Ancestral Population Genomics
- PMID: 31278677
- DOI: 10.1007/978-1-4939-9074-0_18
Ancestral Population Genomics
Abstract
Borrowing both from population genetics and phylogenetics, the field of population genomics emerged as full genomes of several closely related species were available. Providing we can properly model sequence evolution within populations undergoing speciation events, this resource enables us to estimate key population genetics parameters such as ancestral population sizes and split times. Furthermore we can enhance our understanding of the recombination process and investigate various selective forces. With the advent of resequencing technologies, genome-wide patterns of diversity in extant populations have now come to complement this picture, offering an increasing power to study more recent genetic history.We discuss the basic models of genomes in populations, including speciation models for closely related species. A major point in our discussion is that only a few complete genomes contain much information about the whole population. The reason being that recombination unlinks genomic regions, and therefore a few genomes contain many segments with distinct histories. The challenge of population genomics is to decode this mosaic of histories in order to infer scenarios of demography and selection. We survey modeling strategies for understanding genetic variation in ancestral populations and species. The underlying models build on the coalescent with recombination process and introduce further assumptions to scale the analyses to genomic data sets.
Keywords: Ancestral population; Coalescence; Demography; Divergence; Markov model; Migration; Recombination; Selection; Speciation.
Similar articles
-
Ancestral population genomics.Methods Mol Biol. 2012;856:293-313. doi: 10.1007/978-1-61779-585-5_12. Methods Mol Biol. 2012. PMID: 22399464 Review.
-
Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.PLoS Genet. 2011 Mar;7(3):e1001319. doi: 10.1371/journal.pgen.1001319. Epub 2011 Mar 3. PLoS Genet. 2011. PMID: 21408205 Free PMC article.
-
Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.Methods Mol Biol. 2020;2090:167-189. doi: 10.1007/978-1-0716-0199-0_8. Methods Mol Biol. 2020. PMID: 31975168
-
Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.Mol Phylogenet Evol. 2013 Dec;69(3):1172-85. doi: 10.1016/j.ympev.2013.06.006. Epub 2013 Jun 22. Mol Phylogenet Evol. 2013. PMID: 23800835
-
Unraveling recombination rate evolution using ancestral recombination maps.Bioessays. 2014 Sep;36(9):892-900. doi: 10.1002/bies.201400047. Epub 2014 Jul 14. Bioessays. 2014. PMID: 25043668 Free PMC article. Review.
Cited by
-
Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown.PLoS Comput Biol. 2022 Aug 3;18(8):e1010407. doi: 10.1371/journal.pcbi.1010407. eCollection 2022 Aug. PLoS Comput Biol. 2022. PMID: 35921376 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources