Name: <meta charset="utf8"></head><body>Yazar Spotlight: Modern ve Eski Bitki Topluluklarında İklim ve Ekoloji Yeniden Yapılandırması için Yaprak Özelliği Analizi
Uploaded: 2024-10-25T13:40:00
Duration: 1 min 59 s
Description: Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants&#39; leaves. These relationships, particularly in woody ...

<meta charset="utf8"></head><body>Paleoiklim ve Paleoekolojik Rekonstrüksiyon için Dijital Yaprak Fizyonomisi

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
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		<tr>
			<td>Copy stand or tripod</td>
			<td></td>
			<td></td>
			<td>For fossil photography</td>
		</tr>
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			<td>Digital camera</td>
			<td></td>
			<td></td>
			<td>For fossil photography, high resolution camera preferred</td>
		</tr>
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			<td>Image editing software&#160;</td>
			<td></td>
			<td></td>
			<td>For digital preperation. Examples include Adobe Photoshop and GIMP, the latter of which is free (https://www.gimp.org/)</td>
		</tr>
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			<td>ImageJ software</td>
			<td>IJ1.46pr</td>
			<td></td>
			<td>For making digital measurments, free software (https://imagej.net/ij/index.html)</td>
		</tr>
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			<td>Microsoft Excel</td>
			<td>Microsoft</td>
			<td></td>
			<td>Or similar software for data entry</td>
		</tr>
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			<td>R software</td>
			<td>The R foundation</td>
			<td></td>
			<td>For running provided R script (https://www.r-project.org/). R studio offers a user friendly R enviornment (https://posit.co/download/rstudio-desktop/). Both are free.</td>
		</tr>
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			<td>dilp R Package</td>
			<td></td>
			<td></td>
			<td>Can be installed following instructions here: https://github.com/mjbutrim/dilp</td>
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	</tbody>
</table>

reconstructing terrestrial paleoclimate and paleoecology with fossil leaves using digital leaf physiognomy and leaf mass per area

