Research output: Contribution to journal › Article › peer-review
Review of population history reconstruction methods in conservation biology. / Totikov, Azamat A.; Tomarovsky, Andrey A.; Yakupova, Aliya R. et al.
In: Ecological Genetics, Vol. 21, No. 1, 2023, p. 85-102.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 58585081