Abstract Detail

Species tree reconstruction in polyploid complexes

Tomasello, Salvatore [1], Konowalik, Kamil [1], Wagner, Florian [1], Oberprieler, Christoph [2].

Inferring species networks from gene trees in polyploid complexes by minimising deep coalescences: examples from the genera Leucanthemum and Leucanthemopsis (Compositae, Anthemideae).

Polyploidization is an important evolutionary process particularly prominent in plants. Yet phylogenetic reconstructions including polyploids are not trivial due to their genomic complexity. A polyploid can be the result of the genome merging from two or more parental species and this implies that, together with incomplete lineage sorting, hybridization (by allopolyploidization) can be an important process producing incongruence in phylogenetic reconstructions. Disentangling between polyploid hybridization and incomplete lineage sorting is still a hard task when one wants to reconstruct phylogenies in polyploidy groups. We present a simple method for inferring species networks in polyploid complexes from multilocus gene trees by taking a parsimony approach based on a Minimising Deep Coalescences (MDC) criterion. The method uses the MDC principle as implemented in the software program PhyloNet (Than et al. 2008) to find the optimal (most parsimonious) pair-wise mapping of alleles for each underlying gene and every polyploid accession included. In a second step, the same criterion is used to infer the optimal (most parsimonious) combination of allele pairs across the underlying genes/markers for each polyploid accession. Thereafter a reconstruction of a multi-labelled (MUL) tree is carried out, including all diploid and polyploid accessions simultaneously and having terminal branches that represent either diploid accessions or pseudo-diploid parental genome branches giving rise to polyploids. Finally, the inference of a species network is accomplished by joining parental genome branches either into reticulation (allopolyploids) or non-reticulation (autopolyploids) nodes, using the software program PADRE (Lott et al. 2009). The method is demonstrated in the small genus Leucanthemopsis (Compositae, Anthemideae), which comprises diploid, tetraploid, and hexaploid species, as well as for the larger polyploid complex of the genus Leucanthemum (Compositae, Anthemideae), which includes over 20 species, ranging from 2n = 2x to 2n = 22n. For the analyses, a total of six markers (five low-/single-copy nuclear markers plus one single chloroplast locus) and ten markers (nine low-/single-copy nuclear markers and one chloroplast locus) were used in the Leucanthemopsis and the Leucanthemum datasets, respectively. Allelic variation was assessed via 454 next-generation sequencing of amplicons.

Broader Impacts:

1 - University of Regensburg, Institute of Botany, Universitätsstr. 31, Regensburg, 93053, Germany
2 - Institute Of Botany, University Of Regensburg, Universitätsstr. 31, Regensburg, N/A, D-93040, Germany

Keywords:
species network reconstruction
Polyploidy.

Presentation Type: Symposium or Colloquium Presentation
Session: SY09
Location: Grand Ballroom A/Riverside Hilton
Date: Wednesday, July 31st, 2013
Time: 10:15 AM
Number: SY09007
Abstract ID:295
Candidate for Awards:None