Leaves are fundamental production units that facilitate the exchange of energy (e.g., light, heat) and matter (e.g., carbon dioxide, water vapor) between the plant and its surrounding environment1,2. To perform these functions, leaves must mechanically support their own weight against gravity in still and windy air 3,4. Because of these intrinsic links, several aspects of the size, shape, and toothiness of leaves (physiognomy) reflect the details of their function and biomechanics and provide insight into their environment and ecology. Prior work has quantified relationships between leaf physiognomy, climate, and ecology across the modern world to establish proxies that can be applied to fossil leaf assemblages5,6. These proxies provide important opportunities to reconstruct paleoclimate and paleoecology and contribute to a greater understanding of the complex interplay between various systems of the planet throughout its history. This article details the methods necessary for the use of two proxies: 1) the leaf mass per area reconstruction method to elucidate paleoecology, and 2) digital leaf physiognomy to reconstruct paleoclimate.
Leaf dry mass per area (MA) is a frequently measured plant trait in both neo- and paleobotany. The primary value of MA, especially for fossil reconstructions, is that it is part of the leaf economics spectrum, a coordinated axis of well-correlated leaf traits that includes leaf photosynthetic rate, leaf longevity, and leaf nutrient content by mass7. The ability to reconstruct MA from fossils provides a window into these otherwise inaccessible metabolic and chemical processes and ultimately can reveal useful information about plant ecological strategy and ecosystem function.
Royer et al.5 developed a method to estimate the MA of woody non-monocotyledonous (dicot) angiosperm fossil leaves based on the area of the leaf blade and the width of the petiole. Theoretically, the leaf petiole acts as a cantilever, holding the weight of the leaf in the optimal position3,4. The cross-sectional area of the petiole, which makes up the most significant component of beam strength, should, therefore, be strongly correlated with the mass of the leaf. By simplifying the shape of the petiole into a cylindrical tube, the cross-sectional area of the petiole can be represented with the petiole width squared, allowing leaf mass to be estimated from a two-dimensional fossil (for more detail, see Royer et al.5). Leaf area can be measured directly. Together, petiole width squared divided by leaf area (i.e., the petiole metric; Table 1) provides a good proxy for fossil MA and allows paleobotanists to step into modern trait-based ecology. MA reconstruction methods have also been expanded to broadleaf and petiolate gymnosperms5,8, herbaceous angiosperms8, and ferns9, which produced relationships that differ from the relationships observed for woody dicot angiosperms and from each other. An expanded woody dicot dataset and new regressions equations for reconstructing the variance and mean of MA at the site level allow the inference of the diversity of leaf economic strategies and what strategies are most prevalent, among woody dicot angiosperms in fossil floras10.
The relationship between physiognomic leaf traits and their climate has been noted for over a century11,12. Specifically, the physiognomy of woody dicot angiosperm leaves is strongly correlated with temperature and moisture13. This relationship has formed the basis for numerous univariate14,15,16,17 and multivariate6,18,19,20,21,22 leaf physiognomic proxies for terrestrial paleoclimate. Both univariate and multivariate leaf physiognomic paleoclimate methods have been widely applied to angiosperm-dominated fossil floras across all continents spanning the last ~120 million years of Earth&#39;s history (Cretaceous to modern)23.
Two fundamental observations utilized in leaf physiognomic paleoclimate proxies are 1) the relationship between leaf size and mean annual precipitation (MAP) and 2) the relationship between leaf teeth (i.e., outward projections of the leaf margin) and mean annual temperature (MAT). Specifically, the average leaf size of all woody dicot angiosperm species at a locality is positively correlated with MAP, and the proportion of woody dicot angiosperm species at a locality with toothed leaves, in addition to the size and number of teeth negatively correlate with MAT6,12,13,14,15,16,24.
A functional link between these leaf physiognomy-climate relationships is strongly supported by both theory and observation1,2,25. For example, although larger leaves provide greater photosynthetic surface area, they require greater support, lose more water through transpiration, and retain more sensible heat due to a thicker boundary layer 1,26,27. Thus, larger leaves are more common in wetter, hotter environments because water loss through increased transpiration effectively cools leaves and is less problematic. In contrast, smaller leaves in drier hot climates reduce water loss and avoid overheating instead by increasing sensible heat loss28,29. Details of what factors, or combination of factors, contribute most strongly to explaining functional links remain enigmatic for other leaf traits. For example, there have been several proposed hypotheses to explain the leaf teeth-MAT relationship, including leaf cooling, efficient bud packing, enhanced support and supply of thin leaves, guttation through hydathodes, and enhanced early season productivity30,31,32,33.
Most leaf physiognomic paleoclimate proxies rely on categorical division of leaf traits rather than quantitative measurements of continuous variables, leading to several potential shortcomings. The categorical approach excludes the incorporation of more detailed information captured by continuous measurements that are strongly correlated with climate (e.g., number of teeth, leaf linearity), which can reduce the accuracy of paleoclimate estimates6,20,34. Additionally, in some of the leaf trait scoring methods, the traits being categorically scored can be ambiguous, leading to issues in reproducibility, and some traits have limited empirical evidence to support their functional link to climate6,15,16,35,36.
To address these shortcomings, Huff et al.20 proposed digitally measuring continuous leaf traits in a method known as digital leaf physiognomy (DiLP). A key advantage of DiLP over previous methods is its reliance on traits that 1) can be measured reliably across users, 2) are continuous in nature, 3) are functionally linked to climate, and 4) display phenotypic plasticity between growing seasons6,37. This has led to more accurate estimates of MAT and MAP than previous leaf physiognomic paleoclimate methods6. In addition, the method accommodates the imperfect nature of the fossil record by providing steps to account for damaged and incomplete leaves. The DiLP method has been successfully applied to a range of fossil floras from multiple continents spanning a large range of geologic time6,38,39,40,41,42.
The following protocol is an expansion of that described in earlier work5,6,20,34. It will explain the procedures necessary to reconstruct paleoclimate and paleoecology from woody dicot angiosperms fossil leaves using the DiLP and MA reconstruction methods (see Table 1 for an explanation of the variables measured and calculated through the use of this protocol). In addition, this protocol provides steps to record and calculate leaf traits not included in DiLP or MA analysis but that are easy to implement and provide useful characterizations of leaf physiognomy (Table 1). The protocol follows the following format: 1) Imaging fossil leaves; 2) leaf digital preparation, organized into five possible preparation scenarios; 3) leaf digital measurement, organized into the same five possible preparation scenarios; and 4) DiLP and MA analyses, using the R package dilp10.
The protocol for MA reconstructions is embedded within the DiLP protocol because both are convenient to prepare for and measure alongside each other. If a user is interested in MA analyses only, they should follow the preparation steps described in DiLP preparation scenario 2, whether or not the leaf margin is toothed, and the measuring steps describing petiole width, petiole area, and leaf area measurements only. A user can then run the appropriate functions in the dilp R package that performs the MA reconstructions.

