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.     

Mitochondrial DNA evolution in the Anaxyrus boreas species group

The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group.     

Combining phylogenetic and ecological niche modeling approaches to determine distribution and historical biogeography of Black Hills mountain snails (Oreohelicidae)

We aim to show how a combination of molecular systematics and ecological niche modelling approaches can be used to test historical biogeographical hypotheses for species of conservation concern. We focus on the land snail genus Oreohelix (Oreohelicidae), a group found throughout the Rocky Mountains. In addition to its larger distribution, a group of Oreohelix is also found in the Black Hills of Wyoming and South Dakota, an isolated, easternmost extension of the Rocky Mountains. We determine the number, distribution, and relationships of Black Hills Oreohelicids, which are a current conservation concern due to their fragmented distribution. We compared Black Hills groups to those in the main part of the Rockies to test historical biogeographical patterns that explain current diversity. We collected mtDNA data (COI and 12S sequences) from multiple populations of Oreohelix throughout the Black Hills and in adjacent populations in the Rocky Mountains to construct phylogenetic hypotheses. To determine whether favourable environmental conditions currently exist between the Black Hills and the north-eastern Rocky Mountains, we used DesktopGARP to generate an ecological niche model for distinct lineages discovered in the molecular phylogenetic analysis. Results show that all Black Hills populations are likely Oreohelix cooperi and that little genetic differentiation exists within this clade. In addition, Black Hills groups are genetically similar or identical to populations found in the Judith Mountains and Bighorn Mountains (north-eastern Rockies). Ecological niche models show that suitable environmental conditions may exist between eastern Rockies and Black Hills O. cooperi samples. Taken together, the phylogenetic and niche model data, along with the low vagility of the snails, support passive long-distance dispersal as a likely explanation for current arrangement of biodiversity.     

Reexamination of relationships, habital evolution, and phylogeography of checker mallows (Sidalcea; Malvaceae) based on molecular phylogenetic data

Phylogenetic analysis of nuclear ribosomal DNA external and internal transcribed spacer region (ETS and ITS) sequences for Sidalcea (Malvaceae) resolved five major, well-supported lineages, three of which represent species groups that have each been noted for complex patterns of morphological variation: the oregana, malviflora, and glaucescens clades. Very low variation within each of the three groups in the sequenced regions is consistent with recent radiation of each clade. We reject the previously suggested hypothesis of monophyly for the annual species of Sidalcea. Based on our findings, the annual habit in Sidalcea arose at least four times, probably as an adaptation to seasonally dry habitats. The hypothesis that the perennial species S. hickmanii and S. malachroides represent basally divergent groups within Sidalcea is supported, but the more recently discovered S. stipularis represents an additional basally divergent lineage. The previous suggestion that the genus spread northward from Mexico along two major routes (through the Rocky Mountains and the Sierra Nevada foothills), with the Rocky Mountain species S. candida and S. neomexicana representing basally divergent lineages, is not supported. Sidalcea neomexicana is nested within the malviflora clade and is likely a lineage of relatively recent descent that originated in California and subsequently spread to the Rocky Mountains.     

Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas

We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene-Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert-Colorado Plateau) and Western (Mojave-Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene-early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.     

Effects of Wolbachia on mtDNA variation in two fire ant species

Wolbachia are endosymbiotic bacteria that infect arthropods. As they are maternally transmitted, the spread of Wolbachia variants within host populations may affect host mtDNA evolution. We sequenced a portion of the mitochondrial cytochrome oxidase I gene from numerous individuals of two Wolbachia-infected fire ant species, Solenopsis invicta and S. richteri, to determine how these bacteria influence patterns of mtDNA variation. As predicted, there was a strong association between Wolbachia strain and host mtDNA lineage within and between these fire ant species. However, there was no consistent association between the presence of Wolbachia and a reduction in mtDNA diversity. Moreover, patterns of mtDNA variation within Wolbachia-infected populations did not differ consistently from neutral expectations, despite our prediction that strong positive selection acting on Wolbachia influences the evolutionary dynamics of other cytoplasmic genomes. Specifically, while values of Tajima's D consistently were less than zero for all six samples of fire ants harbouring Wolbachia, MacDonald-Kreitman tests suggested that the patterns of variation were different from those expected under neutrality in only two of the samples. We conclude that these neutrality tests do not unambiguously reveal a clear effect of Wolbachia infection on patterns of mtDNA variation and substitution in fire ants. Finally, consistent with an earlier study, our data revealed the presence of two divergent mtDNA haplotype lineages and Wolbachia strains within S. invicta. Recognition of these two lineages has important consequences for interpreting patterns of mtDNA evolution and genetic differentiation between conspecific social forms of this species.     

