10.5061/DRYAD.71S06
Doronina, Liliya
University of Münster
Churakov, Gennady
University of Münster
Kuritzin, Andrej
St. Petersburg State Technological Institute
Shi, Jingjing
University of Münster
Baertsch, Robert
4Department of Biomolecular Engineering, University of California, Santa
Cruz, California 95064, USA
Clawson, Hiram
4Department of Biomolecular Engineering, University of California, Santa
Cruz, California 95064, USA
Schmitz, Juergen
University of Münster
Data from: Speciation network in Laurasiatheria: retrophylogenomic signals
Dryad
dataset
2018
Carnivora
Cetartiodactyla
Eulipotyphla
phylogenomic network
Retrotransposons
genome mosaic
retrophylogenomics
Perissodactyla
Chiroptera
Pholidota
Laurasiatheria
2018-03-03T00:00:00Z
2018-03-03T00:00:00Z
en
https://doi.org/10.1101/gr.210948.116
4082019 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Supplemental_Material_S3-S5Supplemental Material S3: Alignments of
retrotransposon markers for
Chiroptera-Perissodactyla-Cetartiodactyla-Carnivora relationships.
Supplemental Material S4: Concatenated alignments of retrotransposon
flanking regions. Supplemental Material S5: Alignments of deletion
markers.
Laurasia