Species tree inference in a recent radiation of orioles (Genus Icterus): Multiple markers and methods reveal cytonuclear discordance in the northern oriole group

[Display omitted] ► Reliable species tree methods crucial for recently diverged groups. ► We inferred a phylogeny of 11 New World orioles using four methods. ► Multiple nuclear loci and individuals resolved most species-level relationships. ► Overall agreement among different methods and data sets....

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Bibliographic Details
Published in:Molecular phylogenetics and evolution 2011-11, Vol.61 (2), p.460-469
Main Authors: Jacobsen, Frode, Omland, Kevin E.
Format: Article
Language:English
Subjects:
Animals
Bayes Theorem
Bayesian analysis
Bayesian MCMC
Biological Evolution
Cell Nucleus - genetics
Coalescing
Computational Biology
Congruence
data collection
DNA, Mitochondrial - genetics
Evolution
Icterus
Inference
Introns
Loci
Markers
mitochondrial DNA
Models, Genetic
Multi-allelic
Multi-locus
new species
nuclear genome
Oriole
Phylogeny
Sequence Analysis, DNA
Songbirds - classification
Songbirds - genetics
Sorting
Trees
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Summary:[Display omitted] ► Reliable species tree methods crucial for recently diverged groups. ► We inferred a phylogeny of 11 New World orioles using four methods. ► Multiple nuclear loci and individuals resolved most species-level relationships. ► Overall agreement among different methods and data sets. ► Most striking cytonuclear discordance due to gene flow within northern group. Recent computational advances provide novel opportunities to infer species trees based on multiple independent loci. Thus, single gene trees no longer need suffice as proxies for species phylogenies. Several methods have been developed to deal with the challenges posed by incomplete and stochastic lineage sorting. In this study, we employed four Bayesian methods to infer the phylogeny of a clade of 11 recently diverged oriole species within the genus Icterus. We obtained well-resolved and mostly congruent phylogenies using a set of seven unlinked nuclear intron loci and sampling multiple individuals per species. Most notably, Bayesian concordance analysis generally agreed well with concatenation; the two methods agreed fully on eight of nine nodes. The coalescent-based method ∗BEAST further supported six of these eight nodes. The fourth method used, BEST, failed to converge despite exhaustive efforts to optimize the tree search. Overall, the results obtained by new species tree methods and concatenation generally corroborate our findings from previous analyses and data sets. However, we found striking disagreement between mitochondrial and nuclear DNA involving relationships within the northern oriole group. Our results highlight the danger of reliance on mtDNA alone for phylogenetic inference. We demonstrate that in spite of low variability and incomplete lineage sorting, multiple nuclear loci can produce largely congruent phylogenies based on multiple species tree methods, even for very closely-related species.
ISSN:1055-7903
1095-9513
DOI:10.1016/j.ympev.2011.06.017