at consuming either seed type, thus are selected against<sup>5</sup>.</p>
<p>One of the most important ways natural selection impacts the lives of humans is through the rise of antibiotic resistant bacterial strains in hospitals and due to agricultural practices which utilize significant amounts of antibiotics<sup>6</sup>. The phenomenon of antibiotic resistance is a sort of inadvertent form of natural selection imposed by humans.</p>
<p>A question moving forward is whether natural populations will be able to adapt to the effects of climate change quickly enough to avoid extinction. This is dependent not only on existing variation in populations, but also on the strength of selection being high enough to affect quick change in the population. In this regard, reduced population sizes of many species around the world are of special concern.</p>
<h4>References</h4>
<ol class="references">
	<li><strong>Marketa Zimova, L. Scott Mills, Paul M. Lukacs, Michael S. Mitchell.</strong> Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage. <em>Proc of the Royal Society. </em>2014, Vol. 281, 1782.</li>
	<li><strong>Nowak, Marketa Zimova L. Scott Mills J. Joshua.</strong> High fitness costs of climate change-induced camouflage mismatch. <em>Ecology Letters. </em>2016, Vol. 19, 3 (299-307).</li>
	<li><strong>R. Craig Albertson, J. Todd Streelman, and Thomas D. Kocher.</strong> Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. <em>PNAS. </em>2003, Vol. 100, (9) 5252-7.</li>
	<li><strong>Susan E. Hiby, Richard Apps, Olympe Chazara, Lydia E. Farrell, Per Magnus, Lill Trogstad, H&#229;kon K. Gjessing, Mary Carrington and Ashley Moffett.</strong> Maternal KIR in Combination with Paternal HLA-C2 Regulate Human Birth Weight. <em>J. Immunology. </em>2014, Vol. 192, (11) 5069-73.</li>
	<li><strong>Clabaut C, Herrel A, Sanger TJ, Smith TB, Abzhanov A.</strong> Development of beak polymorphism in the African seedcracker, Pyrenestes ostrinus. <em>Evol Dev. </em>2009, Vol. 11, (6) 636-46.</li>
	<li><strong>Witte, Wolfgang.</strong> Medical Consequences of Antibiotic Use in Agriculture. <em>Science. </em>1998, Vol. 279, (5353) 996-7.</li>
</ol>

Natural Selection: Calculating Fitness and Selection - Concept

Sélection naturelle

Fitness
Widespread variation of phenotypes in natural populations provides the raw material for evolution, which is the change in the inherited traits of ...

Enseignement

JoVE Lab Manual

Biologie

Artificial Selection

<h4>Natural Selection and Adaptive Evolution</h4>
<p>In natural settings, adaptive evolution takes place by natural selection, a process in which differences in traits lead to differences in survival and reproductive success between individuals. This happens because individuals with certain phenotypes have a higher probability of survival and/or produce more surviving offspring than individuals with other phenotypes. <br />
A classic example of this was demonstrated by Rosemary and Peter Grant studying the population of Medium Ground Finches on Daphne Major Island, in the Galapagos archipelago<sup>1</sup>. In the late 1970&#8217;s, the islands experienced a drought during which few plants flowered and produced seeds. The birds were forced to survive on large, thick shelled seeds left over from previous years.  Of the population, only the birds with larger beaks could harvest efficiently. As a consequence, birds with small beaks died; the few birds that survived were larger and had thicker, stronger bills. These differences in bill size were genetic, and therefore heritable, so the offspring produced the following year had, on average, larger bill and body sizes than had been present in the population before the drought.  Interestingly, 8 years later there was particularly high rainfall, resulting in a resurgence of small seed producing plants.  The small beaked finches were observed to be more abundant in subsequent years.  Indeed, over the past 5 decades, this finch population has oscillated in accordance with the food type available<sup>1,2</sup>.<br />
More generally, natural selection leads to evolution of populations, because populations contain genetic variation that results in expression of different phenotypes. In the case of the finches, the birds present in the population before the drought varied in bill size and these differences in turn affected the size of seeds each individual was best able to eat. Without such variation, evolution cannot happen because there is no variation for selection to act upon.</p>
<h4>Artificial Selection and Domestication of Plants and Animals</h4>
<p>Humans have taken advantage of natural variation to create a wide variety of domesticated plants and animals through artificial selection, also known as selective breeding. In this case, humans cause selection because they select which phenotypes of animal will breed to produce the next generation. Artificial selection has been used for much of human history to produce crops and animals that are more efficient or have desirable traits, such as plants that produce larger fruits and vegetables, or cows that produce more milk.<br />
If selection is applied consistently for many generations, it is possible to produce an organism that hardly resembles the one it originated from. Dogs as diverse as Chihuahuas and Great Danes were derived from gray wolves in a few thousand years. This rate of change tells us that much of the genetic variation necessary to produce these domestic breeds was present in the population of wolves originally descended from.  Researchers are studying the genetics of modern breeds of dogs to determine what genetic elements differ between them that might be correlated with their obvious differences in appearance and even behavior.  This may then serve as a good model for understanding human genetic diversity<sup>3</sup>.<br />
Artificial selection in plants can clearly be seen in the diversity of cruciferous vegetable crops derived from <em>Brassica olaracea</em>, a large leafy plant native to coastal southern and Western Europe. It has been bred by human populations in multiple locations, over hundreds of years, to produce an estimated 400 different vegetables, such as turnips, cabbage, kale, broccoli, cauliflower, and Brussels sprouts<sup>4</sup>.<br />
Researchers, as well as farmers, have taken advantage of another species in the same genus, <em>B. rapus</em>, a subspecies of which has been bred to have an extremely short life cycle of about one month. This variety is known as &#8220;Wisconsin Fast Plants,&#8221; <sup>5</sup> and is used as a model organism in research and education. <em>B. rapus</em> germinates in a few days, produces flowers after two weeks, and produces viable seeds by the end of four weeks. The plant generally dies at the end of this cycle.</p>
<h4>References:</h4>
<ol class="references">
	<li>Rosemary B. Grant, Peter R. Grant; What Darwin&#39;s Finches Can Teach Us about the Evolutionary Origin and Regulation of Biodiversity, BioScience, Volume 53, Issue 10, 1 October 2003, Pages 965&#8211;975, https://doi.org/10.1641/0006-3568(2003)053[0965:WDFCTU]2.0.CO;2</li>
	<li>Weiner, Jonathan. The Beak of the Finch. Penguin Random House. May 30, 1995 | 352 Pages</li>
	<li>Wayne RK1, Ostrander EA. Lessons learned from the dog genome. Trends Genet. 2007 Nov;23(11):557-67. Epub 2007 Oct 25. PMID: 17963975 DOI: 10.1016/j.tig.2007.08.013</li>
	<li>J.W. Fahey, BRASSICAS, Editor(s): Benjamin Caballero, Encyclopedia of Food Sciences and Nutrition (Second Edition), Academic Press, 2003, Pages 606-615, ISBN 9780122270550, https://doi.org/10.1016/B0-12-227055-X/00118-8. (http://www.sciencedirect.com/science/article/pii/B012227055X001188)</li>
	<li><a target="__blank" href="https://fastplants.org">https://fastplants.org/</a> Retrieved August 21, 2018</li>
</ol>

Artificial Selection: Visualization in Plants and Data Analysis - Concept

Sélection artificielle

Natural Selection and Adaptive Evolution
In natural settings, adaptive evolution takes place by natural selection, a process in which differences in ...

