Lack of mitochondrial DNA divergence between chromosome races of the common shrew, Sorex araneus, in Sweden. Implications for interpreting chromosomal evolution and colonization history

The common shrew, Sorex araneus, has one of the most variable karyotypes among mammals, displaying numerous chromosome races throughout its distribution. The six chromosome races present in Sweden can be categorized in two different karyotypic groups, the west and north European karyotypic groups (western and northern). Three races belonging to the western group are considered to have arisen through whole arm reciprocal translocations (WARTs). Race formation through this process requires a bottleneck event. In the present study we sequenced a part of the mitochondrial DNA (mtDNA) genome to investigate molecular differences between the chromosome races in Sweden. We found no mtDNA differentiation between the mainland chromosome races or the karyotypic groups. Genetic variation is as large between populations within a race as between populations among the races or karyotypic groups, suggesting that the karyotypic groups might have originated in a common glacial refugium. The noticeable exception is the Oland race, which shows higher mtDNA diversity compared to the other Swedish races, indicating a divergent origin difficult to explain. Mitochondrial DNA variation in Sweden suggests that most haplotypes arose in situ and that the populations has undergone a rapid size expansion. Altogether, the mtDNA data are in agreement with the WART hypothesis, which still holds as the most plausible variant of karyotype evolution for three of the chromosome races of the common shrew in Sweden.     

Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quaternary biogeography of high latitudes

A species-wide phylogeographical study of the root vole (Microtus oeconomus) was performed using the whole 1140 base pair mitochondrial (mt) cytochrome b gene. We examined 83 specimens from 52 localities resulting in 65 unique haplotypes. Our results demonstrate that the root vole is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions. Net divergence estimates (2.0-3.5%) between phylogroups, as well as relatively high nucleotide diversity estimates within phylogroups, indicate that the distinct phylogeographical structure was initiated by historical events that predated the latest glaciation. European root voles are divided into a Northern and a Central mtDNA phylogroup. The mtDNA data in concert with fossil records imply that root voles remained north of the classical refugial areas in southern Europe during the last glacial period. The currently fragmented populations in central Europe belong to a single mtDNA phylogroup. The Central Asian and the North European lineages are separated by the Ural Mountains, a phylogeographical split also found in collared lemmings (Dicrostonyx) and the common vole (M. arvalis). The Beringian lineage occurs from eastern Russia through Alaska to northwestern Canada. This distribution is congruent with the traditional boundaries of the Beringian refugium and with phylogeographical work on other organisms. In conclusion, similarities between the phylogeographical patterns in the root vole and other rodents, such as Arctic and subarctic lemmings, as well as more temperate vole species, indicate that late Quaternary geological and climatic events played a strong role in structuring northern biotic communities.     

Phylogeography and the geographic cline in the armament of a seed-predatory weevil: effects of historical events vs. natural selection from the host plant

Japanese camellia (Camellia japonica) and its seed predator, the camellia weevil (Curculio camelliae), provide a notable example of a geographic mosaic of coevolution. In the species interaction, the offensive trait of the weevil (rostrum length) and the defensive trait of the plant (pericarp thickness) are involved in a geographically-structured arms race, and these traits and selective pressures acting on the plant defence vary greatly across a geographical landscape. To further explore the geographical structure of this interspecific interaction, we tested whether the geographical variation in the weevil rostrum over an 800-km range along latitude is attributed to local natural selection or constrained by historical (phylogeographical) events of local populations. Phylogeographical analyses of the mitochondrial DNA sequences of the camellia weevil revealed that this species has experienced differentiation into two regions, with a population bottleneck and subsequent range and/or population expansion within each region. Although these phylogeographical factors have affected the variation in rostrum length, analyses of competing factors for the geographical variation revealed that this pattern is primarily determined by the defensive trait of the host plant rather than by the effects of historical events of populations and a climatic factor (annual mean temperature). Thus, our study suggests the overwhelming strength of coevolutionary selection against the effect of historical events, which may have limited local adaptation.     

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that 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. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.     

Phylogeography and population history of the least weasel (Mustela nivalis) in the Palearctic based on multilocus analysis

The least weasel (Mustela nivalis) is one of the most widely distributed carnivorans. While previous studies have identified distinct western and eastern mitochondrial DNA (mtDNA) lineages of the species in the western Palearctic, their broader distributions across the Palearctic have remained unknown. To address the broad-scale phylogeographical structure, we expanded the sampling to populations in Eastern Europe, the Urals, the Russian Far East, and Japan, and analyzed the mtDNA control region and cytochrome b, the final intron of the zinc finger protein on Y chromosome (ZFY), and the autosomal agouti signaling protein gene (ASIP). The mtDNA data analysis exposed the previous western lineage (Clade I) but poorly supported assemblage extending across Palearctic, whereas the previous eastern lineage (Clade II) was reconfirmed and limited in the south western part of the Palearctic. The ZFY phylogeny showed a distinctive split that corresponding to the mtDNA lineage split, although less phylogeographical structure was seen in the ASIP variation. Our data concur with the previous inference of the Black Sea–Caspian Sea area having an ancestral character. The Urals region harbored high mitochondrial diversity, with an estimated coalescent time of around 100,000 years, suggesting this could have been a cryptic refugium. Based on the coalescent-based demographic reconstructions, the expansion of Clade I across the Palearctic was remarkably rapid, while Clade II was relatively stable for a longer time. It seems that Clade II has maintained a constant population size in the temperate region, and the expansive Clade I represents adaptation to the cold regions.     

Phylogeographic analysis of a recent radiation of Enallagma damselflies (Odonata: Coenagrionidae)

A phylogenetic hypothesis revealed two recent radiations among species of Enallagma damselflies, and extensive ecological work suggests that both adaptive and nonadaptive processes are involved in these radiations. We analysed the geographical pattern of genetic variability at 868 bp of mitochondrial DNA (mtDNA) among 283 individuals of 5 species displaying little ecological differentiation to identify the ancestral lineage, support their independent evolutionary trajectories and identify historical events and the underlying mechanism for one of these radiations. Nested clade analysis results clearly support a past event of range fragmentation in E. hageni. These Atlantic and Continental hageni races experienced distinct dispersal histories and still maintain nearly nonoverlapping ranges All four other species derive from the Continental hageni. Whereas three species endemic to the Atlantic coastal plain show little genetic variation, E. ebrium shared several haplotypes with the Continental hageni. Contrasting levels of genetic differentiation between E. hageni and E. ebrium in geographical areas associated with distinct events of E. hageni's recent history support the recent origin of this species. Altogether, our results are compatible with a process of radiation via divergence in mate recognition systems within the Continental hageni race following secondary contacts between putative refugial races.     

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

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

Phylogeographic structure and mitochondrial DNA variation in true lemmings (Lemmus) from the Eurasian Arctic

The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochrome b region. These data are used to reveal the vicariant history of Lemmus , and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history of Lemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.     

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

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

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers

We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500-5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.     

Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post‐medieval period and comparison with other regions in Eurasia

Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D‐loop of mitochondrial DNA (mtDNA; 213 bp) and the Y‐chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G‐oY1 of the Y‐chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.     

Comparative phylogeography of the two pink salmon broodlines: an analysis based on a mitochondrial DNA genealogy

Over most of their natural northern Pacific Ocean range, pink salmon (Oncorhynchus gorbuscha) spawn in a habitat that was repeatedly and profoundly affected by Pleistocene glacial advances. A strictly two-year life cycle of pink salmon has resulted in two reproductively isolated broodlines, which spawn in alternating years and evolved as temporal replicates of the same species. To study the influence of historical events on phylogeographical and population genetic structure of the two broodlines, we first reconstructed a fine-scale mtDNA haplotype genealogy from a sample of 80 individuals and then determined the geographical distribution of the major genealogical assemblages for 718 individuals sampled from nine Alaskan and eastern Asian even- and nine odd-year pink salmon populations. Analysis of restriction site states in seven polymerase chain reaction (PCR)-amplified mtDNA regions (comprising 97% of the mitochondrial genome) using 13 endonucleases resolved 38 haplotypes, which clustered into five genealogical lineages that differed from 0.065 to 0.225% in net sequence divergence. The lineage sorting between broodlines was incomplete, which suggests a recent common ancestry. Within each lineage, haplotypes exhibited star-like genealogies indicating recent population growth. The depth of the haplotype genealogy is shallow ( approximately 0.5% of nucleotide sequence divergence) and probably reflects repeated decreases in population size due to Pleistocene glacial advances. Nested clade analysis (NCA) of geographical distances showed that the geographical distribution observed for mitochondrial DNA (mtDNA) haplotypes resulted from alternating influences of historical range expansions and episodes of restricted dispersal. Analyses of molecular variance showed weak geographical structuring of mtDNA variation, except for the strong subdivision between Asian and Alaskan populations within the even-year broodline. The genetic similarities observed among and within geographical regions probably originated from postglacial recolonizations from common sources rather than extensive gene flow. The phylogeographical and population genetic structures differ substantally between broodlines. This can be explained by stochastic lineage sorting in glacial refugia and perhaps different recolonization routes in even- and odd-year broodlines.     

Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla)

We characterized the pattern and magnitude of phylogeographical variation among breeding populations of a long-distance migratory bird, the Wilson's warbler (Wilsonia pusilla), and used this information to assess the utility of mtDNA markers for assaying demographic connectivity between breeding and overwintering regions. We found a complex pattern of population differentiation in mitochondrial DNA (mtDNA) variation among populations across the breeding range. Individuals from eastern North America were differentiated from western individuals and the eastern haplotypes formed a distinct, well-supported cluster. The more diverse western group contained haplotype clusters with significant geographical structuring, but there was also broad mixing of haplotype groups such that no haplotype groups were population specific and the predominance of rare haplotypes limited the utility of frequency-based assignment techniques. Nonetheless, the existence of geographically diagnosable eastern vs. western haplotypes enabled us to characterize the distribution of these two groups across 14 overwintering locations. Western haplotypes were present at much higher frequencies than eastern haplotypes at most overwintering sites. Application of this mtDNA-based method of linking breeding and overwintering populations on a finer geographical scale was precluded by the absence of population-specific markers and by insufficient haplotype sorting among western breeding populations. Our results suggest that because migratory species such as the Wilson's warbler likely experienced extensive gene flow among regional breeding populations, molecular markers will have the greatest utility for characterizing breeding-overwintering connectivity at a broad geographical scale.     

Phylogeography of the circumpolar Paranoplocephala arctica species complex (Cestoda: Anoplocephalidae) parasitizing collared lemmings (Dicrostonyx spp.)

The Paranoplocephla arctica complex (Cyclophyllidea, Anoplocephalidae), host-specific cestodes of collared lemmings Dicrostonyx, include two morphospecies P. arctica and P. alternata, whose taxonomical status now must be considered ambiguous. The genetic population structure and phylogeography of the P. arctica complex was studied from 83 individuals sampled throughout the Holarctic distribution range using 600 bp of the mitochondrial cytochrome c oxidase subunit I gene (COI). The mitochondrial DNA (mtDNA) phylogeny divides the species complex into one main Nearctic and one main Palaearctic phylogroup, corresponding to the main phylogenetic division of the hosts. In the Palearctic phylogroup, the parasite clades correspond to the host clades although the parasites from Wrangel Island form an exception as the host on this island, D. groenlandicus, belongs to the Nearctic phylogroup. In the Nearctic, northern refugia beyond the ice limit of the Pleistocene glaciations are proposed for the hosts. All reconstructions of parasite phylogeny show a genetically differentiated population structure that in the Canadian Arctic lacks strict congruence between phylogeny and geography. The parasite phylogeny does not show complete congruence with host relationships, suggesting a history of colonization and secondary patterns of dispersal from Beringia into the Canadian Arctic, an event not proposed by the host phylogenies alone.     

Parasite phylogeographical congruence with salmon host evolutionarily significant units: implications for salmon conservation

Comparative phylogeographical studies between parasites and their hosts or with biogeographical regions are useful to predict parasite dispersal potential over a broad geographical range. We used both microsatellite markers and mtDNA sequence data from a trematode parasite, Plagioporus shawi, to test for congruence across two evolutionarily significant unit (ESU) boundaries of its salmonid hosts (Oncorhynchus spp.). We find congruent patterns with the nuclear loci of P. shawi and the ESU boundaries of its salmonid hosts. This pattern indicates that broad-scale phylogeographical patterns of a parasite can be predicted by the biogeographical history of their hosts. Furthermore, this pattern provides independent support for these ESU boundaries as biologically relevant barriers. The mtDNA shows some discordance with nuclear loci and a level of genetic differentiation greater than can be explained by genetic drift. Thus, the mtDNA cannot be used in isolation to infer the population history of P. shawi. The genetic differentiation at both the nuclear and mtDNA markers will be useful for salmon fisheries management by providing a tool to assign ocean-migrating salmonids back to their freshwater population of origin.     

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.     

