Review of population history reconstruction methods in conservation biology
- Authors: Totikov A.A.1,2, Tomarovsky A.A.1,2, Yakupova A.R.3, Graphodatsky A.S.1, Kliver S.F.4
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Affiliations:
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences
- Novosibirsk State University
- Saint Petersburg National Research University of Information Technologies, Mechanics and Optics
- Independent researcher
- Issue: Vol 21, No 1 (2023)
- Pages: 85-102
- Section: Methodology in ecological genetics
- URL: https://journals.rcsi.science/ecolgenet/article/view/132252
- DOI: https://doi.org/10.17816/ecogen120078
- ID: 132252
Cite item
Abstract
Demographic history reconstruction is based on the estimation of effective population size (Ne), which is inferred and interpreted in various fields of evolutionary and conservation biology. Interest in Ne estimation is growing, as the key evolutionary forces and their are linked to Ne, and genetic data become increasingly accessible. However, what is effective population size, and how can we obtain an estimate of effective population size? In this review, we describe the history of the term “Ne” and explore existing methods for obtaining historical and contemporary estimates of changes in effective population size. We provide a detailed overview of methods based on sequential Markovian coalescence (SMC), generalized phylogenetic coalescence (G-PhoCS), identity by descent (IBD) and identity by state (IBS) similarity, as well as methods using allele frequency spectrum (AFS). For each method, we briefly summarize the underlying theory and note its advantages and disadvantages. In the final section of the review, we present examples of the use of these methods for various non-model species with conservation status.
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##article.viewOnOriginalSite##About the authors
Azamat A. Totikov
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
Author for correspondence.
Email: a.totickov1@gmail.com
ORCID iD: 0000-0003-1236-631X
SPIN-code: 9767-3971
Scopus Author ID: 57265434800
research assistant; postgraduate student
Russian Federation, Novosibirsk; NovosibirskAndrey A. Tomarovsky
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
Email: andrey.tomarovsky@gmail.com
ORCID iD: 0000-0002-6414-704X
SPIN-code: 6727-8664
Scopus Author ID: 57264872500
research assistant; postgraduate student
Russian Federation, Novosibirsk; NovosibirskAliya R. Yakupova
Saint Petersburg National Research University of Information Technologies, Mechanics and Optics
Email: aliyah.yakupova@gmail.com
ORCID iD: 0000-0003-1486-0864
SPIN-code: 4292-0609
Scopus Author ID: 57264122200
master
Russian Federation, Saint PetersburgAlexander S. Graphodatsky
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences
Email: graf@mcb.nsc.ru
ORCID iD: 0000-0002-8282-1085
SPIN-code: 4436-9033
Scopus Author ID: 7003878913
Dr. Sci. (Biol.), head of the Department of Diversity and Evolution of Genomes, head of the Laboratory of Animal Cytogenetics
Russian Federation, NovosibirskSergei F. Kliver
Independent researcher
Email: mahajrod@gmail.com
ORCID iD: 0000-0002-2965-3617
SPIN-code: 8635-4259
Scopus Author ID: 56449314300
independent researcher
Georgia, BatumiReferences
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