Hardy-Weinberg and Genetic Drift

<p>Evolutionary change is interesting and important to study, but changes in populations occur over long periods of time and in huge physical spaces and are therefore very difficult to measure. In general, studying phenomena like this requires the use of mathematical models which are built using parameters that can be conveniently measured. These models are then used to make predictions about how changes to the system might affect the outcome.</p> 
<p>For example, changes to the frequency of genetic alleles at individual loci in species are often observed over long time periods, but are not generally observable over short time periods. The use of computer models allows researchers to predict changes within a species&#8217; gene pool using observations that have already been gathered, and allow for simulations of a potentially unlimited number of generations of the population. This would certainly not be possible within a human lifetime.</p>
<h4>The Hardy-Weinberg Equilibrium Principle</h4>
<p>One equation used to model populations is the Hardy-Weinberg equilibrium equation. It was formulated independently in 1908 by both G. H. Hardy and Wilhelm Weinberg<sup>1,2</sup>. The simple equation describes the expected allele frequency of a population that is<em> not</em> evolving. Because most real-life populations are evolving in response to the forces of natural selection, this formula acts as a useful null hypothesis. It is used to test whether or not different types of selection are, or are not, occurring. If measured allele frequencies differ from those that were predicted using the Hardy-Weinberg equation, then the gene in question is undergoing evolutionary change.</p>
<p>The Hardy-Weinberg equation can be represented as <em>p</em><sup>2</sup> + 2<em>pq</em> + <em>q</em><sup>2</sup> = 1 where <em>p</em> represents the frequency of the dominant allele and q represents the frequency of the recessive allele for the gene in question. Each expression in the equation represents the predicted frequency of one of the three possible diploid genotypes. Homozygous dominant frequency is represented by <em>p</em><sup>2</sup>, homozygous recessive by <em>q</em><sup>2</sup>, and heterozygous by 2<em>pq</em>. If these frequencies are summed, it adds up to 1, which makes sense since the full population had been divided into the three available categories.</p>
<p>It is also possible to describe the population, or gene pool, in terms of the two alleles, without regard to how they are packaged into diploid individuals. This equation is represented as <em>p + q = 1</em>, that is, the frequencies of the dominant and recessive alleles must add up to 1 within the population. Again, this makes sense, since the model includes just two allele possibilities. Notice that the frequency of genotypes in the population is just the quadratic expansion of the frequency of alleles in the population because (<em>p </em>+<em> q</em>)<sup>2</sup> = <em>p</em><sup>2 </sup>+ 2<em>pq </em>+<em> q</em><sup>2</sup>.</p>
<p>The Hardy-Weinberg equation, like most other models, requires a series of assumptions. Usefully, if the real-life data differs from the predicted data, it is possible to hypothesize which of the starting assumptions was false. The assumptions of the Hardy-Weinberg equilibrium equations are: 1) the population is very large, 2) the population is closed, meaning that there are no individuals immigrating into or emigrating out of the population, 3) there are no mutations occurring on the gene in question, 4) individuals within the population are mating at random&#8212;individuals are not choosing their mates, 5) natural selection is not occurring. Again, keep in mind that the Hardy-Weinberg equilibrium equation is a null hypothesis. Frequently, real populations violate one or more of these assumptions. The equation is used to determine if and how evolution is happening.</p>
<h4>Genetic Drift</h4>
<p>In a relatively small population, a condition that violates the first Hardy-Weinberg assumption, it is possible for allele frequencies to have resulted from chance. This phenomenon is referred to as genetic drift. One version of this is referred to as the founder effect. If a small number of individuals move to an isolated location and start a new population, the specific genetics of those particular individuals will shape the future generations. This new small gene pool may have the same allele frequency as the original, but it is also possible, even likely, that it does not. Say the original population included 50% dominant alleles and 50% recessive. In the extreme, if all of the individuals in a migrating founder group are homozygous recessive, then the dominant allele has been lost completely and the recessive is now at 100%. A similar phenomenon, called the bottleneck effect, can occur if a population sustains a large drop in numbers due to a natural disaster, human intervention, or disease.</p>
<p>Importantly, genetic drift represents a type of evolution that is not necessarily adaptive. It does not specifically select for traits that are fit for the environment. Nonetheless, it is an important evolutionary force in shaping populations with a small number of individuals and will cause deviations from Hardy-Weinberg predictions. In populations that are larger, deviations from the predictions are more likely to mean that the population in question is undergoing evolution through natural selection. Under these circumstances, further consideration of the mechanisms causing this evolution can be explored.</p>
<p>Modern applications of the Hardy-Weinberg model include analysis of human and animal populations in terms of how their immune systems relate to their susceptibility to infectious disease<sup>3,4</sup>. Many research groups are cataloging genes which encode specific immune system molecules, such as CCR5 and the major histocompatibility complex (MHC, known in humans as the human leukocyte antigen (HLA), and correlating this information to epidemiological studies regarding disease and its progression<sup>3,5-6</sup>. From comparing these two types of data sets, patterns are emerging showing that some individuals are genetically resistant to particular infections while others are more likely to succumb to disease<sup>4</sup>. Hardy and Weinberg&#8217;s model has been essential to the analysis of this data and has contributed to our understanding of how infections have shaped evolution.</p>
<h4>References</h4>
<ol class="references">
	<li>Hardy, G. H. (Jul 1908). 'Mendelian Proportions in a Mixed Population'<em> (PDF). Science. <strong>28</strong> (706): </em>49&#8211;50. doi:10.1126/science.28.706.49. ISSN 0036-8075. PMID 17779291.</li>
	<li>Weinberg, W. (1908). '&#220;ber den Nachweis der Vererbung beim Menschen'. <em>Jahreshefte des Vereins f&#252;r vaterl&#228;ndische Naturkunde in W&#252;rttemberg</em>. <strong>64</strong>: 368&#8211;382.</li>
	<li>Eguchi S, Matsuura M. Testing the Hardy-Weinberg equilibrium in the HLA system. Biometrics. 1990 Jun;46(2):415-26. PubMed PMID: 2364131.</li>
	<li>Phillips KP, Cable J, Mohammed RS, et al. Immunogenetic novelty confers a selective advantage in host-pathogen coevolution. <em>Proc Natl Acad Sci U S A</em>. 2018;115(7):1552-1557.</li>
	<li>Lim JK, Glass WG, McDermott DH, Murphy PM CCR5: no longer a 'good for nothing' gene--chemokine control of West Nile virus infection. Trends Immunol. 2006 Jul; 27(7):308-12.</li>
	<li><a target="__blank" href="https://hla-net.eu/tools/frequency-estimation/">https://hla-net.eu/tools/frequency-estimation/</a></li>
	<li>Santiago Rodriguez, Tom R. Gaunt and Ian N. M. Day. Hardy-Weinberg Equilibrium Testing of Biological Ascertainment for Mendelian Randomization Studies. American Journal of Epidemiology Advance Access published on January 6, 2009, DOI 10.1093/aje/kwn359. http://www.oege.org/software/hwe-mr-calc.html</li>
</ol>
<h4>Further Reading</h4>
<p>Andrews, C. (2010) The Hardy-Weinberg Principle. Nature Education Knowledge 3(10):65 https://www.nature.com/scitable/knowledge/library/the-hardy-weinberg-principle-13235724</p>

Hardy-Weinberg Equilibrium Principle and Genetic Drift - Concept

Hardy-Weinberg et la dérive génétique

Evolutionary change is interesting and important to study, but changes in populations occur over long periods of time and in huge physical spaces and are ...

Community Diversity

<p>Populations do not live in isolation; thus, every population interacts with others in certain ways. These interactions give rise to a network of populations. Hence, an ecological community is composed of such population networks of various species interacting with each other within the same area. These biological, or biotic, components may also closely interact with non-living, or abiotic, components, forming an ecosystem. Ecosystems may be as small as the microbial communities inside the human digestive tract, structured by the pH and nutrients of their environment, or as large as a forest containing trees and insects closely linked through the carbon cycle. Ecologists and conservationists have become increasingly interested in ecosystems as humans continue to make major changes to them globally through urbanization and climate change. Alterations to any single component of an ecosystem can affect other closely-linked components, potentially causing drastic changes to the entire system. For these reasons, quantifying and predicting the current and future &#8220;health&#8221; of ecosystems has become a major topic of ecological research.</p>

<h4>Biodiversity</h4>

<p>The term &#8220;ecosystem health&#8221; is metaphorical because and it is difficult to compare the health of very different ecosystems and there is no single value that can be used to quantify how healthy an ecosystem is. For example, deserts and forests have very different species diversities but one is not necessarily healthier than the other. Therefore, multiple metrics have been formulated to represent the health of an ecosystem, and their use depends on the goals of the study. Hence, &#8220;ecosystem health&#8221; may refer to how valuable an ecosystem is to humans. For example, the value of ecosystem services like carbon sequestration by trees or pollination by bees are used to quantify the health of ecosystems. Other metrics may measure the number of rare species found in an ecosystem, how resistant an ecosystem is to fire, or some other measurements of biotic and abiotic factors. For ecologists, one very popular health measure is that of biological diversity, or &#8220;biodiversity.&#8221; Biodiversity is a measure of the variety of biological species found in an area and can be calculated using the Shannon-Wiener biodiversity index.</p>

<p>The Shannon-Wiener Index requires two measurements from a local community: species richness and evenness. Species richness is the total number of distinct species within a local community. An area with no species present, such as a freshly paved parking lot, would have a richness value of 0. Rainforests, known for supporting some of the most diverse communities on Earth, have a much greater species richness. While having many species generally coincides with having a diverse and healthy ecosystem, the evenness also needs to be considered. For instance, when one species dominates the area while the others are very rare, the biodiversity in this area is lower than in an area with species of equal abundance. Therefore, areas with many species that are relatively equal in abundance have the highest scores of biodiversity.</p>

<p>Shannon-Wiener is not the only measure of ecosystem biodiversity and health. For example, a popular index, named the EPT index, is used to determine water quality in river systems by assigning values of healthiness to individual organisms. More specifically, this index considers three pollutant-sensitive orders of invertebrates found in rivers, Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies). The presence of these pollutant-intolerant species in a waterway is used as an indication of good water quality and the ecosystem in question is considered to be healthy.</p>

<p>Often, ecologically-relevant areas are too large to be sampled in entirety. To resolve this problem, ecologists sample multiple smaller plots throughout the study area using quadrats, which are small frames of a predetermined size placed at points throughout the study site, in which a researcher identifies and records all individuals of species of interest. When enough quadrat samples are considered, scientists can extrapolate to make accurate estimates of ecological communities.</p>

<h4>Impacts of Ecological Changes</h4>

<p>Most natural ecological changes happen over an extended time scale. In addition, humans continue to alter ecosystems. To assess long-term changes in ecosystems, scientists have set up Long Term Ecological Research sites (LTERs). One of the longest running LTERs is the Hubbard Brook Experimental Forest located in New Hampshire, United States. This site and others have increased knowledge about ecosystem scale patterns resulting from deforestation, changes to hydrological regimes, and other long-term ecological disturbances<sup>1</sup>.</p>

<p>When a major change occurs very rapidly, it is called an ecological disturbance. Fires, hurricanes, and floods are examples of ecological disturbances. Disturbances can alter an ecosystem by wiping out nutrients and changing the composition of the biological community. After a disturbance, the most resistant and resilient species are favored for survival. A resistant species or community is one that can survive major disturbances with minimal detriments and quickly recover from a disturbance, like dandelions after a lawn is mowed. Sampling a site for many years before and after disturbances is unfeasible, but comparing different areas with different disturbance regimes offers a partial solution to this problem.</p>

<p>Disturbed habitats are usually patchy; therefore, using randomly-placed quadrats might result in underrepresentation of species and incorrect biodiversity estimates. For this reason, it is essential to consider the surroundings and some of the characteristics of the habitat that is being studied. This is accomplished in landscape ecology by studying both core and edge habitats. A core habitat is located centrally within a patch, surrounded by the same type of habitat. In contrast, an edge habitat, also known as boundary habitat, borders a different habitat type. Edge habitats, such as where a forest habitat meets a meadow habitat, may have increased biodiversity because species from both habitat types may be found in them. Such differences in biodiversity at the edges of habitats are called edge effects. To assess these transitional areas, ecologists use paths along habitats, called transects, and record the biodiversity of small sampling sites at set intervals along the path. However, not all habitats will have edge effects and sometimes edge species are invasive and can grow in a wider range of habitats, thus not be indicative of a &#8220;healthy&#8221; ecosystem.</p>

<p>In addition to species measures scientists may also take measures of the chemical components of an ecosystem to assess its health. For example, they might check for pollution, or examine soil quality by measuring the nutrients present. This information can also be useful to help explain changes in patterns of biodiversity in different regions of a community. There are also many variables including temperature, precipitation over a certain time frame, and functional traits of the species, that would be hard to measure and would require advanced statistical analyses. Ecologists are constantly working on new ways to record these variables across greater scales of time and space. This has given way to new methods such as remote sensing of ecosystems, in which satellite imagery is used to estimate variables of interest across the entire globe<sup>2</sup>. These data require the use of multivariate statistics and other complex mathematical tools that are continually being developed.</p>

<p>As the human populations continue to grow and alter ecosystems worldwide, scientists and concerned citizens work towards conserving and preserving threatened ecosystems. One way to restore heavily altered ecosystems is through bioremediation, which involves the release of biological organisms, usually microorganisms, to break down pollutants and restore favorable traits to an ecosystem<sup>3</sup>. One example of this is the release of microorganisms in wastewater to break down pollution and restore water to a habitable condition for fish<sup>4</sup>. Therefore, inventive ways of restoring ecosystems will become increasingly important to remediate human effects on ecosystems.</p>

<h4>References</h4>

<ol class="references">
	<li><strong>Likens, Gene E.</strong> Fifty years of continuous precipitation and stream chemistry data from the Hubbard Brook ecosystem study (1963&#8211;2013). <em>Ecology. </em>Vol. 98 , 8: 2224.</li>
	<li><strong>Zhaoqin Li, Dandan Xu, Xulin Guo.</strong> Remote Sensing of Ecosystem Health: Opportunities, Challenges, and Future Perspectives. <em>Sensors (Basel). </em>2014, Vols. 14(11): 21117&#8211;21139.</li>
	<li><strong>Garbisu, Itziar Alkorta Lur Epelde Carlos.</strong> Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation. <em>FEMS Microbiology Letters. </em>2017, Vol. 364, 19.</li>
	<li><strong>P. Padmavathi, K. Sunitha, K. Veeraiah.</strong> Efficacy of probiotics in improving water quality and bacterial flora in fish ponds. <em>Afr. J. Microbiol. Res. </em>2012, 6(49). 7471-7478.</li>
</ol>


Community Diversity: Measuring Biodiversity in Different Areas - Concept

Diversité communautaire

Populations do not live in isolation; thus, every population interacts with others in certain ways. These interactions give rise to a network of ...

Ecologie

Group Behavior

<h4>Life in a Population</h4>
<p>Organisms in populations interact with one another in complex ways, where individuals compete for resources such as food, shelter, and mates. These interactions are costly since individuals invest energy to acquire the resource, therefore there are a variety of strategies that organisms adopt to gain an advantage over their competitors. This is observed clearly with polymorphic mating systems, in which one sex, predominantly males, display multiple mating strategies. For example, dominant male sea lions defend harems of females up on the beach, whereas non-dominant males try to increase their chances of mating by staying in or near the water, where they mate with females that have left the beach temporarily <sup>1</sup>. Other types of strategies may determine how often an individual will fight for a resource, or how willing they are to cooperate with others.</p>
<h4>Game Theory and Evolutionarily Stable Strategies</h4>
<p>In order to understand how different behavioral strategies evolve, ecologists turn to the game theory, which is a mathematical modeling approach that investigates the outcomes of multi-individual interactions, in which the payoff for any one individual depends its own strategy as well as the strategies of the others <sup>2</sup>. In this approach, the relative cost of the interaction and the benefits obtained from the resource determines the net gain or, in some cases, loss incurred by the organism. Different strategies can be assigned costs and benefits based on those faced by an organism. For example, fighting for control of a resource may provide a large benefit, but it also comes with costs that reduce an organism&#8217;s net gain. On the other hand, a strategy to avoid conflict will reap fewer benefits but incurs no costs.</p>
<p>The organisms with the best interaction strategy maximize their net gain, which in turn will contribute to their fitness. Therefore, over the course of evolutionary time, one strategy may arise that outcompetes all others in a population. This is called an evolutionary stable strategy (ESS) <sup>2</sup>. Populations evolve to adopt this strategy once it arises through mutation or is introduced through migration. Therefore, these strategies are mostly genetic or adopted at a young age, and changes in the strategies used by a population over time are determined by the action of natural selection. This concept is often illustrated using the Hawk-Dove game, which compares the success of two strategies for obtaining resources <sup>3</sup>. In this example, &#8220;hawks&#8221; are aggressive, and always fight for resources. &#8220;Doves,&#8221; on the other hand, are passive, and never fight for resources. In an interaction between two doves, resources are split evenly. When a hawk and a dove interact, the hawk always wins and obtains all of the resources. However, when two hawks interact, they split resources evenly and suffer the cost of their conflict as well <sup>3</sup>. Assessing these interactions over consecutive interactions allows modeling of how competing strategies in an evolving population fare against each other, thus emergence of ESS in an experimental setting.</p>
<p>As seen with the doves in the Hawk-Dove example, organisms not only compete against each other, but also display cooperative behaviors. The risk of being a population of 100% doves is the arrival of a cheater, or an individual that does not cooperate <sup>4</sup>. Cheaters can invade and outcompete the residents, therefore many cooperating populations have strategies in place to prevent invasion, including the ability to switch strategy as necessary or to identify and cheaters, and in some cases, to communicate this information to others in their group to decrease the chances of cheater success <sup>4</sup>.</p>
<h4>Social Interaction in Nature</h4>
<p>The existence of altruism, or a reduction in an organism&#8217;s immediate fitness in order to benefit another&#8217;s, in wild populations has been held up as a counterpoint to the theory of natural selection, however game theory shows how altruism can evolve under certain conditions. Assuming organisms can identify one another or reasonably expect to interact again in the future, acts of apparent altruism may actually be beneficial over time, as an organism can count on the favor being returned. This is seen when flocks of birds or herds of mammals feed collectively &#8211; one individual may sound an alarm call when they spot a predator, making them more vulnerable to attack <sup>5</sup>. The net benefit, however, of others frequently doing the same makes this act adaptive. Similarly, a vampire bat may regurgitate its food to feed hungry individuals. When it is unable to find food in future, it may benefit from the same behavior of another vampire bat <sup>6</sup>.</p>
<p>In addition to the interactions within a single species, the evolution of social interactions can take place between species as well. Besides predator-prey interactions, different species can compete for the same resources and develop strategies to gain advantage over others. However, individuals of a species may also interact cooperatively with members of another species. Interspecies interaction that require cooperation include mutualisms, or situations in which two organisms provide mutual benefits to one another. Many plants form mutualisms with nitrogen-fixing bacteria in the soil, whereby the plants provide complex sugars to bacteria in exchange for nitrogen <sup>7</sup>. Should bacteria fail to provide nitrogen, then plants can reduce the amount of sugars available.</p>
<p>Since cooperative interactions depend on either being able to identify or retaliate against cheaters, it is possible for invaders to take advantage of existing mutualisms in new environments. Invasive species have the potential to be closely related enough to local species that they are able to form mutualisms with other local species, but distantly related enough that existing recognition or defense mechanisms are ineffective. In Hawaii, an invasive dinoflagellate that forms a mutualism with coral takes more resources than local dinoflagellates. This has a negative impact on coral instead of the expected beneficial one <sup>8</sup>. Therefore, studying intra- and interspecies interactions not only allows understanding the development of behavioral strategies in evolving populations but is also essential to assess the behavioral phenotypes of invasive organisms to develop effective strategies against them.</p>
<h4>References</h4>
<ol>
	<li><strong>P&#246;rschmann, UlrichUniBi, et al.</strong> Male reproductive success and its behavioural correlates in a polygynous mammal, the Gal&#225;pagos sea lion (Zalophus wollebaeki). <em>Molecular Ecology. </em>2010, Vol. 19, 12 (2574-86).</li>
	<li><strong>Price, J. M Smith &#38; G. R.</strong> The Logic of Animal Conflict. <em>Nature. </em>1973, 246 (15-18).</li>
	<li><strong>Sigmund K, Nowak MA.</strong> Evolutionary game theory. <em>Curr Biology. </em>1999, Vol. 9, 14 (R503-5).</li>
	<li><strong>Rose, M. R.</strong> Cheating in Evolutionary Games. <em>J. Theor. Biol. </em>1978, 75 (21-34).</li>
	<li><strong>Trivers, R. L.</strong> Evolution of reciprocal altruism. <em>Q. Rev. Biol. </em>1971, Vol. 46, 1 (35-57).</li>
	<li><strong>Wilkinson, G. S.</strong> Reciprocal food sharing in the vampire bat. . <em>Nature. </em>1984, 308(181-84).</li>
	<li><strong>Francis M. Martin, St&#233;phane Uroz, David G. Barker.</strong> Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. <em>Science. </em>2017, Vol. 356, 6340 (eaad4501).</li>
	<li><strong>Tracy D.Ainsworth, Rebecca VegaThurber, Ruth D.Gates.</strong> The future of coral reefs: a microbial perspective. <em>Trends in Ecology &#38; Evolution. </em>2010, Vol. 25, 4 (233-40).</li>
</ol>

Group Behavior: Hawk-Dove Game and Trading Exercise - Concept

Comportement de groupe

Life in a Population
Organisms in populations interact with one another in complex ways, where individuals compete for resources such as food, shelter, ...

Sexual Selection and Mate Choice

<h4>Choosing Mates</h4>

<p>Evolutionary fitness is largely determined by the ability of an organism to survive and successfully produce offspring.  Critical to this process is sexual selection, which plays a large role in the determination of mating pairs, and thus which genes are passed on to the next generation.  Often, intense competition for mates within a population places selective pressure on traits related to courtship and copulation.  Natural selection that results from these pressures is called sexual selection.  Sexually selected traits include characteristics like ornamentation or coloration for the sole purpose of attracting mates.  These traits can also serve to enhance the distinction between males and females within a species, termed sexual dimorphism.  Dimorphism and other sexually selected traits help individuals of a species determine the fitness of potential mates and select an appropriate breeding partner.  This type of selection occurs in most species, from insects to humans and countless others. </p>

<h4>Inter- and Intra-sexual Selection</h4>

<p>The two basic types of sexual selection are intersexual (between-sex) and intrasexual (within-sex) selection.  Intersexual selection occurs as a result of interactions between males and females of a species.  One sex, typically males, will develop and display traits or behavior patterns to attract the opposite sex.  Examples of such traits include plumage on birds, the mating calls of frogs, and courtship displays in fish.  In contrast, intrasexual selection occurs between members of the same sex.  Competition between males is common, as with deer or horned beetles, which fight for dominance and the ability mate with nearby females.  In such cases, sexual selection acts on traits that facilitate competition among individuals of the same sex.  For example, the strength and size of the &#8220;horn&#8221; of horned beetles or antler size in deer.  Both intersexual and intrasexual selection influence the development of sexually selected traits in numerous species. </p>

<h4>Signaling Fitness and the Operational Sex Ratio (OSR)</h4>

<p>The display of sexually-selected traits can be important signals of individual fitness to potential mates.  Such signals are often energetically costly, and thus indicate the health, genetics, and nutrition status of an individual.  Often, though not always, these traits are displayed by males to attract females.  This is the result of the difference in energetic investment into offspring production and rearing.  Female eggs are produced in fewer numbers and at a higher energetic cost than male sperm, prompting females to be more selective in mate choice.  The level of competition for mates can be quantified by the operational sex ratio (OSR).  The OSR is based on the ratio of sexually mature males to females in a population, and is often male-biased in groups that contain more males or for populations in which males mate with multiple females.  However, the OSR can be skewed by several factors, including the relative investment by each sex into parental care, mate bonding processes, and the overall rate of reproduction<sup>1-2</sup>.</p>