<meta charset="utf8"></head><body>Yazar Spotlight: Modern ve Eski Bitki Topluluklarında İklim ve Ekoloji Yeniden Yapılandırması için Yaprak Özelliği Analizi

Karasal Paleoiklim ve Paleoekolojinin Fosil Yapraklarla Dijital Yaprak Fizyonomisi ve Alan Başına Yaprak Kütlesi Kullanılarak Yeniden Yapılandırılması

Our research is focused on understanding the relationship between plant traits and climate and ecology in modern plants. Then using these relationships, we can develop proxies or models that we can use to reconstruct climate and ecology in ancient plant communities. Recent research has focused on understanding the biological, physiological, evolutionary underpinnings of the relationship between plant traits and climate and ecology, today and in the past.This research has shown that plant traits respond to climate and ecology, both in the lifetime of a single plant and in evolutionary time scales. Our research has demonstrated that despite the complex factors that influence plant traits, there are very strong empirical relationships between leaf traits and climate and ecology. We've used these relationships to develop models for reconstructing climate and ecology that have been applied in a variety of settings through Earth history.These methods refine the reconstruction of paleoclimate and paleoecology to provide a much more comprehensive understanding of terrestrial ecosystems and climate than is available by just studying our modern Earth. Such a perspective is critical in understanding what our future Earth holds as climates and ecosystems respond to anthropogenic impact. This is a leaf-physionomy-based approach, meaning that it does not require an accurate taxonomic identification.In addition, DiLP uses digital measurements of continuous leaf characters as opposed to qualitative and categorical, which allows for greater reproducibility, and these leaf characters have a functional relationship to climate.

Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants&#39; leaves. These relationships, particularly in woody ...

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Reconstructing Terrestrial Paleoclimate and Paleoecology with Fossil Leaves Using Digital Leaf Physiognomy and Leaf Mass Per Area

JoVE Journal

Environment

Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants&#39; leaves. These relationships, particularly in woody non-monocotyledonous angiosperms, have been used to develop leaf-based proxies for paleoclimate and paleoecology that have been applied to reconstruct ancient terrestrial ecosystems for the last ~120 million years of Earth&#39;s history. Additionally, given that these relationships have been documented in living plants, they are important for understanding aspects of plant evolution and how plants respond to climatic and environmental changes. To conduct these types of analyses on modern and fossil plants, leaf physiognomy must be measured accurately using a reproducible methodology. This protocol describes a computer-based method for measuring and analyzing a variety of leaf physiognomic variables in modern and fossil leaves. This method allows for the measurement of leaf physiognomic traits, in particular variables related to leaf serrations, leaf area, leaf dissection, and linearity that are used in the digital leaf physiognomy proxy for reconstructing paleoclimate, as well as petiole width and leaf area, which are used for reconstructing leaf mass per area, a paleoecological proxy. Because this digital leaf trait measurement method can be applied to fossil and living plants, it is not limited to applications related to reconstructing paleoclimate and paleoecology. It can also be used to explore leaf traits that may be informative for understanding the function of leaf morphology, leaf development, phylogenetic relationships of leaf traits, and plant evolution.

The protocol presented shows digital measurement and analysis of continuous leaf physiognomic traits on fossil leaves to reconstruct paleoclimate and paleoecology using the digital leaf physiognomy and leaf mass per area reconstruction methods.

Çevre

Digital Preparation of Fossil Leaves for the Measurement of Leaf Physiognomic Traits

