Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jeffrey L Peters, Trina E Roberts, Kevin Winker, Kevin G McCracken
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7d58445a3aa245c091ade24759820a37
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:7d58445a3aa245c091ade24759820a37
record_format	dspace
spelling	oai:doaj.org-article:7d58445a3aa245c091ade24759820a372021-11-18T07:27:03ZHeterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.1932-620310.1371/journal.pone.0031972https://doaj.org/article/7d58445a3aa245c091ade24759820a372012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22384117/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.Jeffrey L PetersTrina E RobertsKevin WinkerKevin G McCrackenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e31972 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeffrey L Peters Trina E Roberts Kevin Winker Kevin G McCracken Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
description	Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.
format	article
author	Jeffrey L Peters Trina E Roberts Kevin Winker Kevin G McCracken
author_facet	Jeffrey L Peters Trina E Roberts Kevin Winker Kevin G McCracken
author_sort	Jeffrey L Peters
title	Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
title_short	Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
title_full	Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
title_fullStr	Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
title_full_unstemmed	Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
title_sort	heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/7d58445a3aa245c091ade24759820a37
work_keys_str_mv	AT jeffreylpeters heterogeneityingeneticdiversityamongnoncodinglocifailstofitneutralcoalescentmodelsofpopulationhistory AT trinaeroberts heterogeneityingeneticdiversityamongnoncodinglocifailstofitneutralcoalescentmodelsofpopulationhistory AT kevinwinker heterogeneityingeneticdiversityamongnoncodinglocifailstofitneutralcoalescentmodelsofpopulationhistory AT kevingmccracken heterogeneityingeneticdiversityamongnoncodinglocifailstofitneutralcoalescentmodelsofpopulationhistory
_version_	1718423419447410688

Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.

Ejemplares similares