<p>Because ORS is often male skewed, males of a species tend to experience stronger inter- and intra-sexual selective pressures.  In this context, natural selection has favored the development of traits to attract females or compete with other males, even when these traits come at a significant energetic or fitness cost.  Traits to attract females, for instance, are often colorful or flashy, making individuals more easily seen by predators.  These traits may require significant energy to produce and can reduce immune function in individuals.  Furthermore, males put themselves at risk when competing with other males.  Battles between males, mating dances, vocalizations, and displays are often not only physically demanding, but may also be loud, flashy and distracting, reducing awareness to predators and potentially injuring individuals.  Because of this, natural selection and sexual selection are often in conflict, seemingly pulling such traits in opposite directions. The influence of natural selection prevents sexually selected traits from becoming too extravagant.  As a result, sexually associated traits that significantly reduce an individual&#8217;s ability to survive long enough to mate will be selected against.  This balance between natural and sexual selection causes most individuals within a population to exhibit fitness and sexual traits of average or intermediate quality to maximize reproductive success and survival.</p>

<h4>Trading Off: Sexual Selection Versus Natural Selection</h4>

<p>However, under unique circumstances, sexually selected traits may not be constrained by survival pressures.  For instance, birds within the &#8220;bird-of-paradise&#8221; family include a variety of species that occupy remote areas lacking natural predators.  As a result, males have developed extravagant colorations and mating displays that would normally be selected against due to predation.  Such &#8220;runaway selection&#8221; can produce beautiful and highly ornamented species.  Unfortunately, due to human activity, the introduction of new predators like cats threatens the survival of these endangered species. </p>

<p>Understanding sexual selection influences the way we view animal traits, behaviors, and mate choice, including humans<sup>3</sup>.  There is often more to sexual selection than visual cues, with many species relying solely on smell or sound to find mates.  In humans, the influence of smell was demonstrated in an experiment by <em>Wedekind et al, </em>which showed a female preference for the smell of males who were more different, genetically<sup>4</sup><em>.  </em>Enhanced genetic diversity, especially as it relates to immune function, may provide offspring with greater fitness.  In this and other ways, sexual selection has influenced the way humans and organisms of all types evolve, behave, select mates, and reproduce. </p>

<h4>Further Reading:</h4>

<ol class="references">
	<li>Verdade, L. M. (1996). 'The influence of hunting pressure on the social behavior of vertebrates.' Rev Bras Biol <strong>56</strong>(1): 1-13.</li>
	<li>Lifshitz, N. and C. C. St Clair (2016). 'Coloured ornamental traits could be effective and non-invasive indicators of pollution exposure for wildlife.' Conserv Physiol <strong>4</strong>(1): cow028.</li>
	<li>Stanyon, R. and F. Bigoni (2014). 'Sexual selection and the evolution of behavior, morphology, neuroanatomy and genes in humans and other primates.' Neurosci Biobehav Rev <strong>46P4</strong>: 579-590.</li>
	<li>Wedekind, C. and S. Furi (1997). 'Body odour preferences in men and women: do they aim for specific MHC combinations or simply heterozygosity?' Proc Biol Sci <strong>264</strong>(1387): 1471-1479.</li>
</ol>


Sélection sexuelle et choix du partenaire

Choosing Mates

Evolutionary fitness is largely determined by the ability of an organism to survive and successfully produce offspring.  Critical to this ...

Eusociality and Division of Labor

<h4>Social Organization</h4>

<p>Varying levels of social organization are observed within the animal kingdom, ranging from simple to highly complex. These systems can greatly enhance the survival and reproductive success of an individual or a population. Of these, eusociality is the highest level of social organization, involving divisions of labor based on social castes. However, this system is rarely observed in nature, as it requires individuals to help others in the population at great survival or reproductive costs to themselves<sup>1</sup>. When this behavior pattern, termed altruism, was originally observed in species like the honeybee, it caused early evolutionary biologists to reconsider their antiquated definition of evolutionary fitness. Original theories considered fitness only on an individual level. However, in light of eusocial systems, W. D. Hamilton first proposed a theory of inclusive fitness. This postulates that the measure of an individual&#8217;s fitness can include the reproductive fitness of family members, who also carry a proportion of that individual&#8217;s genes. In this way, it can make evolutionary sense for individuals to make personal sacrifices for the benefit of related individuals.</p>

<h4>Relatedness</h4>

<p>Hamilton&#8217;s theory is driven by the concept of relatedness, which is defined as the proportion of shared genes between two individuals. For example, 50% of an individual&#8217;s genes are shared with direct offspring, while only 25% are present in the following generation. Accordingly, investment in a closely-related individual confers greater fitness than investment in those less closely-related. The following equation describes this relationship:</p>

<p>r (relatedness) &#215; B (benefit to the recipient) > C (cost to the altruist)</p>

<p>In this equation, &#8220;benefit to the recipient&#8221; (B) is equivalent to the increase in number of offspring produced by that individual while &#8220;cost to the altruist&#8221; (C) is equivalent to the decrease in the number of offspring produced by the altruist. In situations where the product of &#8220;r&#8221; times &#8220;B&#8221; is not greater than &#8220;C&#8221;, altruism is not favored by natural selection. However, as relatedness increases, so does the value of &#8220;r&#8221; times &#8220;B.&#8221; Thus, altruistic behavior becomes more likely when the altruist and recipient are more closely related.</p>

<h4>Eusociality</h4>

<p>Not every species that exhibits altruistic behavior is considered eusocial. Ultimately, eusociality is characterized by three main traits. First, the division of labor (including reproduction) into social castes leads some individuals to forego reproduction to enhance the reproductive success of family members. Other characteristics include overlapping generations, in which individuals of multiple generations live and work together, as well as cooperative brood care, in which non-parent individuals assist in the care of offspring.</p>

<p>One well-known example of eusociality is displayed by the honeybee. A typical beehive contains different groups of bees performing varied tasks. Only one reproductive female, the queen bee, repopulates the hive while other females act as workers. Reproductive males, called drones, are fairly uncommon. Honeybees belong to the order Hymenoptera along with ants and wasps<sup>2-3</sup>. This order contains the most eusocial species, but is not the only order with eusociality. Other groups that contain eusocial species include termites, marine snapping shrimp, and naked mole rats. Some have even proposed that humans may be eusocial. Though overlapping generations and cooperative brood care are generally present, humans appear to lack a separation between reproductive and non-reproductive groups. Though it is not a perfect fit, aspects of eusociality and altruism are frequently observed in humans and play a large role in our own social structure.</p>

<p>Though <em>non</em>-eusocial communities structures are much more commonly observed, eusociality confers evolutionary advantages to the species in which it is found. Two main hypotheses have been proposed to explain the evolution of eusociality: the ecological hypothesis and haplo-diploidy hypothesis.</p>

<p>The first, the ecological hypothesis, considers the many ecological drivers that may favor eusocial structures. These include the ability of eusocial communities to utilize common nest sites, facilitate group protection from predators, and reduce competition among individuals. The second theory, the haplo-diploidy hypothesis, takes into account the complex genetic structure of many eusocial groups, including bees and ants. In these groups, males commonly exhibit haploidy. This means that they carry only one copy of each chromosome, and thus contain half the genetic information of females. As a result, fathers pass 100% of their genes to their daughters while mothers, who are diploid, pass on 50%. Accordingly, when calculating the relatedness between sisters in a haplo-diploid species, 75% of genes are shared. This is significantly more than the 50% observed in diploid species. Increased relatedness among sisters may explain why workers in a colony are generally exclusively female and are able to work together for the good of the colony. This pattern is seen in honeybees which include haploid males and diploid females<sup>4</sup>. However, not all eusocial species exhibit haplo-diploidy. Both the ecological and the haplo-diploidy hypotheses likely play a role in the evolution of eusociality.</p>

<h4>Further Reading:</h4>

<ol class="references">
	<li>Sun, Q., et al. (2018). 'Managing the risks and rewards of death in eusocial insects.' Philos Trans R Soc Lond B Biol Sci <strong>373</strong>(1754).</li>
	<li>Krasnec, M. O. and M. D. Breed (2012). 'Eusocial evolution and the recognition systems in social insects.' Adv Exp Med Biol <strong>739</strong>: 78-92.</li>
	<li>Meunier, J. (2015). 'Social immunity and the evolution of group living in insects.' Philos Trans R Soc Lond B Biol Sci <strong>370</strong>(1669).</li>
	<li>Holland, J. G., et al. (2013). 'Queen control of a key life-history event in a eusocial insect.' Biol Lett <strong>9</strong>(3): 20130056.</li>
</ol>


Eusocialité et division du travail

Social Organization

Varying levels of social organization are observed within the animal kingdom, ranging from simple to highly complex. These systems ...

