Problems of molecular systematics of the genus Salvelinus based on nucleotide sequence variability of the major noncoding region of mitochondrial DNA

Variability of the major noncoding mitochondrial DNA region of char (Salvelinus alpinus complex) was analyzed by the median network method on the basis of the literature data on nucleotide sequences of this region. A significant portion (21%) of the polymorphic sites of char mtDNA was shown to be evolutionarily unstable, which results in mutation homoplasia at these sites. Using median-joining analysis the chars were divided into three phylogeographical groups: Arctic, Beringian, and chars occurring in the vast region from Lake Baikal and Taimyr Peninsula to the Atlantic Ocean. The latter group includes three subgroups (Siberian, Atlantic, and Acadian), which diverged from a common ancestor. In the Arctic group, the branch of Taranetz char S. taranetzi is clearly separated. It diverged from the common ancestor earlier than S. boganidae and S. elgyticus occurring on the Chukotka Peninsula species and S. a. erythrinus occurring in Alaska. The Beringian group, which includes dolly varden char from various regions of Asia and America, is an intermediate between the two char groups. The main problems of char systematics inferred from the major noncoding mtDNA region variability arise from the high level of mutation homoplasia.     

Variability of Nucleotide Sequences of Mitochondrial DNA Cytochrome b Gene in Chars of the Genus Salvelinus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome b gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus–S. malma malmacomplex group. Within the S. alpinus–S. m. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma–Chukotka group includes lake S. taranetzi, S. boganidae, andS. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northernS. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene–Pleistocene.     

Change in nucleotide sequence of mitochondrial DNA from cytochrome b gene in chars of Salvelinus genus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome c gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus-S. malma complex group. Within the S. alpinus-S. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma-Chukotka group includes lake S. taranetzi, S. boganidae and S. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northern S. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene-Pleistocene.     

Mitochondrial DNA data imply a stepping‐stone colonization of Beringia by arctic warbler Phylloscopus borealis

Arctic warbler Phylloscopus borealis is one of several high‐latitude Passerines which are widely distributed across one northern continent but restricted to the Beringian part of the other. Most species with such asymmetric intercontinental ranges are monomorphic across Beringia, suggesting either recent colonization of the second continent or considerable gene flow across the Bering Strait. Arctic warbler is the only migratory species in this group that has three different subspecies in Beringia: Ph. b. borealis (Scandinavia to western Beringia, south to Mongolia), Ph. b. xanthodryas (Japan, Sakhalin, Kamchatka, western Beringia), and Ph. b. kennicotti (Alaska). This polymorphism may indicate that Arctic warbler has a unique and complex phylogeographic history that differs significantly from other species with similar ranges. Our analyses of complete mtDNA ND2 sequences of 88 Arctic warblers collected across the species range showed that the clade comprised of birds breeding on Sakhalin Island and Kamchatka Peninsula diverged from the Palearctic/Beringian clade by 3.8% in ND2 sequence. Beringian birds formed a recently derived clade embedded within the Palearctic clade. Nucleotide diversity declined sharply eastward from Palearctic to western Beringia and then to eastern Beringia. Our data provided no support for currently recognized subspecies. They suggested that the barrier at the western edge of Beringia was crossed by Arctic warbler earlier than the Bering Strait resulting in a stepping‐stone colonization of Beringia by this species. Gene flow appears to be restricted across the western border of Beringia but not the Bering Strait.     

Genetic divergence of mitochondrial DNA in white char <Emphasis Type="Italic">Salvelinus albus</Emphasis> and northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis>

Comparative analysis of mitochondrial DNA variation was performed in white char Salvelinus albus Glubokovsky and in its putative ancestor species, northern Dolly Varden char Salvelinus malma malma Walbaum. Highly statistically significant differentiation of S. albus and S. m. malma in the areas of sympatric (Kamchatka River basin) and allopatric (Kronotskoe Lake and Kronotskaya River) residence was demonstrated. The mtDNA divergence between S. albus and S. m. malma did not exceed the range of intraspecific variation in the populations of northern Dolly Varden char. At the same time, clusterization pattern of the Salvelinus chars provides hypothesis on the common origin of two allopatric populations of white char. Genealogical analysis of haplotypes indicates that S. albus and S. m. malma currently demonstrate incomplete divergence of mitochondrial lineages. The low nucleotide divergence estimates between S. albus and S. m. malma reflect the short time period since the beginning of the divergence of ancestral lineages. These estimates are determined by ancestral polymorphism and haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.     

