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Abstract Detail



Phylogenomics

Baum, David A. [1], Grover, Corrinne E. [2], Karimi, Nisa [3], Stenz, Noah [3], Gallagher, Joseph P. [4], Wendel, Jonathan [5].

Genealogical concordance in Adansonia (Malvaceae) as inferred from hyb-seq data.

Baobabs (Adansonia) are iconic trees of tropical deciduous forests and savannahs, with one species in northwestern Australia, one or two species in continental Africa, and six species in Madagascar. A clear understanding of the phylogeny of the genus is needed to date the Africa-Australia disjunction and to elucidate patterns of evolution within Africa and Madagascar. In particular, we are interested in clarifying the origins of the tetraploid African species, A. digitata, and evaluating whether a putative African diploid species (A. kilima) could be one of two allopolyploid parents. Also, in Madagascar, we ultimately hope to resolve the relationships among the florally diverse, hawkmoth pollinated, section Longitubae and assess the frequency of hybridization and introgression. To provide data for these purposes, we have adopted a targeted sequence capture (hyb-seq) strategy. We obtained leaf transcriptomes for A. digitata and another member of Bombacoideae (Pachira sp.), and used these data to identify 380 targets that are all at least 800bp in length and show high levels of conservation among Adansonia, Pachira, and Gossypium. An initial hyb-seq analysis was conducted using three outgroups (Scleronema, Bombax, and Pseudobombax) and nine Adansonia individuals: three African, five Malagasy (three Brevitubae, two Longitubae), and one Australian. The African accessions included the designated type of A. kilima, which we have recently shown to be tetraploid (in contradiction to the species description). Following library construction and hybrid capture, a single lane of MiSeq was run, yielding assemblies for all individuals for all targets. Additionally the ~60% off-target reads allowed assembly of ITS and much of the plastid genome of most accessions. Exonic regions of all genes were readily aligned and almost all yielded resolved gene trees for one or two paralogs. Preliminary analysis corroborate the ITS phylogeny, supporting monophyly of the Malagasy species, and a clear division into Brevitubae (mammal pollinated) and Longitubae (hawkmoth pollinated). Many gene trees show allele-intermingling between the A. kilima type and two greenhouse grown A. digitata, casting further doubt on the validity of A. kilima. To analyze discordance, we will use Bayesian discordance analysis and a recently developed test to evaluate whether all discordance can be accounted for by incomplete lineage sorting. We also plan to redesign the bait-set for use in phylogeographic studies in Africa and Madagascar.


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1 - University Of Wisconsin, Department Of Botany, Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
2 - Iowa State University, Department of Ecology, Evolution, & Organismal Biology, Ames, IA, 50011, USA
3 - U. Wisconsin, Botany, 430 Lincoln Drive, Madison, WI, 53706, United States
4 - Iowa State University, Ecology, Evolution, & Organismal Biology, Ames, IA, 50011, USA
5 - Iowa State University, Department Of Ecology, Evolution, And Organismal Biology, 251 Bessey Hall, Ames, IA, 50011-1020, USA

Keywords:
Sequence capture
genealogical concordance.

Presentation Type: Oral Paper:Papers for Topics
Session: 32
Location: Salon 11/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 10:15 AM
Number: 32009
Abstract ID:544
Candidate for Awards:None


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