Work

Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia

Year: 2019

Type: preprint

Abstract: We present Champagne, a whole-genome method for generating cha racter m atrices for p hylogenomic a nalysis using large g e n omic e vents that, by rigorously picking orthologous genes and locating large, virtually homoplasy-free insertion and deletion events, delivers a character matrix that outperforms existing morphological and nucleotide-based matrices on both established phylogenies, and difficult-to-resolve nodes in the mammalian tree. Champagne harbors distinct theoretical advantages, and can easily be run on any clade of related species, of the many currently being sequenced. Champagne considerably improves the retention index in the parsimony analysis of a number of widely established topologies, observes incomplete lineage sorting (ILS) at the root of Paenungulata, finds little evidence for human-chimp-gorilla ILS, and most surprisingly, offers convincing evidence for a reconsideration of squirrel’s position in the rodent tree.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/803957

Authors: James Kusik Schull, Yatish Turakhia, William J. Dally, Gill Bejerano

Institutions: Stanford University, Nvidia (United States)

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Human Genome Research Institute

Award: The 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome.