Phylogenetic status of brown trout Salmo trutta populations in five rivers from the southern Caspian Sea and two inland lake basins,Iran: a morphogenetic approach

Interrelationships, origin and phylogenetic affinities of brown trout Salmo trutta populations from the southern Caspian Sea basin, Orumieh and Namak Lake basins in Iran were analysed from complete mtDNA control region sequences, 12 microsatellite loci and morphological characters. Among 129 specimens from six populations, seven haplotypes were observed. Based on mtDNA haplotype data, the Orumieh and southern Caspian populations did not differ significantly, but the Namak basin–Karaj population presented a unique haplotype closely related to the haplotypes of the other populations (0·1% Kimura two‐parameter, K2P divergence). All Iranian haplotypes clustered as a distinct group within the Danube phylogenetic grouping, with an average K2P distance of 0·41% relative to other Danubian haplotypes. The Karaj haplotype in the Namak basin was related to a haplotype (Da26) formerly identified in the Tigris basin in Turkey, to a Salmo trutta oxianus haplotype from the Aral Sea basin, and to haplotype Da1a with two mutational steps, as well as to other Iranian haplotypes with one to two mutational steps, which may indicate a centre of origin in the Caspian basin. In contrast to results of the mtDNA analysis, more pronounced differentiation was observed among the populations studied in the morphological and microsatellite DNA data, except for the two populations from the Orumieh basin, which were similar, possibly due to anthropogenic causes.     

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.     

Mitochondrial DNA variation and the evolutionary history of chromosome races of collared lemmings (Dicrostonyx) in the Eurasian Arctic

Collared lemmings (Dicrostonyx) demonstrate extensive chromosome variation along their circumpolar distribution in the high Arctic. To reveal the history of this genus and the origin of chromosome races in the Palearctic, we studied the geographical pattern of mtDNA variation in lemmings from 13 localities by using eight tetranucleotide restriction enzymes. The main split in mtDNA phylogeny is at the Bering Strait and corresponds to the main chromosome division between the Beringian and the Eurasian groups of karyotypes. Nucleotide divergence estimate of 6.8% suggests that, despite the Bering Land Bridge, Palearctic and Nearctic forms have been separated since the mid-Pleistocene. Five distinct phylogenetic groups of mtDNA haplotypes, with average divergence of 1.5%, corresponding to geographical regions, were found along the Palearctic coast. Low nucleotide and haplotype diversity and a star-like phylogeny within phylogeographical groups of haplotypes suggest regional bottleneck events in the recent past, most probably due to warming events during the Holocene. There is congruence between phylogeographical pattern of mtDNA variation and geographical distribution of chromosome races; 69% of the total mtDNA variation is allocated among chromosome races. This congruence implies that historical events such as fragmentation and allopatric bottleneck events have been important for the origin of chromosome races. However, historical factors do not explain the fixed autosome fusions found to distinguish certain populations.     

Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.     

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 bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae)

Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individuals from 25 Mexican populations allowed to us identify 53 geographically structured haplotypes. High haplotype and low nucleotide diversities and Tajima’s D indicate that D. mexicanus experienced rapid population expansion during its dispersal across mountain systems within its current range. The nested clade phylogeographic analysis indicates that the phylogeographic pattern of D. mexicanus is explained by continuous dispersion among lineages from the Sierra Madre Occidental, the Sierra Madre Oriental and the Trans-Mexican Volcanic Belt. However, we also observed isolation events among haplotypes from the Cofre de Perote/Trans-Mexican Volcanic Belt/Sierra Madre Oriental and the Trans-Mexican Volcanic Belt/Sierra Madre del Sur, which is consistent with the present conformation of mountain systems in Mexico and the emergence of geographical barriers during the Pleistocene.     

Differentiation among Austrian populations of Norway spruce [Picea abies (L.) Karst.] assayed by mitochondrial DNA markers

Thirty-seven populations of Norway spruce [Picea abies (L.) Karst.] across the Austrian Alps and Bohemian Massif were sampled to elucidate the geographical pattern of genetic differentiation. Three polymorphic mitochondrial DNA (mtDNA) loci were surveyed. Two or three alleles were detected at each locus, resulting in seven multilocus mtDNA haplotypes (A–F). Western populations proved to be monomorphic, whereas eastern and central Austrian populations were slightly to highly polymorphic, respectively. As revealed by spatial analysis of molecular variance and Monmonier’s analysis, the two main haplotypes A and B are not randomly distributed. Haplotype A was restricted to central and eastern Austria, whereas haplotype B occurred in all Austrian populations but was the only haplotype identified in western populations. This pattern may be explained by different glacial refugia located in the Dinaric Alps and the Carpathian mountains.     

Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area

Sixty‐four samples from 46 salmon populations totalling 2369 specimens were used for polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of the mitochondrial ND1 region. The final analyses included 3095 specimens from 60 populations in Northern Europe. A subsample was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from different parts of the distribution area were sequenced and the phylogeny of European haplotypes and their relations to the North American lineage was described. The four common European haplotypes derive from the ancestral ND1‐BBBA (rooting the European clade to the North American) by one‐step substitutions: AAAA < AABA < BBBA > BBBB. The Swedish west‐coast populations differ from the geographically close southern Baltic, indicating absence of inward and limited outward gene flow through the Danish straits during the last 8000 years. Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vänern, Ladoga and Onega the haplotype AABA dominated. Proposed postglacial colonization routes to the Baltic Sea are discussed in relation to the haplotype distribution pattern.     

Genetic differentiation between populations of swimming crab <Emphasis Type="Italic">Portunus trituberculatus</Emphasis> along the coastal waters of the East China Sea

Portunus trituberculatus is a commercially important species widely spread in the East China Sea. Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 213 individuals from six localities (Changjiang Estuary, Shengsi Islands, Zhoushan Islands, Dongtou Islands, Dinghai Bay, and Quanzhou Bay) ranging from north (31°21′N) to south (24°55′N) coastal waters of the East China Sea. Overall, a total of 27 mtDNA haplotypes and 21 variable sites were detected in the 787 bp segment of COI gene. Analysis of mtDNA COI sequence data revealed that crabs from the six localities were characterized by moderately high haplotypic diversity (h = 0.787 ± 0.026), while sequence divergence values between haplotypes were relatively low (π = 0.00241 ± 0.00098). Each population was characterized by a single most frequent haplotype, shared among all six localities, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population. However, neither the neighbor-joining tree nor the minimum spanning network (MSN) based on the haplotype data exhibited geographical patterns of the six populations. Mismatch distribution analysis of P. trituberculatus individuals sampled from the six localities suggested that sudden population expansion might have occurred in CJ and SS population that might be consistent with over-exploitation of the swimming crab. Analysis of molecular variance (AMOVA) and F _ST statistics showed that significant genetic differentiation existed among the SS, ZS, DT, DH, and QZ populations, suggesting that gene flow might be reduced, even between the geographically close sites, despite the high potential of dispersal. The possible causes of the observed genetic heterogeneity among the P. trituberculatus populations and the potential applications of the mtDNA COI marker in the artificial breeding and fisheries management are discussed. Handling editor: C. Sturmbauer     

REPEATED REVERSALS OF HOST-PREFERENCE EVOLUTION IN A SPECIALIST INSECT HERBIVORE

A tree of mitochondrial DNA (mtDNA) haplotypes was constructed to estimate the number of evolutionary changes of host-plant preference needed to account for variation among 24 populations of the butterfly Euphydryas editha. Using 17 restriction endonucleases, 22 mtDNA haplotypes were found among 24 populations of this butterfly species. We allowed for the possibility of haplotypes to acquire particular preferences either from evolutionary change at their local sites or from migration to populations where those preferences occurred. After we had taken these estimates of migration into account, a minimum of 10 evolutionary changes of host preference (reduced from 22) was needed to explain the pattern of use of five host-plant genera among these populations. Analysis of allozyme variation among a partially overlapping set of populations also suggested multiple host shifts. Although genetic variation of host preference is largely responsible for interpopulation variation of diet, repeated reversals of preference evolution have occurred. However, host preferences were not distributed randomly with respect to phylogeny, and some tendency toward evolutionary conservation of preference also was indicated. The haplotype of E. editha most closely related to the sister species, E. chalcedona, used a principal host of E. chalcedona. Our results suggest that host shifts occur frequently in E. editha, are a result of both migration and local evolution, and have not been associated with speciation in these insects.     

Genetic differentiation of Mediterranean horse mackerel (Trachurus mediterraneus) populations as revealed by mtDNA PCR-RFLP analysis

The genetic population structure of Mediterranean horse mackerel, Trachurus mediterraneus , from seven locations throughout the Black, Marmara, Aegean and eastern Mediterranean seas was investigated using restriction fragment length polymorphism (RFLP) analysis of the mtDNA 16S rDNA region. An approximately 2000-bp segment was screened in 280 individuals using six restriction enzymes, resulting in 10 composite haplotypes. The most common haplotype was present in 56.42% individuals; the next most frequent haplotype was present in 22.85% individuals. Average haplotype diversity within samples was moderate (0.38), and nucleotide diversity was low (0.00435). Mean nucleotide divergence for the seven sampling sites was 0.0028. Nucleotide divergence among samples was moderate, with the highest value detected between the Aegean Sea (Izmir) and the eastern Black Sea (Trabzon) populations (0.007055), and the lowest (−0.000043) between the Marmara Sea (Adalar) and the western Black Sea (Sile) populations. In Monte Carlo pairwise comparisons of haplotype frequencies, the Sinop from the middle Black Sea, Trabzon from the eastern Black Sea, and Iskenderun Bay from the north-eastern Mediterranean Sea exhibited highly significant (P   <   0.001) geographical differentiation from each other and from all other populations. Mantel's test indicated that the nucleotide divergence among populations of T. mediterraneus was not significantly associated with their geographical isolation ( r  = −0.2963; P   >   0.05). Consequently, the mtDNA 16S rDNA region provided evidence for the existence of three distinct T. mediterraneus populations (Sinop, Trabzon and Iskenderun Bay) in the Black and north-eastern Mediterranean seas.     

The phylogeography of European Atlantic salmon (Salmo salar L.) based on RFLP analysis of the NDl/16sRNA region of the mtDNA

The diversity and distribution of mtDNA haplotypes in Atlantic salmon (Salmo salar L.) from 13 river systems across the species' European range was investigated. Salmon were screened by agarose electrophoresis for variation in a 1400 base pair fragment spanning the ND-1 and 16SrRNA genes. The fragment was amplified by PCR and digested using the restriction endonucleases Avail, Dral, Haelll, Hinfl and Rsal. Nine haplotypes were identified and resolved by parsimony analysis into two major clades. Clade I was ubiquitous and predominated in all samples while Clade II was restricted to eight out of 94 individuals in two of the 13 rivers. The first clade shows two sublineages whose frequency distribution is strongly associated with geography. One sublineage dominated in river systems draining into the Baltic sea and in Iceland, and the other in the river systems elsewhere in Europe. No geographical patterns were apparent within these regions but haplotype frequencies among samples, both within and outside the Baltic region, were significantly heterogeneous. Approximately 8% of haplotype frequency variation occurred among samples, 44% between Baltic and non-Baltic samples and 48% within samples. Baltic samples had a significantly lower haplotype and nucleotide diversity than non-Baltic samples. Current and historical factors potentially responsible for the observed levels and distribution of the haplotype variation are discussed.     

ASYMMETRIC INTROGRESSION OF MITOCHONDRIAL DNA AMONG EUROPEAN POPULATIONS OF BLUE MUSSELS (MYTILUS SPP.)

Abstract.—Mytilus edulis and M. galloprovincialis are two blue mussel species that coexist in western Europe. Previously, we reported that M. galloprovincialis populations contain female and male haplotypes that are fixed in M. edulis populations as well as unique haplotypes. This study assesses whether paraphyly for these species is due to introgression or incomplete lineage extinction. The lineage extinction hypothesis predicts that the shared mtDNA haplotypes in M. galloprovincialis will be significantly diverged from those in M. edulis and form distinct sequence clades. In contrast, the introgression hypothesis proposes that M. edulis haplotypes have only recently been introduced into M. galloprovincialis through hybridization with relatively little divergence accumulating between the shared RFLP haplotypes. We examined 80 mtl6S gene sequences for both the maternal and paternal mtDNA lineages from mussels sampled from various European populations and found strong support for the introgression hypothesis. In addition, we found that M. edulis mtDNA haplotypes appear to be introgressing into mussel populations in the Baltic Sea, which have predominantly M. trossulus nuclear genotypes, indicating that introgressive hybridization is prevalent among European mussel populations.     

