Phylogenetic analysis of the genus Thymallus (grayling) based on mtDNA control region and ATPase 6 genes, with inferences on control region constraints and broad-scale Eurasian phylogeography

We present first insights into the molecular phylogeny of the grayling genus Thymallus (Salmonidae) using sequences from the mitochondrial control region and ATPase6 genes. A suite of analytical approaches were applied for each gene separately and for the combined data. The ATPase6 gene is shown to have a mean divergence rate across the genus of 2.46 times faster than the complete control region. Based on the combined data, four major (internal) clades, presumably originating in the Pliocene, were resolved with high support in all analyses and represented two distinct lineages in the Amur basin, one lineage in all remaining Siberian and Mongolian drainages, and one lineage corresponding to European grayling Thymallus thymallus. The resolution of multiple lineages, from both additional internal and terminal clades, within each major drainage basin underscores the complexity and effects that Pleistocene hydrological dynamics have had on the distribution of biodiversity in Siberia.     

Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.     

Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia,introgression and riverine barriers

The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.     

Diversification in the northern neotropics: mitochondrial and nuclear DNA phylogeography of the iguana Ctenosaura pectinata and related species

While Quaternary climatic changes are considered by some to have been a major factor promoting speciation within the neotropics, others suggest that much of the neotropical species diversity originated before the Pleistocene. Using mitochondrial and nuclear sequence data, we evaluate the relative importance of Pleistocene and pre-Pleistocene events within the evolutionary history of the Mexican iguana Ctenosaura pectinata , and related species. Results support the existence of cryptic lineages with strong mitochondrial divergence (> 4%) among them. Some of these lineages form zones of secondary contact, with one of them hybridizing with C. hemilopha . Evolutionary network analyses reveal the oldest populations of C. pectinata to be those of the northern and southern Mexican coastal regions. Inland and mid-latitudinal coastal populations are younger in age as a consequence of a history of local extinction within these regions followed by re-colonization. Estimated divergence times suggest that C. pectinata originated during the Pliocene, whereas geographically distinct mitochondrial DNA lineages first started to diverge during the Pliocene, with subsequent divergence continuing through the Pleistocene. Our results highlight the influence of both Pliocene and Pleistocene events in shaping the geographical distribution of genetic variation within neotropical lowland organisms. Areas of high genetic diversity in southern Mexico were detected, this finding plus the high levels of genetic diversity within C. pectinata , have implications for the conservation of this threatened species.     

Secondary contact between two divergent lineages of grayling Thymallus in the lower Enisey basin and its taxonomic implications

A contact zone between two widespread divergent lineages of grayling Thymallus sp. has been identified in the lower Enisey basin (Khantaiskoye Lake) in north central Siberia (Russia). Sequences of the mitochondrial DNA control region revealed two lineages with 2·6% divergence. Haplotypes from these two lineages clearly fall within two previously described clades, one presumably corresponding to Arctic grayling Thymallus arcticus found throughout the Siberian coastal zone as well as North America, and the other corresponding to grayling found elsewhere in the Enisey basin, including Lake Baikal and its tributaries. Allelic variation at seven microsatellite loci strongly suggests reproductive isolation in sympatry between these two lineages in Khantaiskoye Lake. Integration of these new data with existing knowledge on Thymallus throughout its Siberian range supports a taxonomic revision. The currently recognized sub-specific lineages of Arctic grayling along the Siberian Arctic coast as well as grayling from North America should probably be regarded as T. arcticus . Arctic grayling, however, are limited to the coastal zone and lower reaches of the Enisey. Most of the Enisey basin, including Lake Baikal and its tributaries are occupied by another taxon, which should be recognized as Thymallus baicalensis . This perspective strictly follows evolutionary principles, eliminates the use of four sub-specific names and circumvents the illogical mosaic distribution of T. arcticus arcticus , which nevertheless does not represent a monophyletic lineage.     

Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog,Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai‐Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA partial sequences from protein‐coding genes ND1 and ND2, and intervening areas including complete tRNA^Ile, tRNA^Gln and tRNA^Met. Two null hypotheses were tested: (i) that genetic patterns do not correspond to the development of drainage systems and (ii) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well‐supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed via population fragmentation during the rearrangement of paleodrainage basins in the Early Pliocene and Early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.     

Genetic lineages and postglacial colonization of grayling (Thymallus thymallus, Salmonidae) in Europe, as revealed by mitochondrial DNA analyses

In stark contrast to other species within the Salmonidae family, phylogeographic information on European grayling, Thymallus thymallus, is virtually nonexistent. In this paper, we utilized mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (mtDNA PCR-RFLP) and sequence variation to infer the postglacial dispersal routes of T. thymallus into and within northern Europe, and to locate geographically, potential evolutionarily distinct populations. Mitochondrial analyses revealed a total of 27 T. thymallus haplotypes which clustered into three distinct lineages. Average pairwise interlineage divergence was four and nine times higher than average intralineage divergence for RFLP and sequence data, respectively. Two European grayling individuals from the easternmost sample in Russia exhibited haplotypes more genetically diverged from any T. thymallus haplotype than T. arcticus haplotype, and suggested that hybridization/introgression zone of these two sister species may extend much further west than previously thought. Geographic division of the lineages was generally very clear with northern Europe comprising of two genetically differentiated areas: (i) Finland, Estonia and north-western Russia; and (ii) central Germany, Poland and western Fennoscandia. Average interpopulation divergence in North European T. thymallus was 10 times higher than that observed in a recent mtDNA study of North American T. arcticus. We conclude that (i) North European T. thymallus populations have survived dramatic Pleistocene temperature oscillations and originate from ancient eastern and central European refugia; (ii) genetic divergence of population groups within northern Europe is substantial and geographically distinct; and (iii) the remainder of Europe harbours additional differentiated assemblages that likely descend from a Danubian refugium. These findings should provide useful information for developing appropriate conservation strategies for European grayling and exemplify a case with a clear need for multinational co-operation for managing and conserving biodiversity.     

Genetic variation of European grayling (Thymallus thymallus) populations in the Western Balkans

In order to elucidate genetic composition of European grayling (Thymallus thymallus) populations in the Western Balkans, the partial mitochondrial DNA (mtDNA) control region was sequenced and 12 microsatellite loci genotyped in 14 populations originating from tributaries of the Adriatic and Danube drainages. Eleven mtDNA haplotypes were found, one confined to the Adriatic clade, one to the Alpine group and the rest to the ‘Balkan’ grayling phylogenetic clade. Haplotypes from the Balkan clade were confined to the Danube drainage and constituted two groups: northern group with haplotypes found in the Slovenian part of the Danube drainage, and southern group, consisting from Bosnia–Herzegovina and Montenegro. Substantial genetic distance between northern and southern groups of haplotypes (0.75–1.8%) and well supported divisions within the northern group indicate very structured grayling population within the studied Danube basin that most probably did not evolve due to vicariance but rather as a consequence of multiple colonization waves that might have occurred during the Pleistocene. Furthermore, genetic distance of ~4% between Adriatic and Danube populations’ haplotypes, suggest that their separation occurred in mid-Pliocene. These findings imply a complex colonization pattern of the Western Balkans drainages. Microsatellite data also confirm high genetic diversity in Western Balkans populations of grayling (on average 7.5 alleles per microsatellite locus and H _exp 0.58). Limited stocking activities were detected based on microsatellites and mtDNA data. Regarding current knowledge of grayling phylogeography appropriate management strategies were proposed to preserve unique, autochthonous grayling populations in Western Balkan.     

