Anomalous networks under the multispecies coalescent: theory and prevalence

Journal of Mathematical Biology, Journal Year: 2024, Volume and Issue: 88(3)

Published: Feb. 19, 2024

Language: Английский

Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages

Systematic Biology, Journal Year: 2023, Volume and Issue: 72(6), P. 1357 - 1369

Published: Sept. 12, 2023

The evolutionary implications and frequency of hybridization introgression are increasingly being recognized across the tree life. To detect from multi-locus genome-wide sequence data, a popular class methods based on summary statistics subsets 3 or 4 taxa. However, these often carry assumption constant substitution rate lineages genes, which is commonly violated in many groups. In this work, we quantify effects variation D test (also known as ABBA-BABA test), D3 test, HyDe. All tests used widely range taxonomic groups, part because they very fast to compute. We consider species lineages, their lineage-by-gene interaction, gene-tree edges. simulated networks according birth-death-hybridization process, so capture realistic phylogenies. For all tested, found marked increase false discovery reticulation (type-1 error rate) when there lineages. was most sensitive, with around 80% type-1 error, such that appears more sensitive departure clock than presence reticulation. tests, power events decreased number increased, indicating multiple can obscure one another if occur within small subset Our study highlights need using site-based statistics, points advantages do not require assumptions rates genes.

Language: Английский

Anomalous networks under the multispecies coalescent: theory and prevalence

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 21, 2023

Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an

Language: Английский