Variation of mitochondrial DNA in Far Eastern mullet pilengas, Liza haematocheilus Temminck and Schlegel, acclimatized in the Azov-Black Sea basin

This study continues the investigation of genetic variation in the populations of native and acclimatized in the Azov-Black Sea basin pilengas from the Sea of Japan. The previous comparison based on allozyme analysis was supplemented by analysis of restriction polymorphism of a mitochondrial DNA fragment containing the cytochrome b gene and the D-loop. Five out of fifteen tested endonucleases detected polymorphic sites. In the samples of native and acclimatized pilengas, five common haplotypes were found; ten and three “unique” haplotypes were detected in the Far Eastern and the Azov populations, respectively. The differences in haplotype distributions between these populations were highly significant (P < 0.001). The mtDNA variation was lower in the Azov than in the Far Eastern population (haplotype diversity μ respectively 6.35 ± 0.27 and 9.14 ± 0.55), which is in good agreement with the decrease in the number of polymorphic loci and the mean number of alleles per locus, found earlier for allozyme markers in this population. The reasons for these differences in the acclimatized population are discussed.     

Glacial refuges for three‐spined stickleback in the Iberian Peninsula: mitochondrial DNA phylogeography

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Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci

The population genetic structure of the Anopheles gambiae in western Kenya was studied using length variation at five microsatellite loci and sequence variation in a 648-nt mtDNA fragment. Mosquitoes were collected from houses in villages spanning up to 50 km distance, The following questions were answered, (i) Are mosquitoes in a house more related genetically to each other than mosquitoes between houses? (ii) What degree of genetic differentiation occurs on these geographical scales? (iii) How consistent are the results obtained with both types of genetic markers? At the house level, no differentiation was detected by F_ST and R_ST, and the band sharing index test revealed no significant associations of alleles across loci. Likewise, indices of kinship based on mtDNA haplotypes in houses were even lower than in the pooled sample. Therefore, the hypothesis that mosquitoes in a house are more related genetically was rejected. At increasing geographical scales, microsatellite allele distributions were similar among all population samples and no subdivision of the gene pool was detected by F_ST or R_ST. Likewise, estimates of haplotype divergence of mtDNA between populations were not higher than the within population estimates, and mtDNA-based F_ST values were not significantly different from zero. That sequence variation in mtDNA provided matching results with microsatellite loci (while high genetic variation was observed in all loci), suggested that this pattern represents the whole genome. The minimum area associated with a deme of A. gambiae in western Kenya is therefore larger than 50 km in diameter.     

Phylogeography of an estuarine mysid, Neomysis integer (Crustacea, Mysida), along the north-east Atlantic coasts

Aim The brackish water mysid, Neomysis integer, is one of the most common mysid species along the coasts of the north‐east Atlantic. In the present study, the phylogeographical patterns were examined throughout the distribution range of N. integer. In particular, the latitudinal trends in genetic diversity and the distribution of genetic variation were examined in order to elucidate the imprints of the Pleistocene glaciations. Location North‐east Atlantic coasts from the Baltic Sea to the south of Spain. Methods A total of 461 specimens from 11 populations were analysed by means of single‐stranded conformation polymorphism analysis combined with DNA sequencing of a fragment of the mitochondrial cytochrome c oxidase I gene. The genetic structure was examined by using a progression of phylogenetic, demographic and population genetic analyses to elucidate not only the geographical structure, but also the evolutionary history producing that structure. Results The levels of genetic diversity were relatively uniform throughout the distribution range, with the exception of a decline at the northern and southern edges of distribution. A high heterogeneity was observed between the populations analysed (global Φ_ST = 0.787). This is caused by the disparate distribution of the cytochrome oxidase I haplotypes, with several population‐specific haplotypes. A clear genetic break (2.4% sequence divergence) occurred between the southernmost Guadalquivir population and all other populations. Main conclusions The present study corroborates the expectations of the genetic patterns typically observed in an estuarine species. The within‐population variability was low, whereas a significant (moderate to high) divergence was observed between populations. Phylogeographical analysis revealed that northern populations within the English Channel, North Sea and Baltic Sea are characterized by several widespread haplotypes, while the Irish population and all sites south of the Bay of Biscay consist solely of unique haplotypes. This pattern, combined with the relative high levels of genetic diversity, could be indicative for the presence of a glacial refugium in the English Channel region. Under this scenario N. integer must have survived the Last Glacial Maximum in the palaeoriver system present in that region.     

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 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.