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Cited by 30Genetic diversity and population structureForensic and Genetic ResearchGenetic Mapping and Diversity in Plants and Animals

Whole‐exome sequencing reveals a long‐term decline in effective population size of red spruce (Picea rubens)

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Capblancq, Thibaut, Butnor, John R., Deyoung, Sonia, Thibault, Ethan, Munson, Helena, Nelson, David M., Fitzpatrick, Matthew C., Keller, Stephen R.·2020·Evolutionary Applications
DOI 10.1111/eva.12985PMC PMC7513712
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Abstract

Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo‐genetic history can have immediate conservation implications. We used a whole‐exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high‐elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop “sky islands.” Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome‐derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small N e, with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce.

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  • Stampy's use of hashing to accommodate high sequence variability allows researchers to study populations with significant genetic differences, making it invaluable for evolutionary biology and conservation genetics.

    “Stampy's use of hashing to accommodate high sequence variability allows researchers to study populations with significant genetic differences, making it invaluable for evolutionary biology and conservation genetics [55];”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [55]

    The Materials & Methods section (Sequence alignment and genotype likelihood estimation; page not provided) confirms that the authors tested Stampy as a read aligner in a red-spruce population-genetics study. It does not describe Stampy using hashing to accommodate high sequence variability or establish that it is invaluable; for their data, mapping quality was similar to BWA, but BWA was much faster and was preferred. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Capblancq, T., Butnor, J. R., Deyoung, S., Thibault, E., Munson, H., Nelson, D. M., Fitzpatrick, M. C., & Keller, S. R.
Affiliations
  • University of Vermont (US)
  • University of Maryland Center for Environmental Science (US)
Corresponding author
  • Capblancq, Thibaut
  • Keller, Stephen R.
ORCID
Venue
Evolutionary Applications
Publisher
Wiley
Published
2020-05-22
Volume
13
Issue
9
Pages
2190-2205
ISSN
  • 1752-4563 (ISSN-L)
  • 1752-4571
DOI
10.1111/eva.12985
PMC
PMC7513712
OpenAlex
W3022005556
Cited by
30
References
5
Citations by year
2026: 5 · 2025: 4 · 2024: 5 · 2023: 3 · 2022: 8 · 2021: 5
FWCI
2.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Evolutionary Applications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Science Foundation (1656099)
  • U.S. Department of Agriculture (1006810)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
red spruce, effective population size decline, population bottleneck, genetic diversity, population structure (demography), ancestry groups, sky islands, population fragmentation, exome capture, Picea glauca, tree conservation, non-model organisms, Appalachian Mountains

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