Phylogenetic tree building in the genomic age

P Kapli, Z Yang, MJ Telford - Nature Reviews Genetics, 2020 - nature.com
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

Prevalence and adaptive impact of introgression

NB Edelman, J Mallet - Annual Review of Genetics, 2021 - annualreviews.org
Alleles that introgress between species can influence the evolutionary and ecological fate of
species exposed to novel environments. Hybrid offspring of different species are often unfit …

Widespread introgression across a phylogeny of 155 Drosophila genomes

A Suvorov, BY Kim, J Wang, EE Armstrong, D Peede… - Current Biology, 2022 - cell.com
Genome-scale sequence data have invigorated the study of hybridization and introgression,
particularly in animals. However, outside of a few notable cases, we lack systematic tests for …

Phylogenomic approaches to detecting and characterizing introgression

MS Hibbins, MW Hahn - Genetics, 2022 - academic.oup.com
Phylogenomics has revealed the remarkable frequency with which introgression occurs
across the tree of life. These discoveries have been enabled by the rapid growth of methods …

Efficient Bayesian inference under the multispecies coalescent with migration

T Flouri, X Jiao, J Huang… - Proceedings of the …, 2023 - National Acad Sciences
Analyses of genome sequence data have revealed pervasive interspecific gene flow and
enriched our understanding of the role of gene flow in speciation and adaptation. Inference …

The evolution of insect biodiversity

E Tihelka, C Cai, M Giacomelli, J Lozano-Fernandez… - Current Biology, 2021 - cell.com
Insects comprise over half of all described animal species. Together with the Protura
(coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form …

Multispecies coalescent: theory and applications in phylogenetics

S Mirarab, L Nakhleh, T Warnow - Annual Review of Ecology …, 2021 - annualreviews.org
Species tree estimation is a basic part of many biological research projects, ranging from
answering basic evolutionary questions (eg, how did a group of species adapt to their …

Species delimitation

B Rannala, Z Yang - 2020 - discovery.ucl.ac.uk
Species delimitation is the process of determining which groups of individual organisms
constitute different populations of a single species and which constitute different species …

Estimation of species divergence times in presence of cross-species gene flow

GP Tiley, T Flouri, X Jiao, JW Poelstra, B Xu… - Systematic …, 2023 - academic.oup.com
Cross-species introgression can have significant impacts on phylogenomic reconstruction of
species divergence events. Here, we used simulations to show how the presence of even a …

Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American …

J Ji, DJ Jackson, AD Leaché, Z Yang - Systematic Biology, 2023 - academic.oup.com
In the past two decades, genomic data have been widely used to detect historical gene flow
between species in a variety of plants and animals. The Tamias quadrivittatus group of North …