Divergent mitochondrial lineages arose within a large,panmictic population of the Savannah sparrow (Passerculus sandwichensis)

Unusual patterns of mtDNA diversity can reveal interesting aspects of a species’ biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next‐generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA‐based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus‐specific patterns.     

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.     

Range-wide chloroplast and mitochondrial DNA imprints reveal multiple lineages and complex biogeographic history for Douglas-fir

The contemporary genetic structure of species offers key imprints of how organisms responded to past geological and climatic events, which have played a crucial role in shaping the current geographical distribution of north-temperate organisms. In this study, range-wide patterns of genetic variation were examined in Douglas-fir (Pseudotsuga menziesii), a dominant forest tree species distributed from Mexico to British Columbia in western North America. Two organelle DNA markers with contrasting modes of inheritance were genotyped for 613 individuals from 44 populations. Two mitotypes and 42 chlorotypes were recovered in this survey. Both genomes showed significant population subdivision, indicative of limited gene flow through seeds and pollen. Three distinct cpDNA lineages corresponding to the Pacific Coast, the Rocky Mountains, and Mexico were observed. The split time of the two lineages from the Rockies lineage was dated back to 8.5 million years (Ma). The most recent common ancestors of Mexican and coastal populations were estimated at 3.2 and 4.8 Ma, respectively. The northern populations of once glaciated regions were characterized by a high level of genetic diversity, indicating a large zone of contact between ancestral lineages. A possible northern refugium was also inferred. The Mexican lineage, which appeared established by southward migration from the Rockies lineage, was characterized by the lowest genetic diversity but highest population differentiation. These results suggest that the effects of Quaternary climatic oscillations on the population dynamics and genetic diversity of Douglas-fir varied substantially across the latitudinal section. The results emphasize the pressing need for the conservation of Mexican Douglas-fir.     

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.     

Genetic surfing,not allopatric divergence,explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern—local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation—not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male‐biased dispersal.     

Composition of native and introduced mtDNA lineages in <Emphasis Type="Italic">Coregonus</Emphasis> sp. in two Austrian lakes: evidence for spatio-temporal segregation of larvae?

We hypothesized that there is spatio-temporal genetic (mtDNA) structure of native and introduced larval whitefish (Coregonus sp.) in two Austrian lakes (Traunsee and Hallstättersee). Larval whitefish were sampled from 12 sites in each lake and screened for variation in the mtDNA NADH-1 gene. Based on the sequencing of adult fish together with existing GenBank sequences, an RFLP protocol was developed to assign haplotypes from larval samples into one of two divergent lineages. All but one site (pelagic) in Traunsee contained both haplotypes, thus there was no support for spatial segregation of mtDNA groups in that lake. However, weekly sampling from December to May in Traunsee revealed a temporal pattern, with the native haplotypes dominating in December and January before the appearance of the introduced Baltic clade. In Hallstättersee, only three of the 12 sites sampled revealed haplotypes from the introduced clade and thus spatial segregation seems operative on that lake. Our results imply that differences in the spawning ecology of the two groups maintain sufficient reproductive isolation to be reflected in distinct larval occurrence in space and time highly consistent with genetic differences on the mtDNA level. If the two lineages were highly introgressed, we would expect to find little or no correspondence between spatio-temporal patterns in larval distribution and the differentiated mtDNA lineages.     

Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populations

Despite increasing information about postglacial recolonization of European freshwater systems, very little is known about pre-Pleistocene history. We used data on the recent distribution and phylogenetic relationships of stone loach mitochondrial lineages to reconstruct the initial colonization pattern of the Danube river system, one of the most important refuges for European freshwater ichthyofauna. Fine-scale phylogeography of the Danubian populations revealed five highly divergent lineages of pre-Pleistocene age and suggested the multiple origin of the Danubian stone loach. The mean sequence divergence among lineages extended from 7.0% to 13.4%, which is the highest intraspecific divergence observed so far within this river system. Based on the phylogeographical patterns, we propose the following hypothesis to relate the evolution and dispersal of the studied species with the evolution of the Danube river system and the Carpathian Mountains: (i) during the warmer period in the Miocene, the areas surrounding the uplifting Alps and Carpathians served as mountainous refuges for cold-water adapted fish and promoted the diversification of its populations, and (ii) from these refuges, colonization of the emerging Danube river system may have taken place following the retreat of the Central Paratethys. Co-existence of highly divergent mtDNA lineages in a single river system shows that range shifts in response to climatic changes during the Quaternary did not cause extensive genetic homogenization in the stone loach populations. However, the wide distribution of some mtDNA lineages indicates that the Pleistocene glaciations promoted the dispersal and mixing of populations through the lowlands.     

