High-resolution species trees without concatenation - PubMed (original) (raw)

Comparative Study

. 2007 Apr 3;104(14):5936-41.

doi: 10.1073/pnas.0607004104. Epub 2007 Mar 28.

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Comparative Study

High-resolution species trees without concatenation

Scott V Edwards et al. Proc Natl Acad Sci U S A. 2007.

Abstract

The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

The distribution of gene trees for the 106-gene yeast data set. (A) The number of genes (y axis) yielding each of 24 topologies according to the maximum posterior probability criterion (x axis) is shown for each of four analyses: independent (green) and joint (yellow) model with a molecular clock and independent (red) and joint (blue) model without a molecular clock. (B) The two most commonly encountered maximum posterior probability trees (for both species and genes) are shown below, with the next four most common shown in the bottom row (trees 3–5 and 9). The asterisk in tree 1 indicates the branch whose length differed drastically between BEST and MCMCcoal (30). The complete posterior distribution of gene trees for all four analyses is given in

SI Tables 1–4

.

Fig. 2.

Fig. 2.

Shifting phylogenetic landscapes for gene trees under different models. The complete posterior probability distributions for the independent (A) and joint (B) models without a molecular clock are shown.

Fig. 3.

Fig. 3.

Robustness and efficiency of the joint model for estimating species trees. (A) The number of genes required to resolve the correct species tree with four and eight species when the proportion of gene trees matching the species tree is high. Here this proportion varies between ≈83% and 90% (in blue and green, 100 gene trees per simulation) because the critical internodes in the species tree are relatively long on the scale of the effective population size (θ). The gamma-distributed prior on θ for each node was (1, 200), indicating a mean θ of 1/200 and variance of 1/40,000. A prior mean of 1/200 is consistent with what we know about θ in natural populations of yeast (45, 46). (B) The number of genes required to resolve the correct four-species tree when the proportion of gene trees matching the species tree (in blue) is low (≈40%). Prior 1 on θ is (1, 200), and prior 2 is (1, 1,000). (C) The number of genes required to resolve the correct eight-species tree when the proportion of gene trees matching the species tree (in blue) is low (<10%). Prior 1 on θ is (1, 100), prior 2 is (1, 500), and prior 3 is (1, 1,000).

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