Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting

Abstract

Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful implementation of species tree models that take population genetic parameters into account. However, these models have not included allopolyploid hybridization and the special problems imposed when species trees of allopolyploids are inferred. Here, 2 new models for the statistical inference of the evolutionary history of allopolyploids are evaluated using simulations and demonstrated on 2 empirical data sets. It is assumed that there has been a single hybridization event between 2 diploid species resulting in a genomic allotetraploid. The evolutionary history can be represented as a species network or as a multilabeled species tree, in which some pairs of tips are labeled with the same species. In one of the models (AlloppMUL), the multilabeled species tree is inferred directly. This is the simplest model and the most widely applicable, since fewer assumptions are made. The second model (AlloppNET) incorporates the hybridization event explicitly which means that fewer parameters need to be estimated. Both models are implemented in the BEAST framework. Simulations show that both models are useful and that AlloppNET is more accurate if the assumptions it is based on are valid. The models are demonstrated on previously analyzed data from the genera Pachycladon (Brassicaceae) and Silene (Caryophyllaceae).

Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing

“…Polyploid evolution in Cystopteridaceae. (a) The maximum clade credibility multi‐labeled tree inferred by AlloPPnet (Jones et al ., ) from four single‐copy nuclear loci. The subtree connecting extant diploid species has thickened branches and extant diploid species names are in bold face.…”

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

“…Research into the origin of polyploid species and their subsequent adaptation will continue to benefit from the advent of short read and other sequencing technologies (Burrell et al, 2015;Qi et al, 2015;Rothfels et al, 2017;Stetter & Schmid, 2017). Newly developed data analysis methods will make the identification of allopolyploids and studies of their evolution tractable (Jones et al, 2013;McKinney et al, 2017;Gompert & Mock, 2017). GBS data, coupled with network analysis, provides an affordable option to sample more accessions than previous methods and investigate additional questions about polyploid evolution.…”

Computational approaches to species phylogeny inference and gene tree reconciliation

“…For integrative likelihood approaches, a method for computing the probability of a gene tree given a species tree assuming both ILS and DL was given in [50], assuming DL and HGT was given in [60], and assuming ILS and HGT in a special case was given in [61]. Methods have been developed for computing the probabilities of gene trees under hybridization and ILS in special, limited cases [62, 63, 53, 64], and then for computing the probabilities in general cases [49]. Marcussen et al [65] recently developed a method for inferring phylogenetic networks in the presence of ILS that is aimed at modeling polyploid hybridization.…”