Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River

Aim To assess the roles of dispersal and vicariance in shaping the present distribution and diversity within Hypentelium nigricans, the northern hogsucker (Teleostei: Cypriniformes). Location Eastern United States. Methods Parsimony analyses, Bayesian analyses, pairwise genetic divergence and mismatch plots are used to examine patterns of genetic variation across H. nigricans. Results Species relationships within the genus Hypentelium were consistent with previous hypotheses. However, relationships between haplotypes within H. nigricans revealed two deeply divergent groups, a clade containing haplotypes from the New and Roanoke rivers (Atlantic Slope) plus Interior Highlands and upper Mississippi River and a clade containing haplotypes from the Eastern Highlands, previously glaciated regions of the Ohio and Wabash rivers, and the Amite and Homochitto rivers of south‐western Mississippi. Main conclusions The phylogenetic history of Hypentelium was shaped by old vicariant events associated with erosion of the Blue Ridge and separation of the Mobile and Mississippi river basins. Within H. nigricans two clades existed prior to the Pleistocene; a widespread clade in the pre‐glacial Teays‐Mississippi River system and a clade in Cumberland and Tennessee rivers. Pleistocene events fragmented the Teays‐Mississippi fauna. Following the retreat of the glaciers H. nigricans dispersed northward into previously glaciated regions. These patterns are replicated in other clades of fishes and are consistent with some of the predictions of Mayden's (Systematic Zoology, 37, 329, 1988) pre‐Pleistocene vicariance hypothesis.     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background  

The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat.     

Post-glacial expansion into the Paleozoic Plateau: evidence of an Ozarkian refugium for the Ozark minnow Notropis nubilus (Teleostei: Cypriniformes)

Genetic variation was examined within the Ozark minnow Notropis nubilus using complete mtDNA cytochrome b gene sequences from 160 individuals representing 30 localities to test hypotheses on the origin of the distribution. Phylogenetic analyses revealed three strongly supported clades of haplotypes consistent with geographic distributions: a clade from the Western Ozarks, a clade from the Southern Ozarks and a clade from the Northern Ozarks and upper Mississippi River basin. The estimated mean ages of these clades indicated that they diverged during pre-Illinoian glacial cycles extending from the late Pliocene into the early Pleistocene. Results of demographic analyses based on coalescent approaches supported the hypothesis that the Paleozoic Plateau was not a refugium for N. nubilus during periodic glacial advances. There is evidence of a genetic signature of northern expansion into the Paleozoic Plateau from a Southern Ozarkian refugium. Populations expanded out of drainages in the Northern Ozarks into the Paleozoic Plateau during the late Pleistocene. Subsequently, the two regions were isolated due to the recent extirpation of intervening populations caused by the loss of suitable habitat.     

Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data

Pleistocene glaciations greatly affected the distribution of genetic diversity in animal populations. The Little Owl is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographical structure of European populations, we sequenced the mitochondrial cytochrome c oxidase I (COI) and control region (CR1) in 326 individuals sampled from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: a western haplogroup distributed in western and northwestern Europe, and an eastern haplogroup distributed in southeastern Europe. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three subgroups within the eastern clade: Balkan, southern Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the western and eastern haplogroups split 2.01–1.71 Mya. Slightly different times for splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04–0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72–0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, whereas expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was probably prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with those recorded between different avian species.     

Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.     

Comparative Phylogeography of Mississippi Embayment Fishes

The Mississippi Embayment is a prominent physiographic feature of eastern North America consisting of primarily lowland aquatic habitats and a fish fauna that is largely distinct from nearby highland regions. Numerous studies have demonstrated that both pre-Pleistocene and Pleistocene events have had a strong influence on the distributions and relationships of highland fishes in eastern North America. However, the extent to which these same events affected Embayment distributed taxa remains largely unexplored. The purpose of this study was to investigate the relative roles of pre-Pleistocene and Pleistocene events in shaping phylogeographic relationships of four stream dwelling fishes in the Mississippi Embayment. Molecular genetic analyses of the mitochondrial gene cytochrome b were performed for three ictalurid catfish species (Noturus miurus, n = 67; Noturus hildebrandi, n = 93, and Noturus phaeus, n = 44) and one minnow species (Cyprinella camura, n = 78), all distributed in tributary streams of the Mississippi Embayment. Phylogenetic relationships and divergence times among haplotypes for each species were estimated using maximum likelihood and Bayesian methods. Phylogenetic analyses recovered 6 major haplotype clades within N. miurus, 5 within N. hildbrandi, 8 within N. phaeus, and 8 within C. camura. All three Noturus species show a high degree of isolation by drainage, which is less evident in C. camura. A clade of haplotypes from tributaries in the southern portion of the Mississippi Embayment was consistently recovered in all four species. Divergence times among clades spanned the Pleistocene, Pliocene, and Miocene. Novel relationships presented here for C. camura and N. phaeus suggest the potential for cryptic species. Pre-Pleistocene and Pleistocene era sea level fluctuations coincide with some divergence events, but no single event explains any common divergence across all taxa. Like their highland relatives, a combination of both pre-Pleistocene and Pleistocene era events have driven divergences among Embayment lineages.     

Genetic differentiation in the Trinidad endemic Mannophryne trinitatis (Anura: Aromobatidae): Miocene vicariance,in situ diversification and lack of geographical structuring across the island

Trinidad offers a unique study system within the Caribbean to assess the processes and patterns of amphibian speciation. We used mitochondrial DNA sequences to investigate the phylogenetic relationships and patterns of intraspecific genetic variation of Mannophryne trinitatis from Trinidad. Molecular clock estimates point to a genetic split between M. trinitatis and its sister species, M. venezuelensis, dating to the Late Miocene (c. 7–8 Mya), suggesting vicariance as a means of speciation when Trinidad pulled apart from northern Venezuela. M. trinitatis phylogenetic population analyses from ten Northern Range and four Central Range localities recovered three well‐resolved clades: a larger clade formed by haplotypes from Northern Range localities and two additional clades, one formed by haplotypes from the Central Range and another including haplotypes from Northern Range localities and one haplotype from the Central Range. Overall, our results show that the genetic diversity in M. trinitatis is not geographically structured but it is distributed among the various Northern and Central Range localities. In congruence with the vicariance speciation hypothesis, we attribute M. trinitatis present distribution and lack of genetic structure to multiple admixture events caused by climate changes that severely affected the topology of Trinidad throughout the Pliocene/Pleistocene periods.     

Phylogeographic analysis detects congruent biogeographic patterns between a woodland agamid and Australian wet tropics taxa despite disparate evolutionary trajectories

Aim To test the congruence of phylogeographic patterns and processes between a woodland agamid lizard (Diporiphora australis) and well‐studied Australian wet tropics fauna. Specifically, to determine whether the biogeographic history of D. australis is more consistent with a history of vicariance, which is common in wet tropics fauna, or with a history of dispersal with expansion, which would be expected for species occupying woodland habitats that expanded with the increasingly drier conditions in eastern Australia during the Miocene–Pleistocene. Location North‐eastern Australia. Methods Field‐collected and museum tissue samples from across the entire distribution of D. australis were used to compile a comprehensive phylo‐geographic dataset based on c. 1400 bp of mitochondrial DNA (mtDNA), incorporating the ND2 protein‐coding gene. We used phylogenetic methods to assess biogeographic patterns within D. australis and relaxed molecular clock analyses were conducted to estimate divergence times. Hierarchical Shimodaira–Hasegawa tests were used to test alternative topologies representing vicariant, dispersal and mixed dispersal/vicariant biogeographic hypotheses. Phylogenetic analyses were combined with phylogeographic analyses to gain an insight into the evolutionary processes operating within D. australis. Results Phylogenetic analyses identified six major mtDNA clades within D. australis, with phylogeographic patterns closely matching those seen in many wet tropics taxa. Congruent phylogeographic breaks were observed across the Black Mountain Corridor, Burdekin and St Lawrence Gaps. Divergence amongst clades was found to decrease in a north–south direction, with a trend of increasing population expansion in the south. Main conclusions While phylogeographic patterns in D australis reflect those seen in many rain forest fauna of the wet tropics, the evolutionary processes underlying these patterns appear to be very different. Our results support a history of sequential colonization of D. australis from north to south across major biogeographic barriers from the late Miocene–Pleistocene. These patterns are most likely in response to expanding woodland habitats. Our results strengthen the data available for this iconic region in Australia by exploring the understudied woodland habitats. In addition, our study shows the importance of thorough investigations of not only the biogeographic patterns displayed by species but also the evolutionary processes underlying such patterns.     

