Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades.

ABSTRACT:

Premise

Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons.

Methods

We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and

SUBMITTER: Morales-Briones DF 

PROVIDER: S-EPMC9328367 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature