Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations

Stover, Daryn A.; Housman, Genevieve; Stone, Anne C.; Rosenberg, Michael S.; Verrelli, Brian C.

doi:10.3390/genes13020183

Cited by 3 publications

(1 citation statement)

References 114 publications

(174 reference statements)

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“…We find that several loci associated with adaptive morphological changes are implicated in disease phenotypes in humans and other organisms, suggesting that the variation we have identified here underlying adaptive phenotypes may be deleterious in nonurban settings but beneficial in urban environments. This pattern may seem paradoxical, but it has also been shown in previous studies that genes most closely tied to functional relevance may also represent candidates for maximizing fitness across diverse environments, such as variation for immunity, diet and subsistence, and bone development linked to positive selection in humans ( 68 – 70 ). Our observation here with anoles opens the possibility that genes of high evolutionary conservation could also be involved in adaptation to urban environments and worth pursuing in the future.…”

Section: Discussionmentioning

confidence: 96%

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Winchell

Campbell‐Staton

Losos

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated “natural experiments” in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus , a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions.

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Section: Discussionmentioning

confidence: 96%

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Winchell

Campbell‐Staton

Losos

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Genome-wide analysis of schizophrenia and multiple sclerosis identifies shared genomic loci with mixed direction of effects

Ahangari¹,

Everest²,

Nguyen³

et al. 2022

Brain, Behavior, and Immunity

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Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider

Miles,

Waterman,

Ayoub

et al. 2024

Journal of Heredity

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Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)—a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs—or retained ancestrally duplicated genes—from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

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Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations

Cited by 3 publications

References 114 publications

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Genome-wide analysis of schizophrenia and multiple sclerosis identifies shared genomic loci with mixed direction of effects

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider

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