Variation of cytochrome b gene in sympatric chars from kronotsky lake (Kamchatka Peninsula)

In previously identified sympatric char forms (species) from Kronotsky Lake (Kamchatka Peninsula) and a number of other chars from the genus Salvelinus, nucleotide sequences of the mtDNA cytochrome b gene were determined and phylogenetic analysis of these chars was performed. The divergence estimate of the cytochrome b gene in the Kronotsky char group (0.48%) coincided with the interpopulation difference estimates in northern Dolly Varden, which indicates a relatively recent divergence of the chars from Kronotsky Lake. Haplotypes of each form of the Kronotsky Lake chars are divided into two groups, which belonged to two different phylogenetic mtDNA lineages of northern Dolly Varden from Chukotka and Kamchatka. The formation of the Kronotsky char forms proved to be unrelated to the observed variability of the mtDNA cytochrome b gene.     

Multiple fossil calibrations,nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae,Pinnipedia)

Aim To better understand the historical biogeography of the true seals, Phocidae, by combining nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) in a divergence time analysis using multiple fossil calibrations. Location Arctic, Antarctic, Pacific and Atlantic Oceans, Lake Baikal, Caspian Sea. Methods Fifteen nuclear genes totalling 8935 bp plus near‐complete mitochondrial genome sequences were used in a Bayesian divergence time analysis, incorporating eight soft‐bound fossil calibrations across the phylogeny. All species of true seals were included, plus the walrus, three otariids and seven carnivore outgroups. The majority of the nuclear sequences and four phocid mitochondrial genomes (plus three non‐phocid mitochondrial genomes) were newly generated for this study using DNA extracted from tissue samples; other sequences were obtained from GenBank. Results Using multiple nuclear genes and multiple fossil calibrations resulted in most divergence time estimations within Phocidae being much more recent than predicted by other molecular studies incorporating only mtDNA and using a single calibration point. A new phylogenetic hypothesis was recovered for the Antarctic seals. Main conclusions Incorporating multiple nuclear genes and fossil calibrations had a profound effect on the estimated divergence times. Most estimated divergences within Phocinae (Arctic seals) correspond to Arctic oceanic events and all occur within the last 12 Myr, a time when the Arctic and Atlantic oceans were freely exchanging and perennial Arctic sea ice existed, indicating that the Arctic seals may have had a longer association with ice than previously thought. The Monachinae (‘southern’ seals) split from the Phocinae c. 15 Ma on the eastern US coast. Several early trans‐Atlantic dispersals possibly occurred, leaving no living descendants, as divergence estimates suggest that the Monachus (monk seal) species divergences occurred in the western Atlantic c. 6 Ma, with the Mediterranean monk seal ancestor dispersing afterwards. The tribes Lobodontini (Antarctic seals) and Miroungini (elephant seals) are also estimated to have diverged in the eastern Atlantic c. 7 Ma and a single Lobodontini dispersal to Antarctica occurred shortly afterwards. Many of the newly estimated dates are used to infer how extinct lineages/taxa are allied with their living relatives.     

Variation of cytochrome b gene in sympatric chars from Kronotsky Lake (Kamchatka oblast)

In previously identified sympatric char forms (species) from Kronotsky Lake (Kamchatka Peninsula) and a number of other chars from the genus Salvelinus, nucleotide sequences of the mtDNA cytochrome b gene were determined and phylogenetic analysis of these forms was performed. The divergence of the cytochrome b gene in the Kronotsky char group (0.48%) coincided with the interpopulation difference estimates in northern Dolly Varden, which indicates a relatively recent divergence of the chars from Kronotsky Lake. Haplotypes of each form of the Kronotsky Lake chars are divided into two groups, which belonged to two different phylogenetic mtDNA lineages of northern Dolly Varden from Chukotka and Kamchatka. The formation of the Kronotsky char forms proved to be unrelated to the observed variability of the mtDNA cytochrome b gene.     

Genetic Divergence of Chars of the Genus <Emphasis Type="Italic">Salvelinus</Emphasis> from Kronotsky Lake (Kamchatka Peninsula)

Chars of the genus Salvelinus, inhabiting lakes and lake-river systems, comprise morphological and ecological forms whose taxonomic status is under dispute. In the present work, we have examined genetic variation and divergence in various chars from the Kronotsky lake basin: the lacustrine chars (white, nose, and longhead) and riverine Dolly Varden Salvelinus malma. The study was conducted using analysis of allozyme and microsatellite loci, myogens, RAPD, and restriction analysis of two mtDNA segments. The estimates of heterozygosity at allozyme and microsatellite loci were similar to the corresponding parameters in populations of northern Dolly Varden and Arctic char. Heterozygote deficit was recorded in both samples of separate forms, and in the total sample of all chars from Kronotsky Lake. For allozyme and microsatellite loci, appreciable genetic differentiation among the samples of different char forms was found, which was comparable to that among the spatially isolated populations of northern Dolly Varden. This result indicates reproductive isolation among the char forms examined. However, this isolation is not complete, because no fixed differences between the forms by any of the genetic systems analyzed were found. The genetic differentiation among different forms of lacustrine chars, which corresponds to the interpopulation rather than interspecific level, is thought to be explained by their comparatively recent divergence.__________Translated from Genetika, Vol. 41, No. 8, 2005, pp. 1096–1107.Original Russian Text Copyright © 2005 by Salmenkova, Omel’chenko, Radchenko, Gordeeva, Rubtsova, Romanov.     

