The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

Handle URI:
http://hdl.handle.net/10754/325448
Title:
The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization
Authors:
Eriksson, Anders ( 0000-0003-3436-3726 ) ; Manica, Andrea
Abstract:
Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.
Citation:
Eriksson A, Manica A (2014) The Doubly Conditioned Frequency Spectrum Does Not Distinguish between Ancient Population Structure and Hybridization. Molecular Biology and Evolution 31: 1618-1621. doi:10.1093/molbev/msu103.
Publisher:
Oxford University Press (OUP)
Journal:
Molecular Biology and Evolution
Issue Date:
13-Mar-2014
DOI:
10.1093/molbev/msu103
PubMed ID:
24627034
PubMed Central ID:
PMC4032131
Type:
Article
ISSN:
15371719
Appears in Collections:
Articles; Integrative Systems Biology Lab

Full metadata record

DC FieldValue Language
dc.contributor.authorEriksson, Andersen
dc.contributor.authorManica, Andreaen
dc.date.accessioned2014-08-27T09:51:46Z-
dc.date.available2014-08-27T09:51:46Z-
dc.date.issued2014-03-13en
dc.identifier.citationEriksson A, Manica A (2014) The Doubly Conditioned Frequency Spectrum Does Not Distinguish between Ancient Population Structure and Hybridization. Molecular Biology and Evolution 31: 1618-1621. doi:10.1093/molbev/msu103.en
dc.identifier.issn15371719en
dc.identifier.pmid24627034en
dc.identifier.doi10.1093/molbev/msu103en
dc.identifier.urihttp://hdl.handle.net/10754/325448en
dc.description.abstractDistinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.en
dc.language.isoenen
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.subjectdemographyen
dc.subjecthybridizationen
dc.subjectNeandertalen
dc.subjectpopulation structureen
dc.subjectAfricaen
dc.subjectalleleen
dc.subjectchimpanzeeen
dc.subjectgene linkage disequilibriumen
dc.subjectgenetic parametersen
dc.subjectgenetic variabilityen
dc.subjectpopulation geneticsen
dc.subjectpopulation modelen
dc.titleThe doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridizationen
dc.typeArticleen
dc.identifier.journalMolecular Biology and Evolutionen
dc.identifier.pmcidPMC4032131en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionEvolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorEriksson, Andersen

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