Biology subjects

Shultz, A. J.

Publications and source records attributed to Shultz, A. J..

6 recordsLinked to original sources

bioRxiv2025

charisma: An R package to perform reproducible color characterization of digital images for biological studies

O_LIAdvances in digital imaging and software tools have provided increasingly accessible datasets and methods for analyzing color evolution. Despite the variety of computational packages available, most rely on color classification before running analyses. Previous methods to characterize color limit the ability to analyze large-scale image databases and are not always representative of biologically relevant color classes, which decrease the accuracy of downstream analyses. C_LIO_LIHere, we present charisma, an R package designed to characterize the distribution of distinct color classes in images suitable for large-scale studies of biological organisms. Here, we demonstrate the utility of our package through an analysis of color evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. C_LIO_LIWe show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre-identified, canonical color swatches. We find that charisma color classifications are consistent with those made by color-pattern experts in the field. Applying charisma to tanager color evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. C_LIO_LIOur results demonstrate that using charisma to manually curate and characterize colors in images provides a standardized, reliable, and reproducible framework for high-throughput color classification. C_LI Anonymized Data/Code for Peer ReviewO_LIAnalytic data/code for this manuscript can be found on the following Open Science Frame-work repo: https://osf.io/cqg59/overview?view_only=29c9786a338e48618fabbab2883937cc C_LIO_LIcharisma package GitHub repo: https://anonymous.4open.science/r/charisma-C87E/ C_LI

evolutionary biology↗

bioRxiv2024

How does Gloger's rule predict near- and mid-infrared radiation in birds?

Animal coloration has diverse functions such as camouflage, communication, thermoregulation, protection from UV damage and more, and can be shaped by environmental selective pressures. Some climactic selective pressures are strong enough to produce consistent patterns in many species across large-scale geographic gradients. One pattern in endothermic animals is Glogers rule, which predicts that populations in hot, humid areas will be darker than those in cool, dry areas. This pattern has been demonstrated in several species across latitudinal gradients and is expected to relate to the selective effects of both local thermoregulatory pressures and humidity. However, shortwave radiation from sunlight extends beyond the visible spectrum [400-700 nm] into the near-infrared; thus, thermal pressures often result in changes in surface reflectance characteristics beyond the visible [e.g., 700-2500 nm]. Further, heat exchange with the environment extends into the mid-infrared, including MIR heat loss through the atmospheric transmission window [7.5 - 14 um]. Here, we examine both UV-NIR absorption and MIR emittance in five species of birds that have been shown to follow, or not follow, Glogers rule. We show that NIR absorption varies by species and population in ways that correspond to their habitat and thermoregulatory strategies. MIR emittance, by contrast, was very stable across both species and populations but differed across populations of Northern Bobwhites. We conclude by highlighting the importance of extending coloration research into the NIR and MIR. Further consideration of infrared radiation is necessary for a complete view of animals phenotypic diversity and possible responses to thermal challenge.

ecology↗

bioRxiv2023

Constraint and innovation in color evolution among species and among plumage patches in five avian radiations

Understanding the causes and limits of phenotypic diversification remains a key challenge in evolutionary biology. Color patterns are some of the most diverse phenotypes in nature. In birds, recent work within families has suggested that plumage complexity might be a key innovation driving color diversity. Whether these patterns hold at larger taxonomic scales remains unknown. Here, we assemble a large database of UV-Vis spectral data across five diverse clades of birds (45791 spectra, 1135 species). Using multivariate phylogenetic comparative methods, we compare evolutionary rates and color space occupancy (i.e., quantification of observed colors) among these clades. Novel color-producing mechanisms have enabled clades to occupy new regions of color space, but using more coloration mechanisms did not result in overall more color space occupancy. Instead, the use of more color-producing mechanisms resulted in faster rates of color evolution and less integrated color among plumage regions. Flexible Bayesian modeling further allowed us to assess the relationship between interpatch and interspecific directions of color variation. We find that interpatch variation generally diverges from interspecies cladewise trends in males but not females, suggesting developmental or selective constraints operating in females across evolutionary scales. By comparing rates among clades and assessing both interpatch and interspecies color variation, we reveal how innovations and constraints operate across evolutionary and developmental scales.

evolutionary biology↗

bioRxiv2023

A fast, reproducible, high-throughput variant calling workflow for evolutionary, ecological, and conservation genomics

The increasing availability of genomic resequencing datasets and high quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in non-model organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analysis.Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with HPC clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing datasets from non-mammalian vertebrates. These variant datasets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public datasets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating rapid use and reuse of large genomic datasets.

genomics↗

bioRxiv2019

Microstructures amplify seemingly honest signals in carotenoid-colored tanagers

Red, orange, and yellow carotenoid-colored plumages have been considered honest signals of condition. We comprehensively quantified carotenoid signals in the social, sexually-dimorphic tanager genus Ramphocelus using scanning electron microscopy (SEM), finite-difference time-domain (FDTD) optical modeling, liquid chromatography-mass spectrometry (LC-MS), and spectrophotometry. Despite males having significantly more saturated color patches, males and females within a species have equivalent amounts and types of carotenoids. Male, but not female, feathers have elaborate microstructures which amplify color appearance. Expanded barbs enhance color saturation (for the same amount of pigment) by increasing the transmission of optical power through the feather. Dihedral barbules (vertically-angled, strap-shaped barbules) reduce total reflectance to generate "super black" plumage, an optical illusion to enhance nearby color. Dihedral barbules paired with red carotenoid pigment produce "velvet red" plumage. Together, our results suggest that a widely cited index of honesty--carotenoid pigments--cannot fully explain male appearance. We propose that males are selected to evolve amplifiers of honest signals--in this case, microstructures that enhance appearance --that are not necessarily themselves linked to quality.

evolutionary biology↗

bioRxiv2018

Immune genes are hotspots of shared positive selection across birds and mammals

Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.

evolutionary biology↗