Molecular systematics of Xenocyprinae (teleostei: cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structure of lineages. We sequenced 1140 bp of cytochrome b from 30 individuals of Xenocyprinae and one putative outgroup (Myxocypris asiaticus) and also sequenced 297 bp of ND4L, 1380 bp of ND4, 68 bp of tRNA(His), and 69 bp of tRNA(Ser) from 17 individuals of Xenocyprinae and the outgroup (M. asiaticus). We detected high levels of nucleotide variation among populations, species, and genera. The phylogenetic analysis suggested that Distoechodon hupeinensis might be transferred to the genus Xenocypris, the taxonomic status of the genus Plagiognathops might be preserved, and species of Xenocypris and Plagiognathops form a monophyletic group that is sister to the genus Distoechodon and Pseudobrama. The introgressive hybridization might occur among the populations of X. argentea and X. davidi, causing the two species to not be separated by mtDNA patterns according to their species identification, and the process and direction of hybridization are discussed. The spatial distributions of mtDNA lineages among populations of Xenocypris were compatible with the major geographic region, which indicated that the relationship between Hubei + Hunan and Fujian is closer than that between Hubei + Hunan and Sichuan. From a perspective of parasite investigation, our data suggested that the fauna of Hexamita in Xenocyprinae could be used to infer the phylogeny of their hosts.     

Indo-Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine-dispersed species, Birgus latro . Crabs were collected from eight locations throughout the species' Indo-Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different ( G _ST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro . Long-term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.     

Biogeographic and phylogenetic patterns in diversity of liverwort-associated endophytes

Liverworts harbor diverse fungi, including endophytes, in their healthy tissues. To address whether patterns of endophyte diversity are correlated with host phylogeny or geography, we designed a broad geographic survey with controlled phylogenetic host sampling. We collected liverworts in North Carolina, Washington, Idaho, British Columbia, Germany, and New Zealand and identified endophytes using culture-based and molecular methods. Of the major lineages of filamentous ascomycetes recovered, 53-88% belonged to the Xylariales. Endophyte accumulation curves did not saturate, and singleton sequences were dominant in each region, suggesting that liverwort endophyte communities are diverse. There was no significant difference in species richness between regional endophyte communities; however, total richness estimators indicated that North Carolina and New Zealand have richer communities than do Germany and the Pacific Northwest. This pattern reflects lower per-host endophyte density and prevalence of a common, shared sequence group in Germany and the Pacific Northwest. Although species richness was relatively low in the Pacific Northwest, the greatest phylogenetic diversity of endophytes was recovered there. Tests for regional and host specificity revealed that endophyte floras of hosts within a geographic area are more similar to one another than to those of closely related hosts. Geographic distance, not host phylogeny, best explains differences among communities.     

Phylogeography of spruce beetles (Dendroctonus rufipennis Kirby) (Curculionidae: Scolytinae) in North America

Tree-feeding insects that are widespread in north temperate regions are excellent models for studying how past glaciations have impacted differentiation and speciation. We used mitochondrial DNA (mtDNA) sequences and allele frequencies at nine microsatellite loci to examine genetic population structure across the current range of the spruce beetle (Dendroctonus rufipennis), an economically important insect in North America. Two major haplotype groups occur across northern North America, from Newfoundland to Alaska, on white spruce (Picea glauca), and a third distinctive haplotype group occurs throughout the Rocky Mountains on Engelmann spruce (Picea engelmannii). The two mtDNA lineages found in northern populations are 3-4% divergent from each other and from the lineages found in the Rocky Mountains. Analyses of microsatellite data also suggest the existence of major population groupings associated with different geographical regions. In the Pacific Northwest, concordant contact zones for genetically distinct populations of spruce beetles and their principal hosts appear to reflect recent secondary contact. Although we could detect no evidence of historical mtDNA gene flow between allopatric population groups, patterns of variation in the Pacific Northwest suggest recent hybridization and introgression. Together with the pollen record for spruce, they also suggest that beetles have spread from at least three glacial refugia. A minimum estimate of divergence time between the Rocky Mountain and northern populations was 1.7 Myr (million years), presumably reflecting the combined effects of isolation during multiple glacial cycles.     

