title: Speciation network in Laurasiatheria: retrophylogenomic signals.
abstract: Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.
authors.forename: Liliya
authors.initials: L
authors.lastname: Doronina
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.|Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany.
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: Department of System Analysis, Saint Petersburg State Institute of Technology, 190013 St. Petersburg, Russia.
authors.forename: Andrej
authors.initials: A
authors.lastname: Kuritzin
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Shi
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Baertsch
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
mesh_terms: D000818:Animals; D002417:Cattle; D002685:Chiroptera / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D004285:Dogs; D005819:Genetic Markers; D049810:Genetic Speciation; D016678:Genome; D006736:Horses / Q000145:classification / Q000235:genetics*; D006824:Hybridization, Genetic; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D018626:Retroelements; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005819:Genetic Markers; D018626:Retroelements