Anomalous networks under the multispecies coalescent: theory and prevalence.

Autor: Ané C; Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA. cecile.ane@wisc.edu.; Department of Botany, University of Wisconsin - Madison, Madison, WI, 53706, USA. cecile.ane@wisc.edu., Fogg J; Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA., Allman ES; Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK, 99775-6660, USA., Baños H; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.; Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada., Rhodes JA; Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK, 99775-6660, USA.
Jazyk: angličtina
Zdroj: Journal of mathematical biology [J Math Biol] 2024 Feb 19; Vol. 88 (3), pp. 29. Date of Electronic Publication: 2024 Feb 19.
DOI: 10.1007/s00285-024-02050-7
Abstrakt: Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of [Formula: see text]-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods.
(© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Databáze: MEDLINE
Externí odkaz: