Regular ArticleMtDNA Phylogeography of the California Newt, Taricha torosa (Caudata, Salamandridae)
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Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)
2021, Molecular Phylogenetics and EvolutionCitation Excerpt :Our time-calibrated analysis was performed using the mitochondrial sequence data only, to avoid over-parameterisation and because no internal Dicroglossidae fossil calibrations are available, and divergence-time estimates from available literature for the split between Dicroglossinae and Occidozyginae differ significantly, ranging from 96.8 Ma to 59.9 Ma (Roelants et al., 2007; Wiens et al., 2009; Zhang et al., 2013). Thus, for our BEAST2 analysis, we used a range of mitochondrial divergence rates, (0.35–0.955% substitutions/my; Macey et al., 1998; 2001; Sanguila et al., 2011; Tan and Wake, 1995; Wang et al., 2008) as a crude general scalar. The standard deviation was set to be lower than one, which means that the standard deviation in branch rates was smaller than the mean rate.
Phylogeography, geographic structure, genetic variation, and potential species boundaries in Philippine slender toads
2011, Molecular Phylogenetics and EvolutionCitation Excerpt :As a test of the Matsui et al. (2010) calibration, we employed an alternative approach and inferred approximate divergence dates with a Bayesian relaxed molecular clock in BEAST v1.6.1. A variety of recent empirical studies of amphibians (using a variety of calibrations, taxa, and mtDNA gene fragments) have inferred model-corrected mitochondrial sequence divergence rates of between 0.8 and 1.9% total divergence per million years (Tan and Wake, 1995; Macey et al., 1998, 2001; Crawford, 2003a, 2003b; Wang et al., 2008) for various parts of the genome. We used this range and a relaxed clock approach as implemented in BEAST, allowing branch lengths to vary according to an uncorrelated lognormal distribution, employing a Yule process tree prior, with all remaining priors set to default.
Phylogeny and evolutionary divergence times in apterosperma and euryodendron: Evidence of a tertiary origin in south China
2011, Biochemical Systematics and EcologyCitation Excerpt :During the period, temperatures reached climatic optimum after a shift from Paleogene greenhouse conditions to icehouse conditions at the Eocene/Oligocene transition (Lear et al., 2008; Eldrett et al., 2009). In addition, the Neogene mountain uplift events could also contribute to the plant diversification (Riddle, 1995; Tan and Wake, 1995; Shaffer et al., 2004; Jaeger et al., 2005; Devitt, 2006; Douglas et al., 2006; Moore and Jansen, 2006). Taken these together, it is likely that the origin of Euryodendron was correlated with the historical mountain building events and/or the significant climate changes that established cooler temperatures prevailing until today.
Combining genetic structure and ecological niche modeling to establish units of conservation: A case study of an imperiled salamander
2011, Biological ConservationCitation Excerpt :Although we identified a lack of shared haplotypes between regions suggesting a lack of contemporary gene flow, the lack of genetic divergence between regions suggests that further corroborating evidence (e.g. based on behavior) would need to be confirmed before eastern and western regions of N. perstriatus should be considered separate cryptic species. Moreover, estimates of mean pairwise sequence divergence within N. perstriatus were low compared to maximum diversity estimates described within other species (e.g. 9% sequence divergence within Taricha torosa (Tan and Wake, 1995)) versus 3% sequence divergence between haplotypes for N. perstiatus (this study). Distribution models revealed significantly different ecological settings between regions.
Amphibian phylogeography in the Antipodes: Refugia and postglacial colonization explain mitochondrial haplotype distribution in the Patagonian frog Eupsophus calcaratus (Cycloramphidae)
2011, Molecular Phylogenetics and EvolutionCitation Excerpt :No independent fossil or geological evidence is available to calibrate a local molecular clock for populations of Eupsophus, so external calibrations were used. Estimates of amphibian protein-coding mtDNA mutation rates have been shown to vary slightly depending on gene regions and taxonomic group (Tan and Wake, 1995; Macey et al., 1998; Crawford, 2003). For anurans, Crawford (2003) estimated ND2 to evolve at a rate of 0.957% per lineage per million years, based on a recalibration of Macey et al.’s (1998) Eurasian Bufo dataset.
Evolution of the nocturnal Nearctic Sphaeropthalminae velvet ants (Hymenoptera: Mutillidae) driven by Neogene orogeny and Pleistocene glaciation
2010, Molecular Phylogenetics and Evolution