Multiple species of grayling (Thymallus sp.) found in sympatry in a remote tributary of the Amur River

Large-scale phenotypic and genetic studies of the salmonid genus Thymallus (grayling) in the Palaearctic suggest that most major phylogeographic lineages represent good biological species. Evaluating such a premise in areas involved in palaeo-hydrological dynamics where multiple species are found in sympatry should serve to assess the level of reproductive isolation, the traditional sine qua non of species recognition. Molecular sequence (mtDNA) and microsatellite (nDNA, seven loci) analysis of grayling in the upper Bureya River watershed support the occurrence of three distinctive species of grayling living in sympatry in this large oligotrophic tributary of the Amur River. One of these lineages is primarily found throughout the Lena River basin and is recognized as Baikal-Lena grayling Thymallus baicalolenensis; the second, the upper Amur grayling Thymallus grubii is found over large areas of the Amur catchment including the entire headwater region; and the third, the Bureya grayling Thymallus burejensis is endemic to the study area. A limited number of hybrids were identified, primarily between Baikal-Lena grayling T. baicalolenensis and Bureya grayling T. burejensis with little to no signs of introgression among non-hybrid individuals. Morphological distinctiveness among populations of these species living in sympatry was greater than between populations living in allopatry, suggesting character displacement. Divergence estimates among taxa range up to 6.2 MY, and allopatric origins for all three species’ is suggested. To our knowledge, this is the first data-based confirmation of three species of grayling living in sympatry.     

Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci

Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.     

Comparative mtDNA sequence (control region, ATPase 6 and NADH‐1) divergence in Hucho taimen(Pallas) across four Siberian river basins

Hucho taimen from eight populations spanning four drainage basins (Amur, Lena, Enisei and Khatanga) were analysed for nucleotide sequence variation across three mitochondrial genes (ATP6, NADH‐1 and control region). Samples of H. hucho , Brachymystax lenok (sharp‐snouted and blunt‐snouted forms) and Parahucho perryi were also included for comparison. Nucleotide variation across a total of 1826 base pairs in H. taimen revealed shared haplotypes between the Amur and Lena basins, further supporting a previous hypothesis of late to post‐Pleistocene hydrological exchange between these now disjunct basins. In contrast to an earlier study using the control region alone, clear phylogeographic structure was seen at a large geographic scale, reflected by two phylogroups, one corresponding to the Amur and Lena basins, and the other to the Enisei and Khatanga basins. Comparative rates of divergence revealed considerably faster and less heterogeneous substitution rates for the two coding genes, especially at interspecific levels compared to the mtDNA control region.     

Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae

The phylogeography of an endangered salmonid, European grayling (Thymallus thymallus), was studied based on analysis of 17 nuclear microsatellite DNA loci. In agreement with earlier mitochondrial DNA (mtDNA) studies, phylogenetic relationships of the populations suggested that northern Europe was colonized from two distinct Pleistocene refugia. Furthermore, microsatellites revealed highly supported grouping of mainland Swedish, Norwegian, Danish, German and Slovenian populations, suggesting that grayling from the northwestern and central Europe have descended from their southern conspecifics. The level of divergence between populations was substantial, even across short geographical distances. Although this was in part due to postglacial colonization patterns and contemporary barriers for gene flow, the high divergence estimates between hydrologically connected sampling locations implied efficient interpopulation reproductive isolation. Microsatellites revealed that the populations exhibited, on average, only 3.5 (+/-2.2) alleles per locus, indicating that T. thymallus has strikingly low levels of intrapopulation genetic diversity as compared with other freshwater fish species. Accordingly, as indicated by analysis of molecular variance (AMOVA), only 49.1-58.0% of the total grayling microsatellite diversity resided within populations. A latitudinal genetic diversity gradient, potentially resulting from glaciation-mediated founder events, was not evident. Alternatively, it is possible that grayling display limited dispersal behaviour/capability, leading to low long-term effective population sizes and, consequently, depauperate intrapopulation polymorphism. These findings have implications for conservation of T. thymallus. Importantly, they exemplify that microsatellites can be highly informative for intraspecific phylogeography studies dealing with substantial divergence scales.     