Evolutionary Relationships

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Forming an Evolutionary Hypothesis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">NOTE: A cladogram is an important tool for forming an evolutionary hypothesis. A cladogram is a tree-shaped chart used to depict the hypothetical genealogical relationships between species. The tips or leaves of the chart represent specific species and the branches of the tree are different lengths. The different lengths represent the degree of change between each of the species. The common ancestor of all of the species that a specific line branches from is located at a node, where the branches intersect. Species that share a node are called a sister group.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">To begin, look at the provided blank cladogram and make a hypothesis about where the assigned animals should be placed on the tree. If a blank cladogram has not been provided please <a target="_blank" href="/files/ftp_upload/10562/Blank_Cladogram.png">download one here</a>.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Next, observe the image of the fossilized animal.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Using the morphology, or physical characteristics, of the fossil, make a hypothesis about where on your cladogram it should be placed. Add a new line or mark to indicate your proposed position for the fossil.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Comparing Gene Sequences Using BLAST
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">NOTE: Historically, cladograms have been constructed through the comparison of morphology. Now, genetic sequences can also be compared between species of interest to construct cladograms. DNA sequences are not usually preserved in fossils, so for this lab you will use the BLAST database to compare the DNA sequences of living species that are closely related to the fossil to thousands of other living species.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Before beginning this lab, your instructor will have downloaded the three preserved gene sequences to a folder on your desktop.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Navigate to the BLAST homepage, which the instructor should have left open in your browser, and click on Saved Strategies from the menu at the top of the page.
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Click Open on the Evolutionary_Relationships_Gene1.txt file.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Then, click View to go to the Standard Nucleotide BLAST search page. You should be able to see the DNA sequence in the Query Sequence box at the top-right of the screen.
</div></li><li data-sub-note-item="2-6"><div class="lab-step">Scroll to the bottom of the screen and click the BLAST button. Note: It will take a few moments to process and analyze the data. 
</div></li><li data-sub-note-item="2-7"><div class="lab-step">When the data has been processed, a graphic summary will appear.  NOTE: Your query sequence is represented by the blue line at the top of the box. Each of the lines below the blue line represents another sequence in the BLAST database that matches your query. The length and location of these bars represent where and how much of the sequence match up to the query. The color of the bar represents its score, or how identical the sequence is to the query. Below the graphic summary is the Sequences producing significant alignments list, which contains descriptions of the DNA sequences retrieved from the database that most closely align with the query sentence. These are listed in descending order, from the most similar at the top to the least similar at the bottom. On the right, there are several statistics on how closely related each database sequence is to the experimental sequence. The higher the Max, Total, Query Coverage, and Identity scores are, the more similar the query and retrieved sequences are to each other. Similarly, the lower the E value number, the less likely the sequences match was found by random chance and more significantly the alignment is accurate. An E value of 0 indicates a highly significant match.
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Click on the name of the description of the most similar alignment listed. This will take you further down the page to the exact DNA sequence alignment between the retrieved sequence and the query sequence.
</div></li><li data-sub-note-item="2-9"><div class="lab-step">Click on the Sequence ID number. This will open a new tab with more specific information on the retrieved gene sequence.
</div></li><li data-sub-note-item="2-10"><div class="lab-step">Identify and record the scientific and common names of the organism, which should be listed next to Source.
</div></li><li data-sub-note-item="2-11"><div class="lab-step">Identify and record the protein that the gene codes for, which should be listed next to Definition.
</div></li><li data-sub-note-item="2-12"><div class="lab-step">Close the tab and hit Back to return to the Sequences producing significant alignments list.
</div></li><li data-sub-note-item="2-13"><div class="lab-step">Then, repeat steps 7 &#8211; 9 for the next most similar sequences.
</div></li><li data-sub-note-item="2-14"><div class="lab-step">After collecting several species names, return to the Sequences producing significant alignments list and click Select: All to check all of the boxes next to the names of each listed alignment sequence.
</div></li><li data-sub-note-item="2-15"><div class="lab-step">Click on Distance of tree results to create a phylogram based on the similarity of all of the BLAST result gene sequences to the query gene sequence.  Note: Your query fossil relative sequence will be highlighted in yellow.
</div></li><li data-sub-note-item="2-16"><div class="lab-step">Record your sequence&#8217;s location in relation to the other taxon groups shown in the tree.
</div></li><li data-sub-note-item="2-17"><div class="lab-step">Finally, return to the Saved Strategies tab and upload the next saved gene sequence.
</div></li><li data-sub-note-item="2-18"><div class="lab-step">Query the remaining two fossil relative DNA sequences as previously demonstrated (steps 1 &#8211; 16).
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Data Analysis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Based on your gene sequence results, come up with a second hypothesis about where your fossil specimen fit in the original cladogram.
</div></li><li data-sub-note-item="3-2"><div class="lab-step">Compare this placement with your first hypothesis.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Compare your tree with your classmates&#8217;. If any of your classmates put the fossil on a different branch, ask them how they came to that decision.
</div></li></ul></li></ol>

Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Procedure

Relations évolutives

Forming an Evolutionary Hypothesis
ExpandNOTE: A cladogram is an important tool for forming an evolutionary hypothesis. A cladogram is a tree-shaped chart ...

