title: The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads.
abstract: Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
authors.forename: Liliya
authors.initials: L
authors.lastname: Doronina
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Matzke
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.|Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: Core Facility Genomics, Medical Faculty, University of Münster, Münster, Germany.
authors.forename: Monika
authors.initials: M
authors.lastname: Stoll
authors.affiliation: Core Facility Genomics, Medical Faculty, University of Münster, Münster, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Huge
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D018626:Retroelements; D012377:Rodentia / Q000145:classification* / Q000235:genetics*
chemical_list: D018626:Retroelements