The aggregate site frequency spectrum for comparative population genomic inference

Molecular Ecology
Alexander T Xue, Michael J Hickerson

Abstract

Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five pop...Continue Reading

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References

Dec 1, 1992·Genetics·S A Sawyer, D L Hartl
Mar 1, 1997·Genetics·J Wakeley, J Hey
Jun 17, 1998·Molecular Ecology·P TaberletJ F Cosson
Mar 8, 2000·Nature·N MyersJ Kent
Dec 29, 2000·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·N H Barton
Jul 27, 2001·Proceedings of the National Academy of Sciences of the United States of America·H E HoekstraJ G Kingsolver
Oct 30, 2001·Current Opinion in Genetics & Development·P Andolfatto
Jan 22, 2003·Molecular Ecology·Richard J Abbott, Christian Brochmann
Jan 9, 2004·Nature·Chris D ThomasStephen E Williams
Jan 17, 2004·Science·Bryan T GrenfellEdward C Holmes
Apr 8, 2004·Proceedings of the National Academy of Sciences of the United States of America·William A CreskoJohn H Postlethwait
May 25, 2004·Evolution; International Journal of Organic Evolution·Michael A BellNathaniel J Buck
Apr 13, 2005·Proceedings of the National Academy of Sciences of the United States of America·Charles B KimmelWilliam A Cresko
Aug 17, 2005·Molecular Ecology·Staffan Bensch, Mikael Akesson
Sep 30, 2005·Proceedings. Biological Sciences·Susana PedrosaYolanda Bayón
Nov 16, 2005·Annual Review of Genetics·Rasmus Nielsen
Dec 21, 2005·Molecular Biology and Evolution·Joseph Felsenstein
Mar 18, 2006·Journal of Proteome Research·Linda Sage
May 17, 2006·Trends in Ecology & Evolution·Jessica Gurevitch, Dianna K Padilla
Jul 11, 2006·Science·T M BrooksA S L Rodrigues
Oct 4, 2006·Proceedings. Biological Sciences·Jon S BeadellRobert C Fleischer
Nov 17, 2006·Molecular Ecology·Douglas E SoltisPamela S Soltis
Jul 21, 2007·Trends in Ecology & Evolution·Dov F SaxWilliam R Rice
May 10, 2008·Trends in Plant Science·Peter J PrentisAndrew J Lowe
Jun 12, 2008·BMC Evolutionary Biology·Sriramana KanginakudruJ Nagaraju
Aug 19, 2008·The American Naturalist·J G KingsolverP Beerli
Aug 30, 2008·Trends in Ecology & Evolution·Jim Provan, K D Bennett
Sep 13, 2008·Annual Review of Microbiology·Edward C Holmes
Feb 7, 2009·Science·Ana Carolina CarnavalCraig Moritz
Feb 13, 2009·Nature·Gianni LitiEdward J Louis
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 22, 2010·Trends in Ecology & Evolution·Katalin CsilléryOlivier François

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Citations

Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Maria Tereza C Thomé, Bryan C Carstens
Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Anna Papadopoulou, L Lacey Knowles
Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Ivan PratesAna C Carnaval
Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Scott V EdwardsCraig Moritz
Oct 27, 2016·Ecology Letters·Frank T BurbrinkMichael J Hickerson
Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Leslie J Rissler
Jan 19, 2017·Molecular Ecology·Jessica A OswaldBrian Tilston Smith
Jul 1, 2017·Molecular Ecology·Megan L SmithBryan C Carstens
Dec 12, 2017·Molecular Ecology·Alicia Mastretta-YanesBrent C Emerson
Nov 28, 2017·Molecular Ecology·Sally PotterCraig Moritz
Aug 25, 2017·BMC Evolutionary Biology·Isaac OvercastMichael J Hickerson
Mar 5, 2020·Evolution; International Journal of Organic Evolution·Alexander T Xue, Michael J Hickerson
May 20, 2020·Molecular Ecology·Erwan Delrieu-TrottinPablo Saenz-Agudelo
Sep 2, 2020·Evolution; International Journal of Organic Evolution·Jente Ottenburghs
Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Lynsey BunnefeldKonrad Lohse

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