Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

YM Ding, XX Pang, Y Cao, WP Zhang… - Nature …, 2023 - nature.com
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that
differ in gene content and syntenic structure. Presence or absence of genes and …

Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene

H Kong, FL Condamine, L Yang, AJ Harris… - Systematic …, 2022 - academic.oup.com
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide
excellent opportunities to study rapid diversification and to understand the historical …

The genetic basis of a recent transition to live-bearing in marine snails

S Stankowski, ZB Zagrodzka, MD Garlovsky, A Pal… - Science, 2024 - science.org
Key innovations are fundamental to biological diversification, but their genetic basis is poorly
understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina …

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study …

TT Xue, SB Janssens, BB Liu, SX Yu - Molecular Phylogenetics and …, 2024 - Elsevier
Phylogenomic conflicts are widespread among genomic data, with most previous studies
primarily focusing on nuclear datasets instead of organellar genomes. In this study, we …

Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

MJ de Jong, A Niamir, M Wolf, AC Kitchener… - Communications …, 2023 - nature.com
Population-genomic studies can shed new light on the effect of past demographic processes
on contemporary population structure. We reassessed phylogeographical patterns of a …

Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

TW Xiao, HF Yan, XJ Ge - BMC Plant Biology, 2022 - Springer
Abstract Background The East Asian subtropical evergreen broad-leaved forests (EBLFs)
harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain …

Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae)

LH Yang, XZ Shi, F Wen, M Kang - Annals of Botany, 2023 - academic.oup.com
Abstract Background and Aims Hybridization has long been recognized as an important
process for plant evolution and is often accompanied by polyploidization, another prominent …

Detectability of varied hybridization scenarios using genome-scale hybrid detection methods

M Bjorner, EK Molloy, CN Dewey… - arXiv preprint arXiv …, 2022 - arxiv.org
Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to
patterns of genetic heritability that are unexpected under traditional, bifurcating models of …

On the need for new measures of phylogenomic support

RC Thomson, JM Brown - Systematic Biology, 2022 - academic.oup.com
The scale of data sets used to infer phylogenies has grown dramatically in the last decades,
providing researchers with an enormous amount of information with which to draw …

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

JA Rhodes, H Baños, JD Mitchell, ES Allman - Bioinformatics, 2021 - academic.oup.com
MSCquartets is an R package for species tree hypothesis testing, inference of species trees
and inference of species networks under the Multispecies Coalescent model of incomplete …