Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies

    Authors

    C. C. Steiner; A. Mitelberg; R. Tursi;O. A. Ryder

    Comments

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    Abbreviated Journal Title

    Mol. Phylogenet. Evol.

    Keywords

    Phylogeny; Horses; Nuclear genes; Mitochondrial genes; Microsatellites; Ancestral polymorphism; DNA-SEQUENCE DATA; GENUS EQUUS; MIXED MODELS; LINKAGE MAP; HORSE; EVOLUTION; TREES; ZEBRA; INTROGRESSION; INCONGRUENCE; Biochemistry & Molecular Biology; Evolutionary Biology; Genetics &; Heredity

    Abstract

    Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor I gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (V chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals. (C) 2012 Elsevier Inc. All rights reserved.

    Journal Title

    Molecular Phylogenetics and Evolution

    Volume

    65

    Issue/Number

    2

    Publication Date

    1-1-2012

    Document Type

    Article

    Language

    English

    First Page

    573

    Last Page

    581

    WOS Identifier

    WOS:000309636200019

    ISSN

    1055-7903

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