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Abstract Detail



Phylogenomics

Cai, Liming [1], Xi, Zhenxiang [2], Lemmon, Emily [3], Lemmon, Alan [4], Mast, Austin [5], Buddenhagen, Christopher [6], Liu, Liang [7], Davis, Charles [8].

Extensive gene tree discordance in Malpighiales not explained by incomplete lineage sorting and gene tree estimation error.

One of the most difficult challenges in systematics is reconstructing phylogenetic relationships during periods of rapid radiation. The combined effects of short branch lengths and pervasive incomplete lineage sorting (ILS) contributes to spurious phylogenetic estimations. The tremendous growth of genomic data has greatly improved researchers’ ability to investigate rapid radiations by providing hundreds to thousands of unlinked loci. Meanwhile, the application of the multi-species coalescent (MSC) model in phylogenomic inference has become widely embraced to accommodate genealogical heterogeneity and ILS. Here, we generate an anchored hybrid enrichment data set including 423 loci from 65 taxa representing 39 families to infer a species tree of the flowering plant clade Malpighiales. This clade remains one of the thorniest nodes in angiosperm tree of life, and the recalcitrant relationships along the backbone of the order has been hypothesized to arise from its rapid radiation during the Albian and Cenomanian stage. We estimated the species tree using both concatenated maximum likelihood and coalescent-based methods. We additionally applied locus subsampling to examine the consistency of species tree estimations from these two methods. Our results demonstrate that the phylogenetic analysis using the concatenation model yields extensive, well-supported, incongruence among subsampled data set. In contrast, coalescent-based methods do not confidently resolve the backbone relationships of Malpighiales. We additionally use computational simulation to investigate the role of ILS and gene tree estimation error in generating discordant species tree inferences. Here, we identify that under inferred levels of ILS and gene tree estimation error, both the concatenation and coalescent method could recover the true species tree. These results indicate that the most common MSC model is insufficient when dealing with some rapid radiations as exemplified in Malpighiales.


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1 - Harvard University, Department of Organismic and Evolutionary Biology, 22 Divinity Ave, Cambridge, MA, 02138, USA
2 - Sichuan University, Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, Chengdu, Sichuan, 610064, China
3 - Florida State University, Department of Ecology and Evolution, Tallahassee, FL, 32306, USA
4 - Florida State University, Department of Scientific Computing, Tallahassee, FL, 32306, USA
5 - Florida State University, Department Of Biological Science, 319 Stadium Drive, Tallahassee, FL, 32306, United States
6 - AgResearch, New Zealand
7 - University of Georgia, Department of Statistics, Athens, GA, 30602, USA
8 - Harvard University Herbaria, Organismic and Evolutionary Biology, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States

Keywords:
Anchored hybrid enrichment
Subsampling
Gene tree-species tree conflict
Hybridization
Rapid radiation
Coalescent method.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 114/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 8:45 AM
Number: 1004
Abstract ID:185
Candidate for Awards:None


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