Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake.
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| Title: | Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. |
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| Authors: | Mathur, Samarth1,2, Mason, Andrew J.1,2, Bradburd, Gideon S.3,4, Gibbs, H. Lisle1,2 gibbs.128@osu.edu |
| Source: | Proceedings of the National Academy of Sciences of the United States of America. 10/24/2023, Vol. 120 Issue 43, p1-9. 25p. |
| Subjects: | Rattlesnakes, Genetic variation, Endangered species, Inbreeding, Genomics |
| Abstract: | Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future. [ABSTRACT FROM AUTHOR] |
| Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 173580550 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Mathur%2C+Samarth%22">Mathur, Samarth</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Mason%2C+Andrew+J%2E%22">Mason, Andrew J.</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Bradburd%2C+Gideon+S%2E%22">Bradburd, Gideon S.</searchLink><relatesTo>3,4</relatesTo><br /><searchLink fieldCode="AR" term="%22Gibbs%2C+H%2E+Lisle%22">Gibbs, H. Lisle</searchLink><relatesTo>1,2</relatesTo><i> gibbs.128@osu.edu</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22">Proceedings of the National Academy of Sciences of the United States of America</searchLink>. 10/24/2023, Vol. 120 Issue 43, p1-9. 25p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Rattlesnakes%22">Rattlesnakes</searchLink><br /><searchLink fieldCode="DE" term="%22Genetic+variation%22">Genetic variation</searchLink><br /><searchLink fieldCode="DE" term="%22Endangered+species%22">Endangered species</searchLink><br /><searchLink fieldCode="DE" term="%22Inbreeding%22">Inbreeding</searchLink><br /><searchLink fieldCode="DE" term="%22Genomics%22">Genomics</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1073/pnas.2303043120 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 25 StartPage: 1 Subjects: – SubjectFull: Rattlesnakes Type: general – SubjectFull: Genetic variation Type: general – SubjectFull: Endangered species Type: general – SubjectFull: Inbreeding Type: general – SubjectFull: Genomics Type: general Titles: – TitleFull: Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Mathur, Samarth – PersonEntity: Name: NameFull: Mason, Andrew J. – PersonEntity: Name: NameFull: Bradburd, Gideon S. – PersonEntity: Name: NameFull: Gibbs, H. Lisle IsPartOfRelationships: – BibEntity: Dates: – D: 24 M: 10 Text: 10/24/2023 Type: published Y: 2023 Identifiers: – Type: issn-print Value: 00278424 Numbering: – Type: volume Value: 120 – Type: issue Value: 43 Titles: – TitleFull: Proceedings of the National Academy of Sciences of the United States of America Type: main |
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