Phylogeography of Hemibarbus labeo (Cyprinidae): secondary contact of ancient lineages of mtDNA

Lin, C.-J., Lin, H.-D., Wang, J.-P., Chao, S.-C. & Chiang, T.-Y. (2007). Phylogeography of Hemibarbus labeo (Cyprinidae): secondary contact of ancient lineages of mtDNA. —Zoologica Scripta, 39, 23–35. Nucleotide sequences of the D-loop control region of mtDNA were used to assess the genetic structure and phylogeography of Hemibarbus labeo in Mainland China and Taiwan. A hierarchical analysis of molecular variance of populations in 11 major streams from three geographical regions revealed significant structuring among populations and geographical regions. High levels of nucleotide diversity (π = 1.88%) and haplotype diversity (h = 96 ± 0.009%) suggest a large effective population size. A maximum likelihood tree based on mtDNA variation identified two ancient mtDNA lineages, which split approximately 3.39 million years ago. Overlapping distribution of the major lineages displayed low correspondence with geographical regions and reflects a scenario of secondary mergence after long isolation. Gene genealogy further revealed a unidirectional migration. Nevertheless, there existed a phylogeographical structure that mostly agreed with a biogeographical hypothesis. That is, within each lineage, a close phylogeny between populations of the River-Campagna and East-Pacific regions was supported by the mtDNA gene genealogy, although monophyly of each geographical region was not supported. The degree of genetic differentiation was correlated with geographical distances between populations, displaying a pattern of ‘isolation by distance’. Gene genealogy of mtDNA revealed that Yangtzejiang population may act as a divergence centre of H. labeo. In addition, Taiwan population was colonized via a recent a founder event, likely from population Yangtzejiang River about 131 000 years before present. Low haplotype number and genetic variability also suggested possible bottleneck events in the Rongjiang and Dazhangjiang populations.     

Phylogeography and sympatric differentiation of the Arctic charr Salvelinus alpinus (L.) complex in Siberia as revealed by mtDNA sequence analysis

Sequence variation in the mtDNA control region of Arctic charr Salvelinus alpinus and Dolly Varden Salvelinus malma from 56 Siberian and North American populations was analysed to assess their phylogeographic relationships and the origins of sympatric forms. Phylogenetic trees confirm the integrity of phylogroups reported in previous mtDNA studies except that the Siberian group does not separate as a single cluster. Haplotype network analysis indicates the proximity of Siberian and Atlantic haplotypes. These are considered as one Eurasian group represented by the Atlantic, east Siberian (interior Siberia including Transbaikalia, Taimyr) and Eurosiberian (Finland, Spitsbergen, Taimyr) sub-groups. Salvelinus alpinus with presumably introgressed Bering group (malma) haplotypes were found along eastern Siberian coasts up to the Olenek Bay and the Lena Delta region, where they overlap with the Eurasian group and in the easternmost interior region. It is proposed that Siberia was colonized by S. alpinus in two stages: from the west by the Eurasian group and later from the east by the Bering group. The high diversity of Eurasian group haplotypes in Siberia indicates its earlier colonization by S. alpinus as compared with the European Alps. This colonization was rapid, proceeded from a diverse gene pool, and was followed by differential survival of ancestral mtDNA lineages in different basins and regions, and local mutational events in isolated populations. The results presented here support a northern origin of Transbaikalian S. alpinus , the dispersion of S. alpinus to the Lake Baikal Basin from the Lena Basin, segregation of S. alpinus between Lena tributaries and their restricted migration over the divides between sub-basins. These results also support sympatric origin of intralacustrine forms of S. alpinus .     

Species-level phylogeographical history of Myricaria plants in the mountain ranges of western China and the origin of M. laxiflora in the Three Gorges mountain region

Myricaria species in China occur mostly in the major high-altitude mountain areas in and around the Qinghai-Tibetan Plateau. The one major exception to this is M. laxiflora which is restricted to the Three Gorges mountain region. In this study, we investigate species-level phylogeographical patterns of Myricaria species in western China and the origin of M. laxiflora . The results show that most chloroplast haplotypes are species-specific, except for one haplotype which is shared by three widespread species. Higher haplotype diversity within the Qinghai-Tibetan Plateau region supports the hypothesis that the Himalayas are the centre of origin for Myricaria . The phylogeny of Myricaria was geographically structured, and an estimated Bayesian chronology suggested the main divergence events occurred during the Late Pliocene and Early Pleistocene (~1.46–2.30 million years ago). The overall phylogeographical pattern was characterized by vicariance events and regional demographical expansion, reflecting a major influence of geological and climatic events on the evolution of Myricaria species. Our data suggest that M. laxiflora has an ancient origin, but has experienced recent population expansion through the Three Gorges Valley. The origin of M. laxiflora was estimated to be during the Early Pleistocene but its demographical expansion was more recent at about 0.015 million years ago. This highlights the unique phylogeographical history of the Three Gorges mountain region, and the deep imprint of the watercourse connections of the Yangtze River Valley on the phylogeographical structure of the species in this region.