Historical isolation,range expansion,and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum)

Abstract.— The high species diversity of aquatic and terrestrial faunas in eastern North America has been attributed to range reductions and allopatric diversification resulting from historical climate change. The role these processes may have played in speciation is still a matter of considerable debate; however, their impacts on intraspecific genetic structure have been well documented. We use mitochondrial DNA sequences to reconstruct an intraspecific phylogeny of the widespread North American spotted salamander, Ambystoma maculatum , and test whether phylogenetic patterns conform to regional biogeographical hypotheses about the origins of diversity in eastern North America. Specifically, we address the number and locations of historical refugia, the extent and patterns of postglacial colonization by divergent lineages, and the origin and affinities of populations in the Interior Highland region. Despite apparent morphological uniformity, genetic discontinuities throughout the range of this species suggest that populations were historically fragmented in at least two refugia in the southern Appalachian Mountains. The ranges of these two highly divergent clades expanded northward, resulting in two widely distributed lineages that are sympatric in regions previously proposed as suture zones for other taxa. The evolutionary history of spotted salamander populations underscores the generality of biogeographical processes in eastern North America: despite differences in population size, glacial refugia, and vagility, similar signatures of differentiation are evident among and within widespread taxa.     

Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America

Molecular studies of plants from the Pacific Northwest of North America suggest a recurrent pattern of genetic differentiation and geographic structuring. In each of five angiosperms and one fern species representing diverse life histories, cpDNA data indicate two clades of populations that are geographically structured. A northern group comprises populations from Alaska to central or southern Oregon, whereas populations from central Oregon southward to northern California form a southern group. In several of these species, a few populations having southern genotypes may have survived in glacial refugia further north in the Olympic Peninsula, Queen Charlotte Islands, and Prince of Wales Island. Allozyme data reveal a similar pattern of differentiation in several other plants from the Pacific Northwest. North-south partitioning of genotypes has also been reported for several animal species from this region. On a broader geographic scale, northsouth partitioning of genotypes has also been observed in other plants from western North America having a variety of geographic distributions. Some species also display a reduction of genetic variability in the northern portion of their range compared to the south. The data suggest strongly that past glaciation profoundly influenced the genetic architecture of the flora and fauna of the Pacific Northwest. Two alternative hypotheses are advanced to explain the geographic structuring of genotypes. First, past glaciation may have created discontinuities in the geographic distributions of plant species, with populations surviving in several well-isolated northern and southern refugia. Following glaciation, migration of genetically differentiated, once-isolated populations resulted in the formation of a continuous geographic distribution with a major genetic discontinuity. Alternatively, plants survived and subsequently migrated northward from a southern refugium, and a genotype became fixed in one or a few populations at the leading edge of recolonization. Subsequent long-distance dispersal from this leading edge resulted in a relatively uniform northern genotype that differs from the southern genotype(s). Whatever the underlying mechanism, Pleistocence glaciation may have molded the intraspecific genetic architecture of both plants and animals from the Pacific Northwest in a geographically similar manner. Future studies should seek to obtain a comprehensive phylogeography for regions that includes a diversity of both plants and animals.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian,European, and North American populations

To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.     

Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra- and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCR-amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.     

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.     

Phylogeography of the Northern Alligator Lizard (Squamata,Anguidae): Hidden diversity in a western endemic

Western North America includes the California Floristic Province and the Pacific Northwest, biologically diverse regions highlighted by a complex topography, geology, climate and history. A number of animals span these regions and show distinctive patterns of dispersal, vicariance and lineage diversification. Examining phylogeographic patterns in the fauna of this area aids in our understanding of the forces that have contributed to the generation and maintenance of regional biodiversity. Here, we investigate the biogeography and population structure of the Northern Alligator Lizard (Elgaria coerulea), a wide‐ranging anguid endemic to western North America. We sequenced two mtDNA fragments (ND2 and ND4) for 181 individuals across the range of the species and analysed these data with phylogenetic approaches to infer population and biogeographic history, and date major divergences within the taxon. We further used Bayesian clustering methods to assess major patterns of population structure and performed ecological niche modelling (ENM) to aid in our interpretation of geographic structure and diversification of E. coerulea lineages. Our phylogeographic examination of E. coerulea uncovered surprising diversity and structure, recovering 10 major lineages, each with substantial geographic substructure. While some divergences within the species are relatively old (Pliocene, 5.3–2.6 mya), most intraspecific variation appears to be of more recent origin (Pleistocene, 2.6 mya‐11,700 ya). Current diversity appears to have arisen in the Sierra Nevada Mountains and spread west and north since the Pliocene. Finally, our ENMs suggest that much of the Coast Ranges in California provided ideal habitat during the Last Glacial Maxima (LGM) that has since contracted dramatically and shifted northwards, whereas significant portions of the Sierra Nevada were unsuitable during the LGM and have since become more suitable. Interestingly, E. coerulea shares a number of genetic boundaries with other sympatric taxa, suggesting common historical events and geomorphological features have shaped the biota of this region.     

Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (=Yangtze) drainage inferred from cytochrome b sequences

We examined the genetic structure and phylogenetic relationships of some Chinese populations from the Chang Jiang (=Yangtze) drainage of the cyprinid Zacco platypus. We sequenced the complete mitochondrial cytochrome b gene of 64 individuals from 6 upper and middle tributaries of the Sichuan and Hunan Provinces to assess their population structure and systematics. The combined analyses of the phylogenetic information and the population structure suggested that Chinese Z. platypus consist of four distinct mtDNA lineages which exhibit high genetic variation and haplotypic diversity (Zacco A-D). The high molecular divergence observed among Zacco A-D mtDNA lineages (TrN+I (0.76) distance, mean 8.9%+/-1.7%) and their phylogeographic structure indicate that all four lineages have evolved independently. Analysis of molecular variance (AMOVA) indicates that most of the genetic variation observed is found among the four Zacco mtDNA lineages (thetaCT = 0.94) suggesting restricted gene flow among the Chang Jiang populations. Long-term interruption of gene flow was also evidenced by thetaST values higher than 0.9 that could be favoured by the discontinuous distributions of the lineages inhabiting upper (Sichuan Province) and middle (Hunan Province) Chang Jiang tributaries. The significant correlation between the geographic and genetic distances provide support for the importance of geographic discontinuity in shaping the Zacco genetic structure. Nested clade analysis (NCA) results were congruent with phylogenetic relationships recovered and confirm the genetic distinctiveness of four independent Zacco groups. These four groups correspond to the four Zacco A-D mtDNA lineages recovered in the phylogeny and were defined by nucleotide synapomorphies permitting bootstrapped and Bayesian confidence of 95% or greater. The high level of mitochondrial sequence divergence separating all Zacco mtDNA lineages suggested that the Z. platypus populations from the Chang Jiang drainage probably correspond to four different species.     

A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta)

Species of Fucus are among the dominant seaweeds along Northern Hemisphere shores, but taxonomic designations often are confounded by significant intraspecific morphological variability. We analyzed intra- and inter-specific phylogenetic relationships within the genus (275 individuals representing 16 taxa) using two regions of the mitochondrion: a variable intergenic spacer and a conserved portion of the 23S subunit. Bayesian ML and MP analyses verified a shallow phylogeny with two major lineages (previously reported) and resolved some intra-lineage relationships. Significant species-level paraphyly/polyphyly was observed within lineages 1A and 2. Despite higher species richness in the North Atlantic, a North Pacific origin of the genus is supported by a gradient of decreasing haplotype and nucleotide diversities in F. distichus from the North Pacific to the East Atlantic.     

MOLECULAR PHYLOGENETICS AND EVOLUTION OF SEXUAL DICHROMATISM AMONG POPULATIONS OF THE YARROW'S SPINY LIZARD (SCELOPORUS JARROVII)

Understanding evolution of geographic variation in sexually dimorphic traits is critical for understanding the role that sexual selection may play in speciation. We performed a phylogenetic analysis of geographic variation in sexual dichromatism in the Yarrow's spiny lizard (Sceloporus jarrovii), a taxon that exhibits remarkable diversity in male coloration among populations (e.g., black, red, green, yellow, blue, brown). An mtDNA phylogeny based on approximately 880 bp from the 12S ribosomal RNA gene and 890 bp from the ND4 gene was reconstructed for 30 populations of S. jarrovii and eight other species of the torquatus species group using maximum-likelihood and parsimony methods. The phylogeny suggests that S. jarrovii consists of at least five evolutionary species, none of which are sister taxa. Although intraspecific diversity in male coloration is less than indicated by previous taxonomy, two species formerly referred to as S. jarrovii exhibit impressive geographic variation in sexual dichromatism. In one of these species, the phylogeny shows the independent evolution of a distinctive blue color morph in different parts of the species range. This pattern suggests that sexual selection may lead to striking phenotypic divergence among conspecific populations and striking convergence. Results also demonstrate the importance of a phylogenetic perspective in studies of evolutionary processes within nominal species and the problematic nature of “polytypic” species recognized under the biological species concept.     

Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits

The current geographical distribution of the ninespine stickleback (Pungitius pungitius) was shaped in large part by the glaciation events of the Pleistocene epoch (2.6 Mya–10 Kya). Previous efforts to elucidate the phylogeographical history of the ninespine stickleback in North America have focused on a limited set of morphological traits, some of which are likely subject to widespread convergent evolution, thereby potentially obscuring relationships among populations. In this study, we used genetic information from both mitochondrial DNA (mtDNA) sequences and nuclear microsatellite markers to determine the phylogenetic relationships among ninespine stickleback populations. We found that ninespine sticklebacks in North America probably dispersed from at least three glacial refugia—the Mississippi, Bering, and Atlantic refugia—not two as previously thought. However, by applying a molecular clock to our mtDNA data, we found that these three groups diverged long before the most recent glacial period. Our new phylogeny serves as a critical framework for examining the evolution of derived traits in this species, including adaptive phenotypes that evolved multiple times in different lineages. In particular, we inferred that loss of the pelvic (hind fin) skeleton probably evolved independently in populations descended from each of the three putative North American refugia.     