Cyclic habitat displacements during Pleistocene glaciations have induced independent evolution of Tasimia palpata populations (Trichoptera: Tasimiidae) in isolated subtropical rain forest patches

Aim Mechanisms generating biodiversity and endemism are influenced by both historical and ecological patterns, and the relative roles of history vs. ecological interactions are still being debated. The phylogeography of one rain forest‐restricted caddisfly species, Tasimia palpata, thought to have good dispersal abilities, is used to address questions about shifts of highland rain forest habitat during Pleistocene glaciations and about their consequences for haplotype composition and distribution. Location Tasimia palpata occurs in highland subtropical rain forest patches, which are separated from one another by lowland dry bush, in south‐eastern Queensland, Australia. Methods We sequenced 375 base pairs of the mitochondrial cytochrome oxidase I gene from 169 individuals (20 populations) of T. palpata, mainly from three fragmented subtropical rain forest blocks, revealing 46 haplotypes. Analysis of molecular variance (amova ), genetic divergence between populations, nested clade analyses and tests based on coalescent theory were used to analyse phylogeographical relationships among T. palpata populations. Results amova indicates spatial genetic structure between isolated subtropical rain forest patches, with an isolation‐by‐distance effect. Tests based on coalescent theory suggest a repeated process of population reductions and divergence between isolated rain forests during Pleistocene glaciations as a consequence of habitat constrictions followed by population expansions during interglacial periods when subtropical rain forest expanded. In addition, these results suggest that, prior to the Pleistocene, rain forest and T. palpata had more widespread distributions in this region. Main conclusions Historical rain forest expansion and contraction during the Pleistocene resulted in changes in demography and genetic diversity of T. palpata, as well as in an increase in genetic divergence between populations from different patches of subtropical rain forest. Despite the fact that this caddisfly species was isolated in separate highland rain forest patches at various times during the Pleistocene, there is no evidence of allopatric speciation during the Quaternary, which contrasts with other examples of endemism and high diversity in rain forest highlands.     

Evolution of the Cyprinella lutrensis species group. III. Geographic variation in the mitochondrial DNA of Cyprinella lutrensis— the influence of Pleistocene glaciation on population dispersal and divergence

We employed restriction site variation in mitochondrial (mt)DNA to determine if significant phylogeographic structure occurs in the North American cyprinid fish Cyprinella lutrensis. Digestion patterns from 16 restriction endonucleases identified fifty mtDNA haplotypes among 127 individuals of Cyprinella lutrensis assayed from localities in the Gulf Coastal Plain, the Great Plains, and the Central Lowlands. Nucleotide sequence divergence among haplotypes was highly variable (mean ± SE: 2.87%± 0.08; range: 0.14–9.24%). Maximum-parsimony analysis and the neighbour joining method of tree construction revealed three major groupings (clades) of haplotypes that differed in geographic distribution. Divergence estimates between the basal clade, comprised of haplotypes primarily from the Brazos River in east Texas, and the remaining two clades, place C. lutrensis in the western Gulf Coastal Plain prior to Pleistocene glaciation. Nucleotide sequence divergence between the second clade, comprised of haplotypes from the Trinity and Calcasieu rivers in east Texas and southwestern Louisiana, respectively, and the third clade (comprised primarily of haplotypes from localities north of Texas and affected directly by Pleistocene glaciation), suggest that C. lutrensis colonized gladated regions to the north during the mid- to late Pleistocene. This hypothesis is supported by levels of intrapopulational nucleotide diversity in geographic localities outside of Texas and by geological evidence. Despite marked geographic variation in morphometries, meristics, and nuptial coloration, mtDNA variation in glaciated regions was not geographically structured, and subspecies of C. lutrensis were not identifiable by phylogenetic analysis of mtDNA.     

Pleistocene effects on the European freshwater fish fauna: double origin of the cobitid genus Sabanejewia in the Danube basin (Osteichthyes: Cobitidae)

Biogeographical hypotheses of European freshwater fishes were inferred using phylogeographic analysis of the complete cytochrome b and ATP synthase 8 and 6 mitochondrial genes (1982bp). To test the relative importance of drainage origin versus Pleistocene glaciations in the origin of primary freshwater fishes in Europe, we reconstructed the phylogenetic relationships of the genus Sabanejewia which is distributed in European waters. The phylogenetic relationships recovered for the genus Sabanejewia (n=75) provide support for the monophyly of six main evolutionary mtDNA lineages: Sabanejewia larvata, Sabanejewia romanica, Sabanejewia aurata/Sabanejewia caucasica, Sabanejewia kubanica, Sabanejewia baltica, and the Danubian-Balkanian complex. The Caucasian-Caspian mtDNA lineages, S. kubanica, S. aurata/S. caucasica, and the Northern European S. baltica represents the sister group of the Danubian-Balkanian complex mtDNAclade, supporting a Caucasian-Northern European origin of most of mtDNA lineages of the Central European freshwater fish fauna. The mtDNA divergence observed between the Danubian Sabanejewia species is too dissimilar to support their contemporary origin. Rather, the mtDNA data suggest that the Danubian Sabanejewia lineages most likely have a double origin, indicating that the European Sabanejewia lineages have experienced different historical processes for the following reasons. First, the origin of the S. larvata and S. romanica mtDNA clades predates the origin of the Danubian-Balkanian complex, and our results showed that the completion of the Alps and the origin of the Danube drainage seem to have promoted the speciation of the earliest Sabanejewia clades in the Miocene. Second, small genetic distances and the geographical pattern found within the Danubian-Balkanian complex clade indicate that the lineages included in this clade spread recently across the Danube and Greek river drainages. The inclusion of the S. balcanica species within all mtDNA lineages suggests that cyclical cold periods during the Pleistocene glaciations have favoured its rapid expansion and genetic homogenisation across Central European and Greek waters.     

