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Bayesian inference operates under the assumption that the empirical data are a good statistical fit to the analytical model, but this assumption can be challenging to evaluate. Here, we introduce a novel R package that utilizes posterior predictive simulation to evaluate the fit of the multispecies coalescent model used to estimate species trees. We conduct a simulation study to evaluate the consistency of different summary statistics in comparing posterior and posterior predictive distributions, the use of simulation replication in reducing error rates and the utility of parallel process invocation towards improving computation times. We also test P2C2M on two empirical data sets in which hybridization and gene flow are suspected of contributing to shared polymorphism, which is in violation with the coalescent model: Tamias chipmunks and Myotis bats. Our results indicate that (i) probability-based summary statistics display the lowest error rates, (ii) the implementation of simulation replication decreases the rate of type II errors, and (iii) our R package displays improved statistical power compared to previous implementations of this approach. When probabilistic summary statistics are used, P2C2M corroborates the assumption that genealogies collected from Tamias and Myotis are not a good fit to the multispecies coalescent model. Taken as a whole, our findings argue that an assessment of the fit of the multispecies coalescent model should accompany any phylogenetic analysis that estimates a species tree. [ABSTRACT FROM AUTHOR]

The California Channel Islands are a group of eight oceanic islands located off the coast of southern California that are substantially closer to the mainland than most other well-studied island systems. The equilibrium theory of island biogeography proposed by MacArthur and Wilson posits that species diversity on an island will be positively impacted by island area and negatively impacted by isolation, which has been confirmed for the Channel Islands. In this study, we have extended MacArthur and Wilson's theory to examine how levels of genetic diversity relate to four island characteristics (island area, distance to the mainland, distance to the nearest island, plant diversity) in the endemic perennial taxa of Acmispon ( Fabaceae) on the Channel Islands. We sampled two island species of Acmispon, A. argophyllus and A. dendroideus, from all islands, and mainland sister taxa for nuclear microsatellites, low-copy nuclear sequence and plastid sequence data. We found that only one measure of diversity from one genetic region (low-copy nuclear) was correlated with island area, that there was no support for a relationship between genetic diversity and distance to the mainland and that distance to the nearest island was a predictor of low-copy nuclear genetic diversity. Plant diversity was a significant predictor of plastid genetic diversity when considering all samples. We conclude that the equilibrium theory of island biogeography does not hold for measures of genetic diversity in the Channel Island endemic Acmispon based on island area and distance to the mainland. The short distance between individual islands and the mainland probably facilitates a moderate rate of mainland to island dispersal, preventing the islands from functioning as isolated biogeographic units. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 289-304. [ABSTRACT FROM AUTHOR]