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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]

Our understanding of the evolution of social mating systems is largely based on an atemporal ecological framework, whereas macroevolutionary and phylogenetic perspectives looking at the causes of mating systems variation are less developed. Here, we present analyses of the evolution of social mating systems in birds at an unprecedented scale, including 66% of the world's birds and using trait-dependent speciation and extinction models. We found that lekking (no social bond between the sexes) is very rarely lost, in accordance with the hypothesis that a male shifting to investing in one rather than multiple mates would suffer a severe fitness cost. In contrast, resource-defense polygamous lineages (with a weak, transient socio-sexual bond) frequently revert back to monogamy (strong, durable socio-sexual bond) and have an elevated extinction fraction. We tentatively attribute this to the impossibility for females to settle on an optimal parental care strategy under this system. Finally, we found that most gains of lekking have been directly from monogamy, rather than through an intermediate stage of resource-defense polygamy., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)