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Demonstrating the genetic and environmental bases of adaptive phenotypes is a central goal of biology. Bird colors have a storied tradition at the forefront of conceptual advances in evolutionary biology. With recent increases in our ability to generate and analyze large phenotypic, environmental, and genetic data sets, we are in an excellent position to connect the environment-phenotype and phenotype-genotype links for bird color traits, illuminating potentially more general patterns and processes. I review selected advances in that arena, seeking to identify the most successful research approaches (with their strengths and pitfalls), so that they can be applied to the environment-phenotype-genotype nexus of other traits and taxa. At a macroevolutionary level, mechanistic models are well suited to compare evolutionary hypotheses of trait-environment correlations, and have revealed differences in tempo and mode of color evolution across clades, sexes, and body regions. At a microevolutionary scale, systems with ongoing gene flow along environmental gradients are conducive to addressing the genetics and ecology of phenotypic evolution. I weigh the strengths and weaknesses of two approaches to detecting genomic loci underpinning phenotypic variation in such systems: divergence scans and genome-wide association studies. I also discuss experimental approaches targeted at both the environment-phenotype and the phenotype-genotype links. I conclude by highlighting the importance of synthetic approaches that include environment, phenotype, and genotype within the same framework, and I suggest ideas for developments in that direction. [ABSTRACT FROM AUTHOR]

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops , whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.] [ABSTRACT FROM AUTHOR]

Sexual selection often drives traits in a direction that is disfavored by natural selection. The balance between these two types of selection can shift rapidly in response to environmental changes. Gallagher et al. (2024) report such a shift in the cricket population following the introduction of a parasitoid fly. The ancestral male morph, though still preferred by females, has been supplanted by multiple novel morphs that are more difficult for the parasitoid to detect. [ABSTRACT FROM AUTHOR]

Selection on signals that mediate social competition varies with resource availability. Climate regulates resource availability, which may affect the strength of competition and selection on signals. Traditionally, this meant that more seasonal, colder, or dryer—overall harsher—environments should favor the elaboration of male signals under stronger male‐male competition, increasing sexual dimorphism. However, females also use signals to compete; thus, harsher environments could strengthen competition and favor elaboration of signals in both sexes, decreasing sexual dimorphism. Alternatively, harsher environments could decrease sexual dimorphism due to scarcer resources to invest in signal elaboration in both sexes. We evaluated these contrasting hypotheses in antbirds, a family of Neotropical passerines that varies in female and male signals and occurs across diverse climatic regimes. We tested the association of sexual dimorphism of plumage coloration and songs with temperature, precipitation, and their seasonality. We found that greater seasonality is associated with lower sexual dimorphism in plumage coloration and greater elaboration of visual signals in both sexes, but not acoustic signals. Our results suggest that greater seasonality may be associated with convergent elaboration of female and male visual signals, highlighting the role of signals of both sexes in the evolution of sexual dimorphism. [ABSTRACT FROM AUTHOR]

Ecogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts that endothermic animals should have darker colors in warm/rainy climates. This rule also predicts that animals should be more rufous in warm/dry climates, the so-called complex Gloger's rule. Empirical studies frequently demonstrate that animals are darker in cool/wet climates rather than in warm/wet climates. Furthermore, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage color in the large Neotropical passerine family Furnariidae. We found that birds in cooler and rainier climates had darker plumage even after controlling for habitat type. Birds in darker habitats had darker plumage even after controlling for climate. The effects of temperature and precipitation interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be more rufous in warm/dry habitats but also, surprisingly, in cool/wet locales. We suggest that Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence, and resistance to feather abrasion. [ABSTRACT FROM AUTHOR]

Gloger's rule is a classic ecogeographical principle that, in its simplest version, predicts animals should be darker in warmer and wetter climates. In a rarely tested more complex version, it also predicts animals should be more rufous in warmer and drier climates. The Variable Antshrike (Thamnophilus caerulescens) is a widely distributed South American passerine that presents an impressive amount of plumage color variation and occupies a wide variety of climatic conditions. Moreover, genetic and vocal evidence indicate ongoing hybridization in south-central Bolivia among 3 populations with very distinct plumages. We collected color data from 232 specimens from throughout this species' distribution to test the predictions of Gloger's rule. We found a negative correlation between brightness and precipitation, consistent with the simple version of Gloger's rule. In contrast, we found that birds were darker in cooler climates, contrary to the simple version of Gloger's rule, but consistent with recent findings in other taxa. We found support for both predictions of the complex Gloger's rule and suggest it might be driven by background matching. We conclude by concurring with a recent suggestion that the simple version of Gloger's rule should be reformulated exclusively in terms of humidity. [ABSTRACT FROM AUTHOR]

Intraspecific geographic phenotypic variation is a crucial theme in evolutionary biology. Comparing its magnitude across species can provide insights into its ecological and genetic correlates. Here, we developed an index, which we dub the V index, to quantify intraspecific plumage colour variation in typical antbirds (Thamnophilidae), a family which has long interested ornithologists due to a high prevalence of intraspecific variation. The V index is based on a bivariate colour space defined by brightness and redness. Its value for each species equals the mean area occupied by each of its subspecies in that colour space, divided by the area of the species. Lower values indicate greater intraspecific geographic variation. Based on this index, Thamnophilus caerulescens (Variable Antshrike) was exceptionally geographically variable compared to other thamnophilids, as previously suggested based on qualitative evidence. In general, we found that the most variable species had disjunct distributions and deep phylogeographic structure, suggesting an effect of historical population dynamics in producing geographic variation. The V index can be adapted for use with other taxa, traits, and taxonomic levels, and we expect it will instigate novel ways of thinking about phenotypic variation in birds and other animals. [ABSTRACT FROM AUTHOR]

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree’s terminal taxa, but rarely do a tree and data set include all taxa within a clade. Because the probability that a taxon is included in a data set depends on ecological traits that have phylogenetic signal, missing taxa in real data sets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but theproblem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work. [ABSTRACT FROM AUTHOR]