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1. Avian Coloration Genetics: Recent Advances and Emerging Questions

   https://doi.org/10.1093/jhered/esab015  

   Price-Waldman, Rosalyn; Stoddard, Mary Caswell (May 2021, Journal of Heredity)

   vonHoldt, Bridgett (Ed.)

   Abstract The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs—which exhibit a stunning range of cryptic and conspicuous forms—inspired early work on adaptive coloration. More recently, avian color has fueled discoveries on the physiological, developmental, and—increasingly—genetic mechanisms responsible for phenotypic variation. The relative ease with which avian color traits can be quantified has made birds an attractive system for uncovering links between phenotype and genotype. Accordingly, the field of avian coloration genetics is burgeoning. In this review, we highlight recent advances and emerging questions associated with the genetic underpinnings of bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, and orange in most birds and psittacofulvins that produce similar colors in parrots. We then discuss structural colors, which are produced by the interaction of light with nanoscale materials and greatly extend the plumage palette. Structural color genetics remain understudied—but this paradigm is changing. We next explore how colors that arise from interactions among pigmentary and structural mechanisms may be controlled by genes that are co-expressed or co-regulated. We also identify opportunities to investigate genes mediating within-feather micropatterning and the coloration of bare parts and eggs. We conclude by spotlighting 2 research areas—mechanistic links between color vision and color production, and speciation—that have been invigorated by genetic insights, a trend likely to continue as new genomic approaches are applied to non-model species. 

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2. Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel

   https://doi.org/10.1093/molbev/msab177  

   Miranda, Inês; Giska, Iwona; Farelo, Liliana; Pimenta, João; Zimova, Marketa; Bryk, Jarosław; Dalén, Love; Mills, L Scott; Zub, Karol; Melo-Ferreira, José (June 2021, Molecular Biology and Evolution)

   Teeling, Emma (Ed.)

   Abstract Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat coloration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage color moults across regions with varying winter snow. Whole-genome sequence data were obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris coloration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200-kb genomic region to coloration morph, which was validated by genotyping museum specimens from intermorph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change cosegregating with coloration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favored winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter color variation in mammals and that seasonal camouflage can be modulated by changes at single key genes. 

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3. Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations

   https://doi.org/10.1093/beheco/arz134  

   Valvo, Jennifer J.; Rodd, F. Helen; Hughes, Kimberly A.; Herberstein, ed., Marie (August 2019, Behavioral Ecology)

   Abstract How genetic variation is maintained in ecologically important traits is a central question in evolutionary biology. Male Trinidadian guppies, Poecilia reticulata, exhibit high genetic diversity in color patterns within populations, and field and laboratory studies implicate negative frequency-dependent selection in maintaining this variation. However, behavioral and ecological processes that mediate this selection in natural populations are poorly understood. We evaluated female mate preference in 11 natural guppy populations, including paired populations from high- and low-predation habitats, to determine if this behavior is responsible for negative frequency-dependent selection and to evaluate its prevalence in nature. Females directed significantly more attention to males with rare and unfamiliar color patterns than to males with common patterns. Female attention also increased with the area of male orange coloration, but this preference was independent of the preference for rare and unfamiliar patterns. We also found an overall effect of predation regime; females from high-predation populations directed more attention toward males than those from low-predation populations. Again, however, the habitat-linked preference was statistically independent from the preference for rare and unfamiliar patterns. Because previous research indicates that female attention to males predicts male mating success, we conclude that the prevalence of female preference for males with rare and unfamiliar color patterns across many natural populations supports the hypothesis that female preference is an important process underlying the maintenance of high genetic variation in guppy color patterns. 

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4. A new species of Chromis damselfish from the tropical western Atlantic (Teleostei, Pomacentridae)

   https://doi.org/10.3897/zookeys.1008.58805  

   McFarland, Emily P.; Baldwin, Carole C.; Robertson, David Ross; Rocha, Luiz A.; Tornabene, Luke (December 2020, ZooKeys)

   null (Ed.)

   Initially described in 1882, Chromis enchrysurus , the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, this study sought to determine whether the white-tailed Chromis is actually a color morph of Chromis enchrysurus or a distinct species. Phylogenetic analyses of mitochondrial genes cytochrome b and cytochrome c oxidase subunit I separated Chromis enchrysurus and the white-tailed Chromis into two reciprocally monophyletic clades. A principal component analysis based on 27 morphological characters separated the two groups into clusters that correspond with caudal-fin coloration, which was either known or presumed based on the specimen’s collection site according to biogeographic data on species boundaries in the Greater Caribbean. Genetic, morphological, and biogeographic data all indicate that the white-tailed Chromis is a distinct species, herein described as Chromis vanbebberae sp. nov. The discovery of a new species within a conspicuous group such as damselfishes in a well-studied region of the world highlights the importance of deep-reef exploration in documenting undiscovered biodiversity. 

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5. Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel ( Sciurus carolinensis )

   https://doi.org/10.1111/mec.17230  

   Fusco, Nicole A.; Cosentino, Bradley J.; Gibbs, James P.; Allen, Maximilian L.; Blumenfeld, Alexander J.; Boettner, George H.; Carlen, Elizabeth J.; Collins, Merri; Dennison, Catherine; DiGiacopo, Devin; et al (December 2023, Molecular Ecology)

   Abstract Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest‐dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation‐by‐distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas. 

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