Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.

ABSTRACT: We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared with morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister

SUBMITTER: Schull JK 

PROVIDER: S-EPMC8920512 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature