Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

• Published in: Molecular phylogenetics and evolution Vol. 64; no. 1; pp. 145 - 155
• Main Authors: Moody, Michael L., Rieseberg, Loren H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.07.2012
• Subjects: Base Sequence; Bayes Theorem; Cell Nucleus - genetics; Chaff; Cloning, Molecular; DNA Primers - genetics; Gene trees; Genes; Genetics, Population; genotype; Helianthus; Helianthus - classification; Helianthus - genetics; Helianthus annuus; Helianthus sect. Helianthus; Heterogeneity; Hybridization; Hybridization, Genetic - genetics; hybrids; Incongruence; Inference; introgression; methodology; Models, Genetic; Molecular Sequence Data; monophyly; nDNA; nuclear genome; paraphyly; Phylogeny; Polypropylenes; Sequence Analysis, DNA; Speciation; Sunflowers; topology; Trees; nDNA; Incongruence; Helianthus sect. Helianthus; Hybridization; Phylogeny; Gene trees
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2012.03.012

[Display omitted] ► Topological heterogeneity is found among nDNA gene trees for annual sunflowers. ► There is a general lack of reciprocal monophyly of species among gene trees. ► Partitioned Bayesian analyses support monophyly of most annual sunflower species. ► nDNA gene trees provide an effective means for detecting recent hybridization. ► These do not effectively detect ancient hybridization even with linkage considered. The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.