Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris)
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 elucidatin...
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ftlouisianastuir:oai:digitalcommons.lsu.edu:biosci_pubs-4471 2023-06-11T04:11:28+02:00 Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) Shakya, Subir B. Wang-Claypool, Cynthia Y. Cicero, Carla Bowie, Rauri C. K. Mason, Nicholas A. 2022-03-01T08:00:00Z https://digitalcommons.lsu.edu/biosci_pubs/3474 https://doi.org/10.1111/mec.16357 https://onlinelibrary.wiley.com/doi/10.1111/mec.16357 unknown LSU Digital Commons https://digitalcommons.lsu.edu/biosci_pubs/3474 doi:10.1111/mec.16357 https://onlinelibrary.wiley.com/doi/10.1111/mec.16357 Faculty Publications Alaudidae chromosomal inversion elevation genome architecture landscape genomics neo-sex chromosomes Sierra Nevada structural variation GENE FLOW LOCAL ADAPTATION F-STATISTICS TOOL SET DE-NOVO DISTANCE GENOME COLONIZATION AUTOSOMES ISLAND Biochemistry Ecology and Evolutionary Biology Environmental Sciences Molecular Biology text 2022 ftlouisianastuir https://doi.org/10.1111/mec.16357 2023-05-28T18:33:14Z 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. Text Eremophila alpestris LSU Digital Commons (Louisiana State University) Molecular Ecology 31 6 1783 1799 |
institution |
Open Polar |
collection |
LSU Digital Commons (Louisiana State University) |
op_collection_id |
ftlouisianastuir |
language |
unknown |
topic |
Alaudidae chromosomal inversion elevation genome architecture landscape genomics neo-sex chromosomes Sierra Nevada structural variation GENE FLOW LOCAL ADAPTATION F-STATISTICS TOOL SET DE-NOVO DISTANCE GENOME COLONIZATION AUTOSOMES ISLAND Biochemistry Ecology and Evolutionary Biology Environmental Sciences Molecular Biology |
spellingShingle |
Alaudidae chromosomal inversion elevation genome architecture landscape genomics neo-sex chromosomes Sierra Nevada structural variation GENE FLOW LOCAL ADAPTATION F-STATISTICS TOOL SET DE-NOVO DISTANCE GENOME COLONIZATION AUTOSOMES ISLAND Biochemistry Ecology and Evolutionary Biology Environmental Sciences Molecular Biology Shakya, Subir B. Wang-Claypool, Cynthia Y. Cicero, Carla Bowie, Rauri C. K. Mason, Nicholas A. Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
topic_facet |
Alaudidae chromosomal inversion elevation genome architecture landscape genomics neo-sex chromosomes Sierra Nevada structural variation GENE FLOW LOCAL ADAPTATION F-STATISTICS TOOL SET DE-NOVO DISTANCE GENOME COLONIZATION AUTOSOMES ISLAND Biochemistry Ecology and Evolutionary Biology Environmental Sciences Molecular Biology |
description |
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. |
format |
Text |
author |
Shakya, Subir B. Wang-Claypool, Cynthia Y. Cicero, Carla Bowie, Rauri C. K. Mason, Nicholas A. |
author_facet |
Shakya, Subir B. Wang-Claypool, Cynthia Y. Cicero, Carla Bowie, Rauri C. K. Mason, Nicholas A. |
author_sort |
Shakya, Subir B. |
title |
Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
title_short |
Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
title_full |
Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
title_fullStr |
Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
title_full_unstemmed |
Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris) |
title_sort |
neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (eremophila alpestris) |
publisher |
LSU Digital Commons |
publishDate |
2022 |
url |
https://digitalcommons.lsu.edu/biosci_pubs/3474 https://doi.org/10.1111/mec.16357 https://onlinelibrary.wiley.com/doi/10.1111/mec.16357 |
genre |
Eremophila alpestris |
genre_facet |
Eremophila alpestris |
op_source |
Faculty Publications |
op_relation |
https://digitalcommons.lsu.edu/biosci_pubs/3474 doi:10.1111/mec.16357 https://onlinelibrary.wiley.com/doi/10.1111/mec.16357 |
op_doi |
https://doi.org/10.1111/mec.16357 |
container_title |
Molecular Ecology |
container_volume |
31 |
container_issue |
6 |
container_start_page |
1783 |
op_container_end_page |
1799 |
_version_ |
1768386551661723648 |