Geographical patterns of genetic divergence in the widespread Mesoamerican bumble bee Bombus ephippiatus (Hymenoptera: Apidae)

Bumble bees (Bombus Latreille) are an important group of social insects, well recognized throughout northern temperate regions as important pollinators of wild and agricultural plants. Little is known about the biology of this group in southern portions of the Americas, especially in Mesoamerica, a region of geological and ecological complexity from Mexico through Central America. One ubiquitous Mesoamerican species, Bombus ephippiatus, is enigmatic. Like many other Bombus, this species is homogeneous in body structure yet exhibits striking intraspecific color pattern polymorphism across its range, leading to uncertainty about its genealogical boundaries. It has been grouped taxonomically with B. wilmattae, a species narrowly restricted to southern Mexico and northern Guatamala. Furthermore, the relationships between these two taxa and a third species, B. impatiens, found only in America north of Mexico, have been controversial. Our phylogenetic analysis of DNA sequences from mitochondrial COI and nuclear PEPCK and CAD resolves the phylogeny of these three taxa as (B. impatiens, (B. ephippiatus, B. wilmattae)). Additional data from eight nuclear microsatellite markers reveal complex patterns of genetic divergence and isolation among populations of B. ephippiatus across its extensive geographic range, providing evidence for multiple independent evolutionary lineages. These lineages correspond not only to geographic and habitat variation across their range, but also to distinct color pattern groups present in the species. Knowledge of the phylogeny and genetic divergence of the B. ephippiatus group will provide a framework for understanding evolutionary and ecological origins of color pattern polymorphism in bumble bees, as well as providing insight into geographical factors enhancing speciation in Mesoamerica.     

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.     

The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli

We used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both G_ST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.     

Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California

The broad distribution of the Sceloporus magister species group (squamata: phrynosomatidae) throughout western North America provides an appropriate model for testing biogeographical hypotheses explaining the timing and origins of diversity across mainland deserts and the Baja California Peninsula. We inferred concordant phylogenetic trees describing the higher-level relationships within the magister group using 1.6 kb of mitochondrial DNA (mtDNA) and 1.7 kb of nuclear DNA data. These data provide strong support for the parallel divergence of lineages endemic to the Baja California Peninsula (S. zosteromus and the orcutti complex) in the form of two sequential divergence events at the base of the magister group phylogeny. A relaxed phylogenetic analysis of the mtDNA data using one fossil and one biogeographical constraint provides a chronology of these divergence events and evidence that further diversification within the Baja California clades occurred simultaneously, although patterns of geographical variation and speciation between clades differ. We resolved four major phylogeographical clades within S. magister that (i) provide a novel phylogenetic placement of the Chihuahuan Desert populations sister to the Mojave Desert; (ii) illustrate a mixed history for the Colorado Plateau that includes Mojave and Sonoran Desert components; and (iii) identify an area of overlap between the Mojave and Sonoran Desert clades near Yuma, Arizona. Estimates of bidirectional migration rates among populations of S. magister using four nuclear loci support strong asymmetries in gene flow among the major mtDNA clades. Based on the nonexclusivity of mtDNA haplotypes, nuclear gene flow among populations and wide zones of phenotypic intergradation, S. magister appears to represent a single geographically variable and widespread species.     

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity

The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.     

Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central America

We used a phylogeographic approach to elucidate the evolutionary history of a lineage of frogs, known as Pristimantis (formerly Eleutherodactylus) ridens (Anura: Brachycephalidae), restricted to the wet forests occurring along the Caribbean versant of isthmian Central America as well as the disjunct wet forest on the Pacific slope of Costa Rica. We placed our phylogeographic study of P. ridens within a larger molecular phylogenetic analysis of Central American Pristimantis. All phylogenetic inferences were based on a 1455 base pair fragment of mitochondrial DNA, containing the complete ND2 gene and five flanking tRNA genes. Our reconstruction of the intraspecific phylogeny of P. ridens yielded a basal trichotomy dating to an estimated 12+ million years ago (Ma), consisting of central Panama, western Panama, and Costa Rica plus Honduras. Thus, the presence of P. ridens appears to predate the completion of the Isthmus 3.1Ma. Using a parametric bootstrap (SOWH) test, we evaluated four a priori zoogeographic hypotheses for the origin and spread of P. ridens. This analysis suggested that the P. ridens populations on the Caribbean versant of Costa Rica were established by Pacific versant ancestors only recently, in contrast to the very old lineages found in Panama. Our results support a model of Miocene colonization, long-term geographic stasis, followed by rapid dispersal across the Caribbean lowlands during the Pliocene or Pleistocene.