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1. Rapid phenotypic change in a polymorphic salamander over 43 years

   https://doi.org/10.1038/s41598-021-02124-2  

   Hantak, Maggie M.; Federico, Nicholas A.; Blackburn, David C.; Guralnick, Robert P. (December 2021, Scientific Reports)

   Abstract Color polymorphic animals offer a unique system for studying intraspecific phenotypic responses to climate change. Discrete color morphs are easy to identify, and correlated trait responses of morphs can indicate how climate warming may facilitate long-term maintenance of polymorphisms. We use a historical dataset spanning 43 years to examine temporal shifts in color morph frequency and body size in response to climate in the Eastern Red-backed Salamander, Plethodon cinereus , which contains a widespread striped/unstriped color polymorphism. We created a pipeline to extract high-throughput trait data from fluid-preserved museum specimens where we batch-photographed salamanders, de-aggregated individual specimens from photographs, and solicited help of community scientists to score color morphs. We used a linear modeling framework that includes information about spatial population structure to demonstrate that color morph frequency and body size vary in response to climate, elevation, and over time, with an overall trend of higher frequency and decreased body size of the striped morph, but increased size of the unstriped morph. These surprising results suggest that morphs may be responding to multiple climate and geographic drivers through co-adapted morphological changes. This work highlights new practices of extracting trait data from museum specimens to demonstrate species phenotypes response to climate change. 

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2. SeedExtractor: An Open-Source GUI for Seed Image Analysis

   https://doi.org/10.3389/fpls.2020.581546  

   Zhu, Feiyu; Paul, Puneet; Hussain, Waseem; Wallman, Kyle; Dhatt, Balpreet K.; Sandhu, Jaspreet; Irvin, Larissa; Morota, Gota; Yu, Hongfeng; Walia, Harkamal (February 2021, Frontiers in Plant Science)

   Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length ( GS3 ) and width ( qSW5/GW5 ) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. 

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3. Frontiers in Imaging of Specimens in Mollusk Collections

   Leal, José H (April 2024, The Northeast Natural History Conference)

   Goldfarb, Keith (Ed.)

   Natural history collections are important depositories of biodiversity data. Digital photography of natural history collection specimens and subsequent dissemination of the resulting images on the web allow for the virtual discovery of these specimens, enhancing their accessibility to the target audience and the public in general. This presentation discusses digital photography of marine mollusks in collections, including some of the latest techniques for imaging of very small specimens, photography of specimens preserved in liquid, haptobionts, problems of color retention, transparency, 3-D photography, equipment, and other current areas of interest. Despite the focus on mollusks, the discussions can be extrapolated as generalities applicable to invertebrates from other phyla. The presentation also includes a discussion on equipment and the ideal digital parameters for imaging of natural history collection specimens, including image policies on acceptable file-format requirements for data hosts and aggregators such as iDigBio and others. (The presentation includes work funded in part by the NSF Thematic Collections Network grant award 2001528 “Mobilizing Millions of Mollusks from the Eastern Seaboard”). 

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4. Image Analysis to Quantify Coral Bleaching Using Greyscale Model

   https://doi.org/10.17504/protocols.io.bx8wprxe  

   McLachlan, RH; Grottoli, AG (January 2021, Protocolsio)

   This protocol outlines a method of quantitatively measuring the degree of bleaching of a coral colony nondestructively in the field using image analysis. Previous studies have shown that mean intensity grey (MIG), also known as percent whiteness, is highly correlated with chlorophyll a and Symbiodiniaceae density (Chow et al. 2016, Amid et al. 2018), and therefore can be used to quantify the bleaching intensity of a coral colony. Color analysis can be done using digital photographs of live coral colonies either in situ (e.g., Maguire et al. 2003) or exsitu in the lab (Amid et al. 2018; this protocol). Photographs must be taken prior to any preservation or processing of tissue, such as freezing, use of preservatives or fixatives, airbrushing etc., to ensure no alteration of the original coral color occurs. In this protocol, corals are photographed in front of a white reference standard and the resulting color images are subsequently converted to 8-bit greyscale and analyzed. There are two steps to this protocol: 1) Photographing live coral fragments 2) Image analysis of mean grey value 

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5. Color in motion: Generating 3-dimensional multispectral models to study dynamic visual signals in animals

   https://doi.org/10.3389/fevo.2022.983369  

   Miller, Audrey E.; Hogan, Benedict G.; Stoddard, Mary Caswell (September 2022, Frontiers in Ecology and Evolution)

   Analyzing color and pattern in the context of motion is a central and ongoing challenge in the quantification of animal coloration. Many animal signals are spatially and temporally variable, but traditional methods fail to capture this dynamism because they use stationary animals in fixed positions. To investigate dynamic visual displays and to understand the evolutionary forces that shape dynamic colorful signals, we require cross-disciplinary methods that combine measurements of color, pattern, 3-dimensional (3D) shape, and motion. Here, we outline a workflow for producing digital 3D models with objective color information from museum specimens with diffuse colors. The workflow combines multispectral imaging with photogrammetry to produce digital 3D models that contain calibrated ultraviolet (UV) and human-visible (VIS) color information and incorporate pattern and 3D shape. These “3D multispectral models” can subsequently be animated to incorporate both signaler and receiver movement and analyzed in silico using a variety of receiver-specific visual models. This approach—which can be flexibly integrated with other tools and methods—represents a key first step toward analyzing visual signals in motion. We describe several timely applications of this workflow and next steps for multispectral 3D photogrammetry and animation techniques. 

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