Karyological Differentiation of Northern Dolly Varden and Sympatric Chars of the Genus <Emphasis Type="Italic">Salvelinus</Emphasis> in Northeastern Russia

In many cases the taxonomic status of sympatric chars (with exception of white-spotted char Salvelinus leucomaenis) is not clear and is actively debated. We karyotyped three pairs of sympatric chars inhabiting the Russian Far East-northern Dolly Varden, S. malma malma, and Lavanidov's char, S. levanidovi, from the Yama River (northern coast of the Sea of Okhotsk, Magadan Region), northern Dolly Varden and Taranetz's char, S. taranetzi, from Lake Achchen (east Chukotka), and northern Dolly Varden and white char, S. albus, from the Kamchatka River (Kamchatka Peninsula). Three of them had similar chromosome numbers. But all chars studied had an individual and discrete set of karyotypic characters, which enabled reliable identification each of them by chromosome number, chromosome arm number, and number and location of active nuclear organizer regions.     

The extreme disjunction between Beringia and Europe in Ranunculus glacialis s. l. (Ranunculaceae) does not coincide with the deepest genetic split – a story of the importance of temperate mountain ranges in arctic–alpine phylogeography

The arctic–alpine Ranunculus glacialis s. l. is distributed in high‐mountain ranges of temperate Europe and in the North, where it displays an extreme disjunction between the North Atlantic Arctic and Beringia. Based on comprehensive sampling and employing plastid and nuclear marker systems, we (i) test whether the European/Beringian disjunction correlates with the main evolutionary diversification, (ii) reconstruct the phylogeographic history in the Arctic and in temperate mountains and (iii) assess the susceptibility of arctic and mountain populations to climate change. Both data sets revealed several well‐defined lineages, mostly with a coherent geographic distribution. The deepest evolutionary split did not coincide with the European/Beringian disjunction but occurred within the Alps. The Beringian lineage and North Atlantic Arctic populations, which reached their current distribution via rapid postglacial colonization, show connections to two divergent pools of Central European populations. Thus, immigration into the Arctic probably occurred at least twice. The presence of a rare cpDNA lineage related to Beringia in the Carpathians supports the role of these mountains as a stepping stone between temperate Europe and the non‐European Arctic, and as an important area of high‐mountain biodiversity. The temperate and arctic ranges presented contrasting phylogeographic histories: a largely static distribution in the former and rapid latitudinal spread in the latter. The persistence of ancient lineages with a strictly regional distribution suggests that the ability of R. glacialis to survive repeated climatic changes within southern mountain ranges is greater than what recently was predicted for alpine plants from climatic envelope modelling.     

Rapid Evolution of the Intergenic T–P Spacer in the mtDNA of Arctic Cod <Emphasis Type="Italic">Arctogadus glacialis</Emphasis>

A noncoding intergenic spacer has previously been reported in mtDNA of Gadiformes. Here we present sequence information from two other cod species and variation within three species to clarify the evolution of this region. A general feature of the T–P spacer is high variation and folding into two or three hairpins. The variation among species both in structure of the region and sequence variation reflects the phylogenetic relationship of the species. A unique pattern is found within Arctic cod, Arctogadus glacialis, in which tandem repeat motifs result in new stable secondary structures. There is large variation in size of the region both within (heteroplasmy) and among individuals. A duplicated insertion is found in Greenland cod, Gadus ogac, at the same position as a corresponding duplication in Atlantic cod, Gadus morhua.     

Secondary contact between two divergent lineages of charrs of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> in the Northwest Pacific

The present-day contact zone between the Beringian and Arctic phylogenetic lineages of charrs of the genus Salvelinus in the Northwest Pacific is documented. A comparative analysis of the genetic differentiation and divergence indices for allopatric and sympatric populations of charrs and phylogenetic and genealogical analyses of the mtDNA haplotypes indicate that Lake Achchen and the Lake Pekulineiskoe are the zones of secondary contact between S. m. malma and S. taranetzi; Lake Nachikinskoe, between S. m. malma and Salvelinus sp. 4; and Lake Dal’nee, between S. m. malma and S. krogiusae. The level of divergence between phylogenetic groups of haplotypes considerably exceeds the range of intraspecific variability of S. m. malma and could not have been achieved after colonization of the lakes in conditions of sympathy. The obtained data suggest that the territory of Kamchatka was colonized by the common ancestor of the Arctic phylogroup of Taranetz charr.     

