Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds

Thom, Gregory; Moreira, Lucas Rocha; Batista, Romina; Gehara, Marcelo; Aleixo, Alexandre; Smith, Brian Tilston

Abstract

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.

Citation

Thom, G., Moreira, L. R., Batista, R., Gehara, M., Aleixo, A., & Smith, B. T. (in press). Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biology and Evolution, 16(1), evae002. https://doi.org/10.1093/gbe/evae002

• Journal Article Type: Article
• Acceptance Date: Dec 12, 2023
• Online Publication Date: Jan 17, 2024
• Deposit Date: Feb 5, 2024
• Publicly Available Date: Feb 5, 2024
• Journal: Genome Biology and Evolution
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 16
• Issue: 1
• Pages: evae002
• DOI: https://doi.org/10.1093/gbe/evae002
• Keywords: gene flow, chromosomes, natural selection, phylogenomics, recombination rate