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The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].

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In order to test the results of a previous study of didelphid marsupial phylogeny based on IRBP nuclear gene sequences (Jansa and Voss, 2000. Phylogenetic studies on didelphid marsupials I. Introduction and preliminary results from nuclear IRBP gene sequences. Journal of Mammalian Evolution 7: 43-77), we surveyed external, cranial, dental, and karyotypic characters among a more densely taxon-sampled didelphine ingroup. Separate maximum-parsimony analyses of these nonmolecular data and of a new (taxon-dense) IRBP matrix yielded superficially dissimilar strict-consensus topologies. However, no didelphine clade that was even moderately well supported by either separate analysis was contradicted by any equivalently well-supported clade in the other. Instead, all examples of taxonomic incongruence involved weak nodal support from one or both datasets. A maximum-likelihood analysis of the IRBP data produced a consensus topology that was completely congruent with, although slightly more resolved than, the maximum-parsimony consensus. A combined (simultaneous) maximum-parsimony analysis of both datasets (nonmolecular ϩ IRBP) produced a consensus topology that closely resembled the results of analyzing IRBP separately. Most of the didelphine relationships previously reported by Jansa and Voss (op. cit.) are supported by these analytic exercises, with some notable exceptions. The taxon currently known as Marmosa canescens is conspicuously divergent from congeneric species and variously clusters with three different groups (''other Marmosa'' ϩ Micoureus, Monodelphis, or higher didelphines [ϭ clade H of Jansa and Voss, op. cit.]) in several parsimony-equivalent resolutions of a fourfold basal polytomy in the IRBP and combined-data consensus topologies. Even without canescens, however, the genus Marmosa is not demonstrably monophyletic. The nomenclatural consequences of these results are discussed, and a new genus is described for ''Marmosa'' canescens. Future analyses should test the monophyly of other speciose didelphine genera, but new sources of character data will be needed to offset the loss of resolution and decreased nodal support that are often caused by denser taxon sampling.

Models of species ecological niches and geographic distributions now represent a widely used tool in ecology, evolution, and biogeography. However, the very common situation of species with few available occurrence localities presents major challenges for such modeling techniques, in particular regarding model complexity and evaluation. Here, we summarize the state of the field regarding these issues and provide a worked example using the technique Maxent for a small mammal endemic to Madagascar (the nesomyine rodent Eliurus majori). Two relevant model‐selection approaches exist in the literature (information criteria, specifically AICc; and performance predicting withheld data, via a jackknife), but AICc is not strictly applicable to machine‐learning algorithms like Maxent. We compare models chosen under each selection approach with those corresponding to Maxent default settings, both with and without spatial filtering of occurrence records to reduce the effects of sampling bias. Both selection approaches chose simpler models than those made using default settings. Furthermore, the approaches converged on a similar answer when sampling bias was taken into account, but differed markedly with the unfiltered occurrence data. Specifically, for that dataset, the models selected by AICc had substantially fewer parameters than those identified by performance on withheld data. Based on our knowledge of the study species, models chosen under both AICc and withheld‐data‐selection showed higher ecological plausibility when combined with spatial filtering. The results for this species intimate that AICc may consistently select models with fewer parameters and be more robust to sampling bias. To test these hypotheses and reach general conclusions, comprehensive research should be undertaken with a wide variety of real and simulated species. Meanwhile, we recommend that researchers assess the critical yet underappreciated issue of model complexity both via information criteria and performance on withheld data, comparing the results between the two approaches and taking into account ecological plausibility.

Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses. Although each of the six genes yielded a unique phylogeny, several clades were supported by four or more gene trees. Nodes that conflicted between trees were generally characterized by weak support for one or both of the alternative topologies, thus providing no compelling evidence that any individual gene, or part of the genome, was misleading with respect to the evolutionary history of these mice. Analysis of the combined data resulted in a fully resolved tree that strongly supports monophyly of the genus Mus, monophyly of the subgenus Mus, division of the subgenus Mus into Palearctic (M. musculus, M. macedonicus, M. spicilegus, and M. spretus) and Asian (M. cervicolor, M. cookii, and M. caroli) clades, monophyly of the house mice (M. m. musculus, "M. m. molossinus," M. m. castaneus, and M. m. domesticus), and a sister-group relationship between M. macedonicus and M. spicilegus. Other clades that were strongly supported by one or more gene partitions were not strongly supported by the combined data. This appears to reflect a localized homoplasy in one partition obscuring the phylogenetic signal from another, rather than differences in gene or genome histories.

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