"Neo-sex chromosome evolution and phenotypic differentiation across an " by Subir B. Shakya, Cynthia Y. Wang-Claypool et al.

Faculty Publications

Title

Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris)

Authors

Subir B. Shakya, Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USA; Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Cynthia Y. Wang-Claypool, Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA; Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
Carla Cicero, Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA
Rauri C. K. Bowie, Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA; Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
Nicholas A. Mason, Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USA; Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA; Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA

Author ORCID Identifier

Shakya, Subir https://orcid.org/0000-0002-3561-2336

Document Type

Article

Publication Date

3-2022

Abstract

Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD data set of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.

Publication Source (Journal or Book title)

MOLECULAR ECOLOGY

First Page

1783

Last Page

1799

Recommended Citation

Shakya, S. B., Wang-Claypool, C. Y., Cicero, C., Bowie, R. C., & Mason, N. A. (2022). Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris). MOLECULAR ECOLOGY, 31 (6), 1783-1799. https://doi.org/10.1111/mec.16357

Link to Full Text

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