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Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores

Published online by Cambridge University Press:  15 August 2005

XAVIER DOMINGO-ROURA
Affiliation:
Genètica de la Conservació, Institut de Recerca i Tecnologia Agroalimentàries, Centre de Cabrils, Ctra. de Cabrils s/n, 08348 Cabrils (Barcelona), Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain
FRANCESC LÓPEZ-GIRÁLDEZ
Affiliation:
Genètica de la Conservació, Institut de Recerca i Tecnologia Agroalimentàries, Centre de Cabrils, Ctra. de Cabrils s/n, 08348 Cabrils (Barcelona), Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain
MIDORI SAEKI
Affiliation:
Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Landscape and Ecology Division, Environment Department, National Institute for Land and Infrastructure Management, Ministry of Land, Infrastructure and Transport, Asahi 1, Tsukuba, Ibaraki 305-0804, Japan
JOSEP MARMI
Affiliation:
Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain

Abstract

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We sequenced locus Mel08, with complex short repetitive motifs, in 24 carnivore species belonging to five different families in order to explore mutational changes in the region in the context of locus and species evolution. This non-coding locus includes up to four different parts or repetitive motifs showing size variability. The variability consists of repeat additions and deletions; substitutions, insertions and/or deletions creating interruptions in the repeat; and substitutions, insertions and deletions in the flanking regions. The locus has different repeat expansions in different carnivore subfamilies. We hypothesize that the complexity of this locus is due to a high mutation rate at an ancestral DNA sequence and, thus, prompts the emergence of repeats at mutational hotspots. High levels of homoplasy were evident, with nine electromorphs representing 28 haplotypes never shared across species. The variability in flanking regions was informative for phylogenetic inference and their evolutionary content. Tree topologies were congruent with relevant hypotheses on current conflicts in carnivore phylogenies, such as: (i) the monophyly of Lutrinae, (ii) the paraphyly of Mustelinae, (iii) the basal position of the Eurasian badger, Meles meles, in the Mustelidae, (iv) the classification of skunks as a separate family, Mephitidae, and (v) the placement of the red panda, Ailurus fulgens, as a monotypic family, Ailuridae, at a basal position in the Musteloidea.

Type
Research Article
Copyright
© 2005 Cambridge University Press