Lab Manual Sub Articles

Population Growth

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Exponential Population Growth Model
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">NOTE: In these experiments you will use computer software to simulate different types of growth models. HYPOTHESES: The experimental hypothesis might be that if we increase either R, the reproductive rate or the initial population size, NT, that this will increase the population size after 10 generations in an exponential growth model compared to unmanipulated control populations. The null hypothesis may be that populations of different R and initial population size will have the same population size as control groups after 10 generations.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">To build an exponential population growth model, first open a new workbook in Excel.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Save the file to a secure location and name it &#8220;exponential growth&#8221;.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Label cell A1 &#8220;generation&#8221;, and cell B1 &#8220;population size&#8221;.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Type the number zero into cell A2. This row will represent the initial generation.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">In cell A3 type this formula: = 1 + A2
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Now hit enter.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">Click on cell A3 and drag the small box in the bottom right corner to cell A12 for 10 generations.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Type the number two in cell B2. This will represent the initial population size in the model.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Label cell E1 &#8220;growth rate&#8221;, and in cell E2 type the number 0.05. This value represents the proportion of new offspring produced by each individual for each generation, or R in the exponential growth model.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">NOTE: In the classic exponential growth equation, T is the generation, and NT is the number of organisms in the current generation. NT+1 will be is the number of individuals in the next generation.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Enter the exponential growth equation in cell B3 as the formula shown here: = B2 + (1 + E2) * B2
</div></li><li data-sub-note-item="1-13"><div class="lab-step">Now, hit enter.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">Click cell B3 and drag the small square in the bottom right corner down to cell B12 to simulate 10 generations of exponential growth.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">To observe the results, select all data, along with the headers, in columns A and B.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Click &#8220;insert&#8221; and select &#8220;scatter plot with smooth lines and markers&#8221; from the toolbar. A scatter plot should appear in the sheet. TIP: If it does not, check to see if a new sheet was created in the workbook.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Label the Y axis &#8220;population size&#8221; and the X axis &#8220;generation&#8221;. Title the chart &#8220;exponential growth of a population&#8221;.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">Observe how the population increases in a classic exponential growth pattern.
</div></li><li data-sub-note-item="1-19"><div class="lab-step">Next, create Table 1 labeling the &#8220;growth rate R&#8221; as the header of column A, and &#8220;population size after 10 generations&#8221; as the second column.
</div></li><li data-sub-note-item="1-20"><div class="lab-step">Record the population size at generation 10 for the growth rate of 0.05, the rate we just simulated.
</div></li><li data-sub-note-item="1-21"><div class="lab-step">Now, set the growth rate in cell E2 to 0.1, and repeat the steps to generate a new scatter plot.
</div></li><li data-sub-note-item="1-22"><div class="lab-step">Record the population size at generation 10.
</div></li><li data-sub-note-item="1-23"><div class="lab-step">Continue to alter the growth rate using the values in table one, noticing how the Y axis changes to accommodate the increasing values.
</div></li><li data-sub-note-item="1-24"><div class="lab-step">After completing Table 1, set the growth rate back to 0.05 and change the initial population size in cell B2 to 100 individuals.
</div></li><li data-sub-note-item="1-25"><div class="lab-step">Record the population size at generation 10 in a new table, Table 2.
</div></li><li data-sub-note-item="1-26"><div class="lab-step">Proceed to change the initial population size using the values in Table 2. Once the table is complete, save the Excel sheet and close it.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Logistic Population Growth Model
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">HYPOTHESES: In a logistic growth model, the experimental hypothesis could be that populations will approach and meet the carrying capacity, and any populations with sizes greater than the carrying capacity will decrease in the subsequent generation. The null hypothesis might be that population growth will not follow a logistic S-shaped curve in the logistic models, and that generations with population sizes greater than the carrying capacity will continue to increase or stay the same in the next generation.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">To build a logistic population growth model, open a new spreadsheet in Excel.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Save the file as &#8220;logistic growth&#8221; in the same folder as before.
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Then label cell A1 &#8220;generation&#8221; and B1 &#8220;population size&#8221;.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Type the number zero in cell A2. This row will represent the initial generation.
</div></li><li data-sub-note-item="2-6"><div class="lab-step">In cell A3 type the formula: = 1 + A2
</div></li><li data-sub-note-item="2-7"><div class="lab-step">Now, hit enter.
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Now, click on cell A3 and drag the small box in the bottom right corner to cell A12 to number up to the 10th generation.
</div></li><li data-sub-note-item="2-9"><div class="lab-step">Type the number two in cell B2 to represent the initial population size.
</div></li><li data-sub-note-item="2-10"><div class="lab-step">Label cell E1 as &#8220;max growth rate&#8221; and cell F1 as &#8220;carrying capacity&#8221;.
</div></li><li data-sub-note-item="2-11"><div class="lab-step">Finally, set the max growth rate in cell E2 to 0.05. This value will represent the maximum growth rate the population may achieve &#8211; &#8220;R max&#8221; in the discrete logistic equation. NOTE: In the classic logistic growth equation the term K represents carrying capacity. As the population size of the current generation or NT, approaches the carrying capacity, the growth of the population begins to slow.
</div></li><li data-sub-note-item="2-12"><div class="lab-step">Now set the carrying capacity in cell F2 to 50.
</div></li><li data-sub-note-item="2-13"><div class="lab-step">Enter the logistic growth equation in cell B3 as the formula below: = B2 + ((1 + E$2) * B2) * ((F$2 - B2) /F$2)
</div></li><li data-sub-note-item="2-14"><div class="lab-step">Now hit enter.
</div></li><li data-sub-note-item="2-15"><div class="lab-step">Drag the formula down to cell B12 to add it to all 10 generations.
</div></li><li data-sub-note-item="2-16"><div class="lab-step">To observe the results of this exercise, highlight all data and headers in columns A and B, then click &#8220;insert&#8221; and select &#8220;scatter plot with smooth lines and markers&#8221;.
</div></li><li data-sub-note-item="2-17"><div class="lab-step">Label the Y axis population size and the X axis generation.
</div></li><li data-sub-note-item="2-18"><div class="lab-step">Title the chart as logistic growth of a population.
</div></li><li data-sub-note-item="2-19"><div class="lab-step">Observe the growth of the population as it nears carrying capacity and record the generation that the population meets or exceeds carrying capacity in a new table.
</div></li><li data-sub-note-item="2-20"><div class="lab-step">Now set the max growth rate in cell E2 to 1.
</div></li><li data-sub-note-item="2-21"><div class="lab-step">Notice how the population responds when it rises over carrying capacity.
</div></li><li data-sub-note-item="2-22"><div class="lab-step">Continue to set the max growth rate to the values in Table 3 and record the generation at which the population rises two or above carrying capacity.
</div></li><li data-sub-note-item="2-23"><div class="lab-step">Now set the max growth rate back to 0.05 and set the carrying capacity to 1,000.
</div></li><li data-sub-note-item="2-24"><div class="lab-step">Notice how the graph changes as the growth approaches the carrying capacity.
</div></li><li data-sub-note-item="2-25"><div class="lab-step">Drag the formulas in A12 and B12 down to A14 and B14.
</div></li><li data-sub-note-item="2-26"><div class="lab-step">Adjust the plot to include these new data points to show when the population reaches carrying capacity.
</div></li><li data-sub-note-item="2-27"><div class="lab-step">Save the Excel sheet and close it.
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Predator-Prey Model
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Hypotheses: In our third simulation of predator-prey logistics, the experimental hypothesis could be that predator populations will increase as prey populations increase and that the two populations will experience growth and decline dependent on the population of the other species. The null hypothesis may be that the two populations will show patterns of growth unrelated to the other species&#39; population size.
</div></li><li data-sub-note-item="3-2"><div class="lab-step">To build a predator-prey model, open a new spreadsheet in Excel.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Save the file in the same folder as the other two models and name it &#8220;predator-prey model&#8221;.
</div></li><li data-sub-note-item="3-4"><div class="lab-step">Label cell A1 &#8220;time&#8221;, cell B1 &#8220;prey&#8221; and cell C1 &#8220;predator&#8221;.
</div></li><li data-sub-note-item="3-5"><div class="lab-step">In cell A2 type zero and hit enter.
</div></li><li data-sub-note-item="3-6"><div class="lab-step">In cell A3 type the formula below: = 1 + A2
</div></li><li data-sub-note-item="3-7"><div class="lab-step">Now hit enter.
</div></li><li data-sub-note-item="3-8"><div class="lab-step">Drag the formula down to cell A802 as the model will require many time points to visualize changes of both populations.
</div></li><li data-sub-note-item="3-9"><div class="lab-step">Now type 100 into cell B2 to represent the initial prey population and type 25 into cell C2 as the initial predator population.
</div></li><li data-sub-note-item="3-10"><div class="lab-step">Label cell E1 &#8220;prey growth rate&#8221;, cell F1 &#8220;consumption of prey by predator&#8221;, cell G1 &#8220;conversion efficiency&#8221; and cell H1 &#8220;starvation of predator&#8221;.
</div></li><li data-sub-note-item="3-11"><div class="lab-step">Type the number 0.02 in cell E2. This value represents the growth rate of the prey species or R in the prey population model. NOTE: Here the prey population is represented as VT and the predator population as CT. The value A is the per capita attack rate of the predator species on the prey. In the predator population model, variables are introduced for predators produced per prey consumed, F or conversion efficiency as well as for the starvation rate of the predators noted as Q.
</div></li><li data-sub-note-item="3-12"><div class="lab-step">Type 0.0005 in cell F2 for the attack rate in both the prey population and the predator population model.
</div></li><li data-sub-note-item="3-13"><div class="lab-step">Then type 0.8 in cell G2 to represent the conversion efficiency, and 0.05 in cell H2 for the starvation rate in the predator population equation.
</div></li><li data-sub-note-item="3-14"><div class="lab-step">Now type the prey growth equation in cell B3 as the formula below: =B2+(E$2*B2)-(F$2*C2*B2)
</div></li><li data-sub-note-item="3-15"><div class="lab-step">Hit enter.
</div></li><li data-sub-note-item="3-16"><div class="lab-step">Then type the prey growth equation in cell C3 as the displayed formula: =C2 + (F$2*G$2*B2*C2)-(H$2*C2)
</div></li><li data-sub-note-item="3-17"><div class="lab-step">Hit enter.
</div></li><li data-sub-note-item="3-18"><div class="lab-step">Hold down the shift keys and click to select both cells B3 and C3.
</div></li><li data-sub-note-item="3-19"><div class="lab-step">Click the small box at the bottom right corner of cell B3 and drag the two formulas down to row 802 to simulate the predator and prey populations over 800 generations.
</div></li><li data-sub-note-item="3-20"><div class="lab-step">To visualize the data, select all of the data and headers in columns A, B and C.
</div></li><li data-sub-note-item="3-21"><div class="lab-step">Click &#8220;insert&#8221; and select &#8220;scatter plot with smoothed lines&#8221;.
</div></li><li data-sub-note-item="3-22"><div class="lab-step">A chart showing the population change of the predator and the prey populations should appear.
</div></li><li data-sub-note-item="3-23"><div class="lab-step">Label the Y axis of the plot population size and the X axis time.
</div></li><li data-sub-note-item="3-24"><div class="lab-step">Title the plot &#8220;predator-prey interactions&#8221;.
</div></li><li data-sub-note-item="3-25"><div class="lab-step">Observe the interactions between the predator and prey populations.
</div></li><li data-sub-note-item="3-26"><div class="lab-step">Set the initial predator population to zero and observe what happens in the plot.
</div></li><li data-sub-note-item="3-27"><div class="lab-step">Now set the initial predator population to 120 and observe what happens to the predator population when there are more predators than prey.
</div></li><li data-sub-note-item="3-28"><div class="lab-step">Finally set the initial prey population to zero and observe what happens to the population of the predators.
</div></li><li data-sub-note-item="3-29"><div class="lab-step">Experiment with other values to see what other interactions can be created.
</div></li><li data-sub-note-item="3-30"><div class="lab-step">When finished, save the workbook and close it.
</div></li></ul></li><li data-note-item="4" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="4-1"><div class="lab-step">In the exponential growth model built in the first activity, observe the shape of the resulting population growth curve, and consider whether you think this type of growth could be sustained in nature.
</div></li><li data-sub-note-item="4-2"><div class="lab-step">Note how the growth rate R affected the population size after 10 generations in the exponential growth model.
</div></li><li data-sub-note-item="4-3"><div class="lab-step">Also consider how the initial population size affected the population size after 10 generations in the exponential growth model.
</div></li><li data-sub-note-item="4-4"><div class="lab-step">Now, consider the logistic growth model, and observe the shape of this graph, noting how it differs from the exponential growth model.
</div></li><li data-sub-note-item="4-5"><div class="lab-step">Then, note how the populations behave as they approach the carrying capacity in your logistic growth model.
</div></li><li data-sub-note-item="4-6"><div class="lab-step">Decide if you think that the maximum per capita growth rate, R max, influenced how quickly populations reached carrying capacity in the logistic growth model.
</div></li><li data-sub-note-item="4-7"><div class="lab-step">Also, consider what happens to population size when populations are over carrying capacity in the logistic growth model, or what might happen if the carrying capacity is lowered.
</div></li><li data-sub-note-item="4-8"><div class="lab-step">In the predator-prey model, note whether the prey population responded to increasing predator population. Conversely, consider how the predators then respond to decreasing prey populations.
</div></li></ul></li></ol>