Incongruence in the pattern and timing of intra-specific diversification in bronze frogs and bullfrogs (Ranidae)

We compare patterns of lineage divergence in mitochondrial DNA (mtDNA) sequences of two protein-encoding mitochondrial genes (cyt b and ND2) in two ecologically similar, co-distributed, and closely related ranid frogs (Rana clamitans and Rana catesbeiana), that are geographically widespread, and frequently syntopic. We identified three lineages in R. clamitans, separated by 0.5% to 2.1% net corrected sequence divergence, comparable to two R. catesbeiana lineages separated by 0.6%. The geographic pattern of lineage distribution differed notably between the two species. In R. clamitans, we found a Coastal Plain-Appalachian (CPA) lineage restricted to south and east of the Appalachian Mountains and a widespread lineage that encompassing nearly all the sampled range. A third distinct and divergent lineage was detected in one location in the southwest portion of the range (Louisiana). This pattern contrasts with the east-west pattern in R. catesbeiana, and reflects possible differences in refugial dynamics and patterns of range expansion. Although both species have undergone range expansion and population growth, coalescent reconstruction of N(e) reflects larger lineages but more recent divergence in R. clamitans relative to R. catesbeiana, reflecting significant differences in population history or divergent patterns of molecular evolution at mtDNA.     

Genetic differentiation in eastern European and western Asian populations of the liver fluke, Fasciola hepatica, as revealed by mitochondrial nad1 and cox1 genes

Partial sequences of mitochondrial genes nad1 (316 bp) and cox1 (429 bp) were analyzed to estimate the variability of the liver fluke samples collected in 20 localities in Russia, Belarus, Ukraine, Bulgaria, Armenia, Azerbaijan, Georgia, Turkey, Turkmenistan, and China. The sequences had 4.1% (nad1) and 2.3% (cox1) of variable sites, and 13 and 10 haplotypes were identified among nad1 and cox1 genes, respectively. Spatial analysis of genetic and nucleotide diversity indicated little or no structuring of genetic variation between hosts or regions. The analysis of distribution of both separate and combined (nad1 + cox1) haplotypes revealed the existence of 2 well-defined lineages with 2 main haplotypes and a number of shared divergent haplotypes. Our study showed that the first lineage included the main N1-C1 haplotype, which was found in Australia, China, Georgia, Turkey, Armenia, Azerbaijan, and in all European populations (from Russia, Belarus, Ukraine, Bulgaria). The second lineage was found in all European populations and in populations from Armenia and Azerbaijan. It was suggested that one of the lineages (I) has an Asian origin. The possible source of mtDNA variability and associations between lineage divergence of parasite and its definitive hosts (cattle and sheep) are discussed.     

The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri

An amplified fragment length polymorphism (AFLP) assay was performed on individuals representing discrete haplotypes from two genetically distinct mtDNA lineages of the bamboo viper, Trimeresurus stejnegeri (Schmidt), within Taiwan. AFLP (525 polymorphic markers from five primer pairs) and mtDNA genetic distances were highly correlated and an analysis of molecular variance, and a Bayesian approach similarly partitioned estimates of genetic similarity according to the mtDNA phylogeographical pattern. These results are discussed in relation to biogeographical hypotheses, comparative rates of mtDNA molecular evolution, and in the identification of evolutionary significant units of Taiwanese T. stejnegeri. In spite of the high degree of congruence between the genetic datasets, the AFLP phylogenetic analysis did not support the mtDNA tree, suggesting that no contemporary barriers to gene flow exist between individuals from the two mtDNA lineages.     

Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus)

The potential for widespread, mobile species to exhibit genetic structure without clear geographic barriers is a topic of growing interest. Yet the patterns and mechanisms of structure--particularly over broad spatial scales--remain largely unexplored for these species. Bobcats occur across North America and possess many characteristics expected to promote gene flow. To test whether historical, topographic or ecological factors have influenced genetic differentiation in this species, we analysed 1 kb mtDNA sequence and 15 microsatellite loci from over 1700 samples collected across its range. The primary signature in both marker types involved a longitudinal cline with a sharp transition, or suture zone, occurring along the Great Plains. Thus, the data distinguished bobcats in the eastern USA from those in the western half, with no obvious physical barrier to gene flow. Demographic analyses supported a scenario of expansion from separate Pleistocene refugia, with the Great Plains representing a zone of secondary contact. Substructure within the two main lineages likely reflected founder effects, ecological factors, anthropogenic/topographic effects or a combination of these forces. Two prominent topographic features, the Mississippi River and Rocky Mountains, were not supported as significant genetic barriers. Ecological regions and environmental correlates explained a small but significant proportion of genetic variation. Overall, results implicate historical processes as the primary cause of broad-scale genetic differentiation, but contemporary forces seem to also play a role in promoting and maintaining structure. Despite the bobcat's mobility and broad niche, large-scale landscape changes have contributed to significant and complex patterns of genetic structure.     

Molecular genetic evidence for the post-Pleistocene divergence of populations of the arctic-alpine ground beetle Amara alpina (Paykull) (Coleoptera: Carabidae)

Aim This study examines the hypothesis that the biogeographic history of a species is reflected in the distribution of molecular genetic diversity and the phylogenies of extant populations. Location Populations of arctic-alpine ground beetle Amara alpina were analysed from Beringia (Alaska and northernmost British Columbia), the Hudson Bay region, the northern Appalachian Mountains, and the central Rocky Mountains of North America. Methods Mitochondrial restriction site variation of specimens from twenty-two populations were assayed by using radioactively labelled mtDNA to probe Southern membranes containing restriction enzyme digested total DNA. Restriction sites were mapped and genetic distances were calculated by pairwise comparison of presence and absence of restriction sites. Genetic distances were used in a molecular analysis of variance and to construct a minimal spanning tree. Parsimony methods were used to investigate the phylogenetic relationships between the haplotypes. These results were compared to an existing model for postglacial dispersal based on fossil and modern occurrences of arctic-alpine beetles. Results Among the twenty-two populations, fifteen haplotypes were detected. Genetic variation within each of the four regions corresponded to that expected from the palaeontologically based model. Beringian populations were the most genetically diverse. In contrast, no restriction site variation was observed in populations from the Hudson Bay region. Intermediate amounts of variation were observed in alpine populations of the Rocky and Appalachian Mountains. Maximum parsimony and cluster analysis provide evidence that at least two ancestral haplotypes existed in the Southern refugium from which the Rocky and the Appalachian Mountains populations were founded. Main conclusions The genetic results are generally consistent with the palaeontologically based model. The diversity of Beringian populations is consistent with this region having been continuously inhabited by Amara alpina throughout the Pleistocene. The Hudson Bay region was not deglaciated until about 6000 years, and its populations have no restriction site variation. The molecular genetic data support the interpretation that the Hudson Bay region was colonized from Beringia based on the occurrence of the same haplotype in both regions.     

Cryptic speciation in the Anadenobolus excisus millipede species complex on the Island of Jamaica

Anadenobolus excisus is a large species of millipede endemic to the Caribbean Island of Jamaica. Initial detailed morphological studies showed little or no discrete variation across this species' distribution in somatic or, in particular. genitalic morphology. However, a molecular survey based on approximately 1000 base pairs of the mitochondrial (mtDNA) 16S rRNA gene that examines 242 individuals sampled from 54 localities reveals three highly divergent mtDNA lineages. A lack of discrete morphological differentiation suggests that genetic and morphological divergence may be decoupled, a pattern inconsistent with a number of evolutionary models. In contrast to minimal morphological divergence, size variation among mtDNA lineages suggests that character displacement has occurred and that these lineages are cohesive in sympatry. We conclude that A. excisus is actually a complex of three cryptic species and that morphological approaches to delineating millipede species may sometimes underestimate evolutionary diversity.     

Historical stocking data and 19th century DNA reveal human‐induced changes to native diversity and distribution of cutthroat trout

Many species are threatened with extinction and efforts are underway worldwide to restore imperilled species to their native ranges. Restoration requires knowledge of species' historical diversity and distribution. For some species, many populations were extirpated or individuals moved beyond their native range before native diversity and distribution were documented, resulting in a lack of accurate information for establishing restoration goals. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution for cutthroat trout in the Southern Rocky Mountains. We assembled a large archive of historical records documenting human‐mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) and combined these data with phylogenetic analysis of 19th century samples from museums collected prior to trout stocking activities and contemporary DNA samples. Our study of the trout in the Southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historical and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.