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

Graham Jones (Institutionen för biologi och miljövetenskap ; Institutionen för matematiska vetenskaper) ; Serik Sagitov (Institutionen för matematiska vetenskaper, matematisk statistik) ; Bengt Oxelman
Systematic biology (1076-836X). Vol. 62 (2013), 3, p. 467-478.
[Artikel, refereegranskad vetenskaplig]

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, two new models for the statistical inference of the evolutionary history of allopolyploids are evaluated using simulations and demonstrated on two empirical data sets. It is assumed that there has been a single hybridization event between two diploid species resulting in a genomic allotetraploid. The evolutionary history can be represented as a species network or as a multi-labeled species tree, in which some pairs of tips are labeled with the same species. In one of the models (AlloppMUL), the multi-labeled 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 genus Pachycladon (Brassicaceae) and from the genus Silene (Caryophyllaceae).

Nyckelord: Allopolyploid; Bayesian; hybridization; network; phylogenetics


First published online: February 19, 2013



Denna post skapades 2013-02-25. Senast ändrad 2016-07-19.
CPL Pubid: 174095

 

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Institutioner (Chalmers)

Institutionen för biologi och miljövetenskap (GU)
Institutionen för matematiska vetenskaperInstitutionen för matematiska vetenskaper (GU)
Institutionen för matematiska vetenskaper, matematisk statistik (2005-2016)

Ämnesområden

Matematik
Sannolikhetsteori och statistik
Biologiska vetenskaper
Biologisk systematik
Evolutionsbiologi

Chalmers infrastruktur

 


Projekt

Denna publikation är ett resultat av följande projekt:


Stochastic models of gene and species trees (VR//2010-5623)