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Using supernetworks to distinguish hybridization from lineage-sorting

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posted on 2023-05-17, 02:22 authored by Barbara HollandBarbara Holland, Benthin, S, Lockhart, PJ, Moulton, V, Huber, KT
Background A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such as poor taxon-sampling and/or incomplete lineage-sorting. Results Using coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineage-sorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and well-sampled taxa across these loci, we found that it was possible to distinguish incomplete lineage-sorting from hybridization using the filtered Z-closure and Q-imputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that count-based filtering was the most effective filtering technique. Conclusion Filtered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies.

History

Publication title

BMC Evolutionary Biology

Volume

8

Pagination

EJ

ISSN

1471-2148

Department/School

School of Natural Sciences

Publisher

Biomed Central Ltd

Place of publication

Middlesex House, 34-42 Cleveland St, London, England, W1T 4Lb

Rights statement

© 2008 Holland et al

Repository Status

  • Open

Socio-economic Objectives

Expanding knowledge in the mathematical sciences

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