To begin, position the leaf fossil under the camera and ensure it is lying as flat as possible. Photograph the fossil leaf and label the image file appropriately. Then open the image of a tooth leaf whose area is preserved or can be reconstructed in the image processing software and crop the image if necessary.Select Image and then Canvas to increase the width of the working area. Add a new canvas to either the right or left of the current canvas. Now decide on the leaf's preparation method, determining whether to use a whole leaf or half leaf for area and shape measurements.Using a lasso tool, trace the margin of the leaf, including the petiole if present. Copy and paste the selected portion of the leaf onto an open area of the canvas, making two copies, one original and one is a backup to revert to if necessary. Visually follow the leaf margin to the point it contacts the petiole, often darker and without distinctive veins.Place a lasso point there and repeat for the other half. Encircle the entire petiole to finish this selection. Then, cut and paste the petiole.Copy and paste the isolated leaf with the petiole removed and place it in an open area of the canvas. Using the lasso tool, trim excess leaf material to ensure a complete half leaf remains for preparations or leave the complete leaf intact if preparing a full leaf. Using a line or paintbrush tool, repair any damaged areas along the leaf margin with a line of appropriate color and thickness.For tooth measurements of the leaf, copy the leaf and place it in an open area on the canvas. Use the lasso tool to remove the area adjacent to damaged portions of the margin. Begin selection at a point along the margin that bounds the damaged portion and draw a straight line to the major vein perpendicular to it.Start the selection at the preserved primary tooth sinus closest to the damage. Continue the selection along the major vein until level with the other bound of the damaged margin, then draw a straight line perpendicular to the major vein to the margin. Delete the damaged portion of the leaf and repeat the process for all damaged portions.Copy and paste the version of the leaf prepared for tooth measurements and place it in an open area of the canvas. Use a lasso tool to remove the teeth from the leaf. Start at the leaf apex, one of the lobe tips or the tip of a leaf fragment, and select each primary tooth sinus along the leaf, lobe, or fragment.After selecting the apical sinus of the most basal tooth, apply the extension rule to cut the last tooth of the sequence out. Remove the teeth by cutting and pasting them next to the leaf blade, ensuring that the removed teeth do not touch the original blade.

Yaprak fizyonomik özelliklerinin ölçümü için fosil yaprakların dijital olarak hazırlanması

Digital Measurement and Analysis of Continuous Leaf Physiognomic Traits on Fossil Leaves

To begin, open ImageJ software and set the parameters for automatic measurements. Navigate to Analyze and select Set Measurements. Then select the options for area, perimeter, and Feret's diameter.Now open the prepared fossil leaf image by selecting File and Open. Use the straight line tool to zoom in on the scale bar and draw the longest straight line possible across it. To set the scale of the image, click Analyze and Set Scale.Enter the measured length of the scale bar in centimeters and click OK.In the data entry spreadsheet, mark the leaf as zero for toothed or one for entire. Also measure the petiole width if present And record the data in the data entry spreadsheet. Then select Image, Type, and 8-bit to convert the leaf image to black and white.Navigate to Image, Adjust, and Threshold to begin thresholding the image. Using the slider bar, adjust the threshold until the interior of the leaf turns red and is distinctly separate from the background. Zoom in on sections of the margin to ensure accuracy.To measure the leaf prepared for leaf area and shape measurements with the petiole removed, use the wand tool and click on the interior of the leaf to outline it in yellow, ensuring the outline correctly represents the leaf shape. Make measurements using Analyze and Measure or using the designated keyboard shortcut and record the data in the spreadsheet. For a half-leaf analysis, select the segmented line tool in the line tool and trace the entire length of the artificial middle perimeter.Then click Analyze and Measure or use the shortcut to measure the length of the artificial middle perimeter. Record area, perimeter, Feret, minimum Feret, and the length of the artificial middle perimeter. To adjust the measurements for a half-leaf in the data entry spreadsheet, multiply the area and minimum Feret by two and calculate the blade perimeter using the given formula.Measure the area of the cut-out petiole if present and record its area. To measure the raw blade, use the wand tool to select the interior of the blade outlined in yellow. Proceed with measurements by clicking Analyze and Measure or using the keyboard shortcut.In the data entry spreadsheet, record the raw blade's area and perimeter in the designated fields. To measure the internal raw blade, select the interior of the blade and outline the entire leaf in yellow. Make measurements by clicking Analyze and Measure or using the shortcut.Record the area and perimeter of the internal raw blade in the data entry spreadsheet under the respective fields. Clear the threshold to see the leaf clearly by clicking Reset in the Threshold box or using Edit and Undo to remove modifications like the black and white conversion. Then use the segmented line tool to trace the full length of the cut perimeter.Measure the traced perimeter by clicking Analyze and Measure or using the shortcut. To count the number of primary teeth, right-click the point tool first to select the multi-point tool. Click on each primary tooth to number it.To remove a point selected by mistake, press the Alt key or Command or CMD or Option while clicking the point. Record the final number under primary teeth in the data entry spreadsheet. Click Edit, Selection, and Select None to clear the multi-point tool counts and annotations.Then, to count the total number of teeth, right-click the point tool and select the multi-point tool. Click on each tooth, including primary and subsidiary, to number it. Both McAbee H1 and H2 sites showed leaf physiognomy that fits well within the calibration dataset's range, indicating reliability in the derived paleoclimate estimates.The reconstructed mean annual temperature and mean annual precipitation for McAbee H1 and H2 suggested a temperate seasonal biome.