Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Abstract

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.

Phylogeography and Spatial Genetic Structure of the Southern Torrent Salamander: Implications for Conservation and Management

“…The remaining 17 haplotypes were generally found in geographically proximate locations (Table 1 and Figure 1). This pattern is consistent with other genetic analyses of salamanders from the northwestern United States of America (e.g., Jockusch and Wake 2002;Mahoney 2004;Miller et al 2005) and suggests little contemporary gene flow among populations. Supporting this inference are studies of movement patterns in this species along streamside habitats that reveal very small linear movement per individual (0.08 m/month or 0.003 m/day; Welsh and Lind 1992).…”

“…From a conservation perspective, these analyses can prove invaluable for defining conservation units for species management purposes (Moritz 1994a(Moritz , 1994b. Likewise, genetic analyses can also provide information about dispersal abilities, reproductive strategies, and population demography (e.g., Jarne 1995;Miller et al 2002;Mahoney 2004). In the case of endangered taxa, generation of such information can assist with understanding the basic biology and life history of species that facilitates formulation of species conservation strategies.…”

Geographic variation, genetic structure, and conservation unit designation in the Larch Mountain salamander (Plethodon larselli)

“…Clearly, by extension, the probability of observing 11 location-specific haplotypes (Table 1) becomes exceedingly small. Overall, this pattern is consistent with other genetic analyses of salamanders from the northwestern United States (e.g., Jockusch and Wake 2002;Mahoney 2004;Miller et al 2005) and suggests little contemporary gene flow among populations.…”

Barriers to Sympatry Between Avian Sibling Species (Paridae: Baeolophus) in Local Secondary Contact

“…Similarly, tracking the timing of secondary contact relative to the history of isolation is critical for explaining current patterns and processes. Molecular and morphological data often are used both to examine patterns in secondary contact zones and to infer historical events (e.g., Matocq 2002;García-París et al 2003;Mahoney 2004). However, an independent assessment of such events allows for much stronger inference and hypothesis testing.…”

“…In assessing the role of gene flow and environment on patterns of species' distribution and variation, it is essential to separate the effects of history and current processes (Matocq et al 2000;Mahoney 2004). If geographic range limits are attracted to ecotones (Case and Taper 2000), then two species with a history of isolation and adaptation in different ecological regions would be expected to approach sympatry where their preferred habitats and climates meet.…”