Population Growth: Exponential and Logistic Growth and Predator-Prey Model - Procedure

Croissance démographique

Exponential Population Growth Model
ExpandNOTE: In these experiments you will use computer software to simulate different types of growth models. ...

Genetics of Organisms

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">REF and WEF Fly Genetics
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">NOTE: At your station, you should have four vials of flies. They will be labeled as male or female. They will also be labeled with the notation REF for red-eyed flies or WEF for white-eyed flies. The female vial should also be labeled virgin as these flies should be unmated for the purpose of this experiment.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">Make sure you have around five flies in each vial. NOTE: You will perform crosses using these flies to determine if red or white eyes is dominant and if the trait is sex-linked. You should also have two fly anesthesia wands, a paint brush, magnifying glass, fly anesthetic, some empty fly vials, and a sheet of white paper.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Draw a line in the middle of the paper to make a male side and a female side.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Dip the fly anesthesia wand into the solution and insert it into the red-eyed female vial until the flies stop moving.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Then, dip the same wand into the white-eyed male vial until these flies are also anesthetized.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Tap the flies from the two vials onto the sheet - Females on one side and males on the other.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Check to make sure that all the flies from the female vial are female and likewise, confirm that the male flies are male.  NOTE: Males are slightly smaller and have a darker solid pigment on the end of their abdomen. Females are larger and have stripes rather than a solid spot.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">If there are any male flies in the female vial, obtain a new vial as these females likely have sperm from males from their own strain and are unusable.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Now, move the five red-eyed females and five white-eyed males into a new vial using the paintbrush.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Label this vial to indicate that this is a cross between red-eyed females and white-eyed males. HYPOTHESES: Use Punnett squares to formulate hypotheses for this experiment. Consider what you will see in a few days if the white allele is dominant and there is no effect of parental sex. What if red is dominant? Under the potential offspring genotype in each box, write the expected phenotype.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">To set up the reverse cross, again dip the fly anesthesia wand into the solution and insert it this time into the white-eyed female vial and then the red-eyed male vial until all the flies have stopped moving.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Tap the flies onto a sheet of white paper and check to make sure that all the flies from the female vial are female and likewise with the male flies.
</div></li><li data-sub-note-item="1-13"><div class="lab-step">Now, move the five white-eyed females and five red-eyed males into a new vial using the paintbrush.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">Label this vial to indicate that this is a cross between white-eyed females and red-eyed males.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">Finally, place the two tubes containing the new crosses into a rack for incubation at room temperature. NOTE: After about three days, larvae should be moving around in the vial.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Remove the 10 adult flies and dispose of them into the morgue tube containing 70% ethanol.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Now, put the tubes back in the rack and let the larvae mature until they reach the adult stage in up to two weeks.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">Once all of the larvae from these crosses have matured to adulthood, anesthetize the flies in one of the tubes using the wand.
</div></li><li data-sub-note-item="1-19"><div class="lab-step">Then, on a piece of white paper, sort the flies by sex and phenotype and then record these data.
</div></li><li data-sub-note-item="1-20"><div class="lab-step">Now, repeat this process and tally the sexes and phenotypes for the second cross (steps 1 &#8211; 18).
</div></li><li data-sub-note-item="1-21"><div class="lab-step">Finally, once you have counted all of your flies, dispose of them in the morgue vial.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">To begin investigating your results, first compare the data you collected with the hypothesis you made using the Punnett squares.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Did your data match the simple Punnett square hypothesis where red or white is dominant and there is no effect of sex? Compare your data with other lab groups.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">If your data does not match what your Punnett squares predicted, does this indicate that the gene may be sex-linked?
</div></li><li data-sub-note-item="2-4"><div class="lab-step">If the red gene were dominant and sex-linked, when we cross red-eyed females with white-eyed males, all of the offspring would have red eyes. Assuming all of the females were homozygous for the color allele, does this match your data for the first cross?
</div></li><li data-sub-note-item="2-5"><div class="lab-step">If white were dominant and the gene were sex-linked, we would see the exact opposite. So all of the flies would have white eyes. From your data, can you conclude from your first cross whether red or white is dominant?
</div></li><li data-sub-note-item="2-6"><div class="lab-step">When the reciprocal cross of white-eyed females and red-eyed males is performed, if the red phenotype is dominant, all of the females would be red and all of the males would be white. This would also confirm that the gene is specifically x-linked because white-eyed females could then only be produced in crosses with white-eyed males. Did your second cross produce any white-eyed females?
</div></li><li data-sub-note-item="2-7"><div class="lab-step">Finally, if the gene were x-linked and white was dominant, crossing white-eyed females with red-eyed males would result in all of the offspring having white eyes. Does this hypothesis fit with your second cross?
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Look over your data and conclude which of the hypotheses best fits the patterns you found in your crosses. If your data does not fit with any of these, hypothesize why this might be the case.
</div></li></ul></li></ol>

Genetics of Organisms: REF and WEF Fly Genetics - Procedure

Génétique des organismes

REF and WEF Fly Genetics
ExpandNOTE: At your station, you should have four vials of flies. They will be labeled as male or female. They will also be ...