TY - JOUR

T1 - Review of population history reconstruction methods in conservation biology

AU - Totikov, Azamat A.

AU - Tomarovsky, Andrey A.

AU - Yakupova, Aliya R.

AU - Graphodatsky, Alexander S.

AU - Kliver, Sergei F.

N1 - Funding source. The work was supported by a research grant of the Russian Science Foundation (RSF, 19-14-00034-P) and by a research grant of the Russian Foundation for Basic Research (RFBR, project number 20-04-00808-A). Публикация для корректировки.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - conservation biology

KW - demographic history

KW - demography

KW - effective population size

KW - genetic diversity

KW - genomics

KW - population genetics

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85163292808&origin=inward&txGid=8021222da845170a0b1e966ff14dd5e9

UR - https://www.mendeley.com/catalogue/267e99d6-9b6b-3730-bd2a-28beff74d0bd/

U2 - 10.17816/ecogen120078

DO - 10.17816/ecogen120078

M3 - Article

VL - 21

SP - 85

EP - 102

JO - Экологическая генетика

JF - Экологическая генетика

SN - 1811-0932

IS - 1

ER -