Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex.

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.

Shaffer HB ，Fellers GM ，Voss SR ，Oliver JC ，Pauly GB ... -  《MOLECULAR ECOLOGY》

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications.

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.

Spinks PQ ，Shaffer HB 《MOLECULAR ECOLOGY》

Evidence from peptidomic analysis of skin secretions that the red-legged frogs, Rana aurora draytonii and Rana aurora aurora, are distinct species.

Conlon JM ，Al-Ghafari N ，Coquet L ，Leprince J ，Jouenne T ，Vaudry H ，Davidson C ... -  《PEPTIDES》

Molecular phylogenetics of western North American frogs of the Rana boylii species group.

Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and tRNA(Cys) genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation.

Macey JR ，Strasburg JL ，Brisson JA ，Vredenburg VT ，Jennings M ，Larson A ... -  《MOLECULAR PHYLOGENETICS AND EVOLUTION》

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense.

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.

Shaffer HB ，Pauly GB ，Oliver JC ，Trenham PC ... -  《MOLECULAR ECOLOGY》