2016-12-23T18:52:10

Recent studies based on different types of data (i.e., morphology, molecules) have found strongly conflicting phylogenies for the genera of iguanid lizards but have been unable to explain the basis for this incongruence. We reanalyze published data from morphology and from the mitochondrial ND4, cytochrome b, 12S, and 16S genes to explore the sources of incongruence and resolve these conflicts. Much of the incongruence centers on the genus Cyclura, which is the sister taxon of Iguana, according to parsimony analyses of the morphology and the ribosomal genes, but is the sister taxon of all other Iguanini, according to the protein-coding genes. Maximum likelihood analyses show that there has been an increase in the rate of nucleotide substitution in Cyclura in the two protein-coding genes (ND4 and cytochrome b), although this increase is not as clear when parsimony is used to estimate branch lengths. Parametric simulations suggest that Cyclura may be misplaced by the protein-coding genes as a result of long-branch attraction; even when Cyclura and Iguana are sister taxa in a simulated phylogeny, Cyclura is still placed as the basal member of the Iguanini by parsimony analysis in 55% of the replicates. A similar long-branch attraction problem may also exist in the morphological data with regard to the placement of Sauromalus with the Galápagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long branches on parsimony and likelihood methods, and the use of certain protein-coding genes in phylogeny reconstruction.

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Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long-term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.

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Aim: Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction-site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.Location: Baja California and Southern California. Methods:We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).Results: Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern-most portion of the range of C. ruber was not suitable habitat during the LGM. Main conclusions:We provide the first explicitly model-based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa. Grismer, 2002;Lindell, M endez-De La Cruz, & Murphy, 2008;Riddle, Hafner, Alexander, & Jaeger, 2000;Savage, 1960;Zink, 2002) (Aguirre, Morafka, & Murphy, 1999;Murphy, 1983).However, this hypothesis has been weakened by a general lack of direct geological evidence and the finding that mid-peninsular divergences indicate at least two episodes of divergence (Crews & Hedin, 2006;Dolby et al., 2015;Leach e, Crews, & Hickerson, 2007). No strong evidence has been presented to suggest that a seaway crossed the peninsula in the vicinity of Loreto, leaving the drivers of spatially concordant phylogenetic and phylogeographic breaks unclear at all of these regions.The phylogeographic patterns observed could be produced by at least two different processes: (1) Here, we sought to examine the phylogeography of mainland populations of Crotalus ruber (the red diamond rattlesnake), a large rattlesnake that ranges throughout Baja California and into southern California (Figure 1), using genomic data and explicit testing of alternative phylogeographic models. We also inv...

We describe a new species of rainfrog of the Eleutherodactylus fitzingeri species group from central Panama. This species is most similar to members of the E. melanostictus subgroup and can be distinguished from other members of the E. fitzingeri group from Lower Central America by a combination of characters, including a large supraocular tubercle, barred thigh pattern, a granulate venter, marked sexual dimorphism in the tympanic membrane, and basal toe webbing. We analyzed a data matrix of 24 allozyme, morphological, and karyological characters, following the phylogenetic analysis of Miyamoto (1986), and included four additional characters. The 12 species of the E. fitzingeri group are included, in addition to the new species. The relative phylogenetic position of two species, E. emcelae and E. phasma, are proposed for the first time. The new species is hypothesized to be a member of the E. melanostictus subgroup, which contains the predominantly montane species E. melanostictus, E. rayo, E. emcelae, E. monnichorum, and E. cuaquero.

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