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Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae
Journal article   Peer reviewed

Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

Shannon C.K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston and Tatyana Livshultz
Molecular phylogenetics and evolution, v 80(1), pp 169-185
Nov 2014
DOI: https://doi.org/10.1016/j.ympev.2014.07.020
PMID: 25109653
Featured in Collection :   UN Sustainable Development Goals @ Drexel

Abstract

Apocynaceae Long-branch attraction Next-generation sequencing Phylogenomics Plastome Pollen aggregation
[Display omitted] •Whole plastome sequences were assembled for 12 species of Apocynaceae.•Apocynaceae plastomes are similar and highly conserved except in Asclepias.•The rapid radiation of crown clade Apocynaceae was resolved with statistical confidence for the first time.•Aggregated pollen evolved independently in two primary crown clade lineages.•The presented approach provides a model for rigorous analysis of other phylogenomic data sets. Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira–Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.

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Collaboration types
Domestic collaboration
Web of Science research areas
Biochemistry & Molecular Biology
Evolutionary Biology
Genetics & Heredity
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