Genetic structure of Indian scad mackerel Decapterus russelli: Pleistocene vicariance and secondary contact in the Central Indo-West Pacific Seas

Major genetic breaks between the Indian and Pacific oceans have been reported for marine fishes and invertebrates. The genetic structure and history of the Indian scad mackerel, Decapterus russelli, in the Indo-Malay archipelago were investigated using the cytochrome b gene sequence as mitochondrial marker and two length-polymorphic introns as nuclear markers. The existence of two major mitochondrial lineages separated by 2.2% average nucleotide divergence, and their heterogeneous geographical distributions, were confirmed. This indicated past geographic isolation, possibly caused by a Pleistocene drop in sea level. The presence, in sympatry, of the two mitochondrial lineages was thought to result from secondary contact. A recent population bottleneck and subsequent rapid population expansion were indicated by low genetic diversities and strongly negative Tajima's D-values. This evidence supports the hypothesis that the habitat available to D. russelli in the Pleistocene was restricted. Taking into account both mitochondrial and nuclear-DNA data, three geographically distinct populations were identified: one sampled in the Makassar Strait and Sulawesi Sea, one in the Arafura Sea and the third from the entire western region of the Indo-Malay archipelago. Considering the high hydrological connectivity of this region of the Indo-Pacific and the species pelagic life-history, the population structure may be maintained by homing behaviour and, perhaps, the association of spawning with retention zones.     

Genetic diversity of the naked mole‐rat (Heterocephalus glaber)

The naked mole‐rat (Heterocephalus glaber) is used as an animal model in various studies, but not much is known on the genetic diversity of this animal. Here, on the basis of dataset collected from the most part of the distribution range of the naked mole‐rat, we reconstruct phylogenetic relationships between its different lineages using mitochondrial and nuclear markers. We also mapped the distribution of the main genetic lineages, dated the divergence using different Bayesian tree‐calibration techniques, and modeled the distribution of ecological niches for the period of last glacial maximum. Our results show the existence of two deeply divergent clades designated as the eastern clade (East Ethiopia) and the southern clade (South Ethiopia and North Kenya). Additional phylogeographic structure was demonstrated for each of these two clades. Divergence between these two main lineages dated back to the Middle Pleistocene (ca. 1.4–0.8 Mya) and may have been related to climate changes in Africa during the Mid‐Pleistocene Revolution. In light of substantial genetic differences between the eastern and southern lineages of the naked mole‐rat, these two clades can be considered as two deeply divergent subspecies or even as distinct species.     

Mitochondrial and nuclear DNA phylogeography of European grayling (Thymallus thymallus): evidence for secondary contact zones in central Europe

Mitochondrial and microsatellite DNA markers were applied to infer the phylogeography, intraspecific diversity and dynamics of the distributional history of European grayling (Thymallus thymallus) with focus on its central and northern European distribution range. Phylogenetic and nested clade analyses revealed at least four major mtDNA lineages, which evolved in geographical isolation during the Pleistocene. These lineages should be recognized as the basic evolutionary significant units (ESUs) for grayling in central and northern Europe. In addition, and in contrast to previous work on grayling, the results of Bayesian analysis of individual admixture coefficients, two-dimensional scaling analysis and spatial analysis of molecular variance provided evidence for a high level of admixture among major lineages in contact zones between drainages (e.g. the low mountain range of Germany), most likely resulting from glacial perturbations and ancient river connections between drainages during the Pleistocene glaciations. Even within river systems, a high level of differentiation among populations was revealed as indicated by the microsatellite data. Grayling sampled from 29 sites displayed high levels of differentiation (overall F(ST) = 0.367), a high number of private alleles and high bootstrap support for the genetic distance-based population clusters across 12 loci. We specifically discuss our results in context of phylogeograpic studies on other European freshwater fish species with habitat preferences similar to those of grayling. Our study shows that both large-scale phylogeographical and detailed genetic analyses on a fine scale are mandatory for developing appropriate conservation guidelines of endangered species.     

Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

A previous analysis of Pacific herring mitochondrial (mt) DNA with Bayesian skyline plots (BSPs) was interpreted to reflect population growth in the late Pleistocene that was preceded by population stability over several hundred thousand years. Here we use an independent set of mtDNA control region (CR) sequences and simulations to test these hypotheses. The CR haplotype genealogy shows three deeply divided lineages, A, B and C, with divergences ranging from d=1.6% to 1.9% and with similar genetic diversities (h=0.95, 0.96, 0.94; Θ(π)=0.011, 0.012, 0.014, respectively). Lineage A occurs almost exclusively in the NW Pacific and Bering Sea, but lineages B and C are co-distributed in the Northeastern Pacific. This distribution points to a historical allopatric separation between A and B-C across the North Pacific during Pleistocene glaciations. The origins of B and C are uncertain. One hypothesis invokes long-term isolation of lineage C in the Sea of Cortez, but the present-day lack of geographical segregation from lineage B argues for lineage sorting to explain the deep divergence between B and C. BSPs depict rapid population growth in each lineage, but the timing of this growth is uncertain, because of questions about an appropriate molecular clock calibration. We simulated historical demographies under a Pleistocene climate model using observed genetic parameters. BSPs for these sequences showed rapid population growth after the Last Glacial Maximum (LGM) 18-20kyears ago and a flat population history during previous climate fluctuations. Population declines during the LGM appear to have erased signals of previous population fluctuations.     

Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations

Intraspecific phylogeographical patterns largely depend on the life history traits of a species. Especially species with a high degree of cold tolerance, limited requirements towards habitat preferences, and relatively low active dispersal capacities may have responded in a different way to the Pleistocene climatological fluctuations than the majority of taxa studied so far. To evaluate this possibility, we studied Arion fuscus (Muller, 1774), a common and widespread European terrestrial slug, from 88 locations (N = 964). Sequence variation was assessed for fragments of the mitochondrial 16S rDNA and COI genes by means of single-strand conformation polymorphisms (SSCP) and subsequent DNA sequencing. Additionally, eight allozyme loci were scored in 843 individuals. Phylogenetic analysis revealed the presence of two major evolutionary lineages, one in the Balkan region and another in the Alps and the rest of Europe. The sequence divergence between the two lineages was limited (3.3%), but gene flow between the regions was absent, suggesting that the two regions have been isolated since the late Pliocene or early Pleistocene. Allozyme differentiation among geographical regions and mitochondrial DNA (mtDNA) lineages was low. The geographical patterns observed in our data showed that (i) haplotype and nucleotide diversities are very low in northern Europe, suggesting that single haplotypes rapidly colonized large areas; (ii) recently expanded haplotype clades have restricted distribution ranges, suggesting that current gene flow is low; and (iii) genetic diversity in the Alps is much higher than in other regions and estimated past gene flow from the Eastern Alps to other regions was high, suggesting that this was a refugial zone during the Pleistocene. This full-range phylogeography suggests the existence of an alternative refugial zone, situated north of the refugial areas currently recognized in most other taxa.     

Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the african antelope, kob (Kobus kob)

The genetic differentiation among kob populations (Kobus kob) representing two recognized subspecies was examined using mitochondrial control region sequences. Two distinct lineages (estimated sequence divergence of 9.8%) exhibited different geographical distributions and do not coincide with previously recognized ranges of subspecies. The presence of the two lineages was further supported with sequences of mitochondrial cytochrome b gene. One lineage was predominant in the west and southern ranges of the populations studied and the other was commonly found in a more northern distribution (Murchison populations) in Uganda. Murchison and the geographically intermediate Toro populations (Uganda) represented the area of overlap. The existence of the two lineages in the area of overlap is hypothesized to have resulted from a range expansion and secondary contact of the two lineages of kob that evolved in allopatry. The existence of the kob during the Pleistocene offers a plausible explanation for the observed biogeographic pattern. Our mitochondrial data reveal two examples of discordance between a gene tree and presumed species tree as: (i) the two lineages co-occur in the kob subspecies, Kobus kob thomasi (Uganda kob); and (ii) the puku, which was included in the analysis because of its controversial taxonomic status (currently recognized as a distinct species from the kob), is paraphyletic with respect to the kob. Significant degrees of heterogeneity were detected between populations. Relatively high genetic variation was observed in the populations, however, the inclusion of distinct lineages influences the population structure and nucleotide diversity of the kob populations.     

Holarctic phylogeography of the tundra shrew (Sorex tundrensis) based on mitochondrial genes

A range‐wide phylogeographic study of the tundra shrew (Sorex tundrensis) was performed using cytochrome b and cytochrome oxidase I (COI) mitochondrial genes. The results based on 121 specimens from 42 localities demonstrate that the tundra shrew is divided into five main mitochondrial DNA phylogenetic lineages with largely parapatric distribution. In addition to a single Nearctic clade (Alaska) four Palearctic clades are identified: Western (Northen Urals, Kazakhstan, South‐West Siberia), Eastern (from East Transbaikalia and the Middle Amur to Chukotka), South Central (Central Siberia, the Altai, the Dzhungarian Alatau) and North Central (Northern Siberia, Central Yakutia). Date estimates obtained by use of a molecular clock corrected for potential rate decay suggest Late Pleistocene age for the most recent common ancestor of all contemporary tundra shrew populations. Relatively high genetic divergence between phylogroups (0.95–1.6%) indicates that the observed phylogeographic structure was initiated by historical events that predated the Last Glacial Maximum. We assume that, being more cold‐ and arid‐tolerant, tundra shrew underwent expansion during an early cold phase of the Last Glacial and spread through its recent range earlier than most of other Siberian red‐toothed shrews. Comparative phylogeographic analysis of Siberian shrews and rodents suggests that evolutionary histories of species associated with azonal or open habitats show important differences compared to forest species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 721–746.     

Colour variation is incongruent with mitochondrial lineages: cryptic speciation and subsequent diversification in a Gulf of California reef fish (Teleostei: Blennioidei)

The Gulf of California endemic reef fish, Acanthemblemaria crockeri (Blennioidei, Chaenopsidae), reportedly has two colour morphs, one with melanic lateral spots ('Gulf' morph) and one with orange spots ('Cape' morph). In this study, we recorded colour morph in both males and females and collected mitochondrial DNA sequence data for cytochrome c oxidase I (COI) and tRNA-Pro/D-loop of specimens from throughout the Gulf to explore the genetic basis of the colour morphs. Two highly divergent (HKY + I distance = 11.9% for COI), reciprocally monophyletic lineages were identified, consistent with the presence of two parapatric species. A 30-km gap between the distributions of mitochondrial lineages roughly corresponds to a hypothesized former seaway across the Baja California peninsula north of La Paz, although the estimated divergence time (1.84 million years ago) is more recent than the hypothetical seaway (3–4 million years ago). Surprisingly, the distribution of mitochondrial species is not congruent with the distribution of either male or female colour morphs. Our analysis also revealed significant population differentiation within both species and no shared haplotypes among populations. The northern Gulf species includes four populations (NB, CB, NM and CM) corresponding to northern and central Baja and northern and central mainland sites, while the Cape species includes two populations (SB and SM) corresponding to the Baja and mainland sides of the southern Gulf. The NB/CB division corresponds to a hypothesized Plio–Pleistocene mid-peninsular seaway. The level of genetic divergence documented in this lineage is extraordinary for a marine fish with a pelagic larval stage within a semi-enclosed basin.