SPECIATION IN NORTH AMERICAN CHICKADEES: I. PATTERNS OF mtDNA GENETIC DIVERGENCE

We surveyed mitochondrial DNA haplotype divergence within and between populations of six species of North American chickadees (Parus, Subgenus Poecile) with the following results. (1) Genotype diversities (range 0.3 to 0.7) and low nucleotide diversities (range 3 to 27 × 10^?4) within populations were typical of known vertebrates. (2) The two widespread, northern species (atricapillus and hudsonicus) exhibit little mtDNA genetic differentiation throughout their previously glaciated continental distributions, most likely because of recent, postglacial range expansions. (3) Newfoundland populations of atricapillus and maritime province (Newfoundland plus Nova Scotia) populations of hudsonicus have distinct mtDNA haplotypes which differ from continental haplotypes by single restriction site changes. (4) Haplotypes of the southeastern U.S. species P. carolinensis divide into eastern and western sets which have diverged by three percent. This heretofore unrecognized, divided population structure may correspond to the Tombigbee River/ Mobile Bay disjunction known in some other vertebrate taxa. (5) Allopatric populations of the southwestern species sclateri and gambeli exhibit divergences of one and three percent respectively. (6) Prevailing interspecific divergence distances of three to seven percent suggest speciation early in the Pleistocene rather than during late (e.g., Wisconsin) glaciations. (7) Phylogenetic analyses suggest that North American taxa include two clades, hudsonicus-rufescens-sclateri versus carolinensis-atricapillus-gambeli and that carolinensis and atricapillus are not sister species.     

MITOCHONDRIAL DNA VARIATION WITHIN AND BETWEEN SPECIES OF THE PAPILIO MACHAON GROUP OF SWALLOWTAIL BUTTERFLIES

Species limits and phylogenetic relationships in the Papilio machaon species group are potentially confounded by a complex pattern of Pleistocene range fragmentation, hybridization, and ecological race formation. Mitochondrial DNA (mtDNA) restriction-site analysis has been used to define genetic affinities and genetic population structure within this species group. The distribution of mtDNA haplotypes generally confirms prior phylogenetic hypotheses and species delineations, but there is poor correspondence between ecological races and mtDNA haplotypes. The amount and distribution of mtDNA sequence variation within species vary among species, reflecting differences in current patterns of gene flow and/or historical population structure. In spite of wing pattern characters that ally them with P. polyxenes, both P. joanae and P. brevicauda have mtDNA that is closely related to that of P. machaon. We suggest that P. joanae and P. brevicauda are of hybrid origin.     

Ecomorphology and habitat utilization of Cottus species

We investigated relationships between morphological attributes and mesohabitat use in populations of Cottus carolinae. Field studies revealed significant differences between Ozark and prairie stream mesohabitats where populations of C. carolinae occurred. Features of the mesohabitat that were characteristic of each stream type correlated with intra- and inter-specific differences in morphological attributes of Cottus. The morphology of Cottus occurring in the deeper, slower, and siltier prairie stream exhibited larger head width and depth, body width and depth, and caudal peduncle width while those occurring in a shallower, faster flowing Ozark stream had longer pelvic fins, larger eyes, and deeper caudal peduncles. Each population had a morphology tailored to optimize its performance in a specific habitat. Results of laboratory based performance studies using a variable flow chamber revealed that critical current velocities (CCV) of live and preserved specimens were weakly associated with distinct combinations of morphological traits. Specimens with higher CCV measurements typically had longer pelvic fins, larger eyes, and deeper caudal fins (Ozark morphology). Those with lower CCVs had larger head width and depth, body width and depth, and caudal peduncle width (prairie morphology) in studies using cobble as the substrate. Differences in flow regimes between prairie and Ozark streams may generate specific niches for specific morphotypes, and current velocity may exert selective pressure on morphology.     

Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo‐Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.     

Phylogeography of sable (Martes zibellina L. 1758) in the southeast portion of its range based on mitochondrial DNA variation: highlighting the evolutionary history of the sable

To reveal phylogeographic features of sable (Martes zibellina) in the southeast part of its range, we analyzed variability of the mitochondrial DNA (mtDNA) cytochrome b gene, tRNA (Pro), tRNA (Thr) and control region (D-loop) sequences from 78 specimens in populations of the Russian Far East, northeast China, and Mongolia. Our results revealed the presence of 49 different haplotypes split into two major phylogenetic groups—clades A and B, the latter separated into two clades, B1 and B2. Comparative analysis of D-loop haplotypes in populations originating from the southeast (Russian Far East, China and Mongolia) and the west (northern Urals) portions of sable range indicated that all three mtDNA clades were present in different regional groups. However, highest diversity of clade B1 in northeast China and its nearly complete absence from the Urals suggest that the southeast sable range, being a refuge during Pleistocene glacial periods, can be considered the center of genetic diversification and possibly origin of this species. All divergence estimates fall within the Pleistocene suggesting that Quarternary glaciations played an important role in phylogeographic differentiation of sable.     

Recovering cryptic diversity and ancient drainage patterns in eastern North America: historical biogeography of the Notropis rubellus species group (Teleostei: Cypriniformes)

The Central Highlands of North America contain a strikingly diverse assemblage of temperate freshwater fishes and have long been a focus of biogeographic studies. The rosyface shiner complex, Notropis rubellus and related species, is a member of this fauna exhibiting a disjunct highlands distribution occurring in the unglaciated regions of the Central Highlands and glaciated regions of the Central Lowlands. Until recently, N. rubellus was considered a single, widespread species exhibiting geographic variation in morphological characters. However, several studies have revealed that N. rubellus is a multi-species complex with closely related species endemic to drainages within each highland region. We examined genetic variation of the N. rubellus complex using a complete mtDNA cytochrome b gene sequence data set and combined mtDNA and published allozyme data sets. Parsimony and Bayesian analyses of the mitochondrial data set and parsimony analyses of a combined mitochondrial and allozyme data sets were largely consistent. Results of these analyses revealed ancient cryptic diversity within the N. rubellus complex that existed prior to the onset of Pleistocene glaciations. We identified seven strongly supported clades within the N. rubellus complex. Four clades are diagnosed as separate species (N. percobromus, N. rubellus, N. micropteryx and N. suttkusi) and three clades may represent undescribed forms. Relationships among these groups and their biogeographical patterns provided significant inferences on ichthyofaunal distributions in southeastern North America. These include the timing of the origin of the diversity, ancient drainage patterns and barriers to dispersal in the Central Highlands. The observation of increased diversity in N. rubellus suggests there may be greater diversity within other taxa with a similar distribution.     

NO EVIDENCE OF BOTTLENECK IN THE POSTGLACIAL RECOLONIZATION OF EUROPE BY THE NOCTULE BAT (NYCTALUS NOCTULA)

During the Pleistocene, the habitat of the noctule bat (Nyctalus noctula) was limited to small refuge areas located in Southern Europe, whereas the species is now widespread across this continent. Using mtDNA (control region and ND1 gene) polymorphisms, we asked whether this recolonization occurred through bottlenecks and whether it was accompanied by population growth. Sequences of the second hypervariable domain of the control region were obtained from 364 noctule bats representing 18 colonies sampled across Europe. This yielded 108 haplotypes that were depicted on a minimum spanning tree that showed a starlike structure with two long branches. Additional sequences obtained from the ND1 gene confirmed that the different parts of the MST correspond to three clades which diverged before the Last Glacial Maximum (18,000 yrC¹⁴ BP), leading to the conclusion that the noctule bat survived in several isolated refugia. Partitioning populations into coherent geographical groups divided our samples (φ_CT = 0.17; P = 0.01) into a group of highly variable nursing colonies from central and eastern Europe and less variable, isolated colonies from western and southern Europe. Demographic analyses suggest that populations of the former group underwent demographic expansions either after the Younger Dryas (11,000–10,000 yrC¹⁴ BP), assuming a fast mutation rate for HV II, or during the Pleistocene, assuming a conventional mutation rate. We discuss the fact that the high genetic variability (h = 0.69–0.96; π = 0.006–0.013) observed in nursing colonies that are located some distance from potential Pleistocene refugia is probably due to the combined effect of rapid evolution of the control region in growing populations and a range shift of noctule populations parallel to the recovery of forests in Europe after the last glaciations.     

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.