Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora).
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.
Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany doronina@uni-muenster.de jueschm@uni-muenster.de.
Liliya
L
Doronina
Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
Gennady
G
Churakov
Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany.
Jingjing
J
Shi
Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), Neuruppin, Germany.
Jürgen
J
Brosius
Department of Biomolecular Engineering, University of California, Santa Cruz.
Robert
R
Baertsch
Department of Biomolecular Engineering, University of California, Santa Cruz.
Hiram
H
Clawson
Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany doronina@uni-muenster.de jueschm@uni-muenster.de.
Jürgen
J
Schmitz
D000818:Animals; D005075:Biological Evolution; D002335:Carnivora / Q000235:genetics*; D019143:Evolution, Molecular; D049810:Genetic Speciation; D023281:Genomics; D006824:Hybridization, Genetic; D020084:Long Interspersed Nucleotide Elements; D008969:Molecular Sequence Data; D010802:Phylogeny; D020086:Short Interspersed Nucleotide Elements
Arctoidea; Carnivora; Pholidota; phylogeny; retrogenomics; retrophylogenomics; retroposition; truncated LINEs