Cytogenetic identification of genomic elements of brook trout (Salvelinus fontinalis) in the karyotype of Arctic char (Salvelinus alpinus) from the aquaculture broodstock

Growing interest of Arctic char (Salvelinus alpinus) aquaculture in Europe, and the fact that it can easily hybridize with brook trout (Salvelinus fontinalis) resulting in fertile progeny, led us to investigate fish from the farmed stocks. Chromosomes of sampled Arctic char were examined using conventional and molecular cytogenetic (FISH) techniques in order to determine possible contamination of genomic elements of brook trout. Investigated fish possessed karyotypes composed of 80–82 chromosomes and up to three chromosome fragments. Using staining methods and FISH approach enabled identification of the brook trout chromosomes in the eight out of twenty‐two examined Arctic char. Specific location of AT‐, GC‐ positive and NOR sites observed on chromosomes as well as chromosome fragments in the karyotypes of several individuals points on past chromosomal rearrangements in fish from examined broodstock. Based on our results, it may be assumed that individuals with the brook trout genomic elements, although phenotypically identified as Arctic chars, were hybrids. Our results highlights that special care should be taken to protect gene pools of brook trout and Arctic char in farms where both species are cultured.     

Global phylogeography in Sanionia uncinata (Amblystegiaceae: Bryophyta)

Global phylogeographic patterns in Sanionia uncinata are addressed based on information in internal transcribed spacer (ITS) (214 specimens) and the plastid markers trnL‐trnF (221) and rpl16 (217). ITS suggests a monophyletic Sanionia and a paraphyletic S. uncinata; this was neither supported nor rejected by plastid data. Northern or Eastern Eurasia and Alaska appear important in the early evolution of Sanionia and some populations dispersed into the Southern Hemisphere relatively early. Some haplotypes or groups of haplotypes are morphologically and ecologically distinct, biologically meaningful units that correspond with S. orthothecioides, S. symmetrica and S. georgicouncinata s.l. The latter includes two species that are indistinguishable by morphology, S. georgicouncinata s.s. (Southern Hemisphere) and S. nivalis (Northern Hemisphere). Tropical African and South American S. uncinata populations have separate origins and the Southern Hemisphere was colonized at least twice. In the northern circum‐Arctic region, the haplotype composition differs between the North Atlantic and Beringian areas. Eastern Eurasia has a higher S. uncinata haplotype diversity than other Holarctic regions, implying less devastating effects of recurrent glacial periods. For Eastern and Western Eurasia, North America and the Southern Hemisphere, most of the haplotype variation was found within the regions, but 14–18% can be referred to among region variation. Plastid haplotype diversity was lower in the Southern Hemisphere than in the Arctic to subarctic, possibly attributable to founder effects. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 19–42.     

Mitochondrial DNA evolution in lagomorphs: Origin of systematic heteroplasmy and organization of diversity in European rabbits

Summary A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids.The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation.Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.     

Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-eastern Atlantic

Aim The Pleistocene glaciations were the most significant historical event during the evolutionary life span of most extant species. However, little is known about the consequences of these climate changes for the distribution and demography of marine animals of the north‐eastern Atlantic. The present study focuses on the phylogeographic and demographic patterns of the sand goby, Pomatoschistus minutus (Teleostei: Gobiidae), a small marine demersal fish. Location North‐eastern Atlantic, Mediterranean, Irish, North and Baltic seas. Methods Analysis was carried out by sequencing the mtDNA cytochrome b gene of sand gobies from 12 localities throughout the species’ range, and using this information in combination with published data of allozyme markers and mtDNA control region sequences. Several phylogenetic methods and a network analysis were used to explore the phylogeographic pattern. The historical demography of P. minutus was studied through a mismatch analysis and a Bayesian skyline plot. Results Reciprocal monophyly was found between a Mediterranean Sea (MS) clade and an Atlantic Ocean (AO) clade, both with a Middle Pleistocene origin. The AO Clade contains two evolutionary significant units (ESUs): the Iberian Peninsula (IB) Group and the North Atlantic (NA) Group. These two groups diverged during Middle Pleistocene glacial cycles. For the NA Group there is evidence for geographic sorting of the ancestral haplotypes with recent radiations in the Baltic Sea, Irish Sea, North Sea and Bay of Biscay. The demographic histories of the Mediterranean Clade and the two Atlantic ESUs were influenced mainly by expansions dated as occurring during the Middle Pleistocene glaciations and post‐Eem, respectively. Main conclusions The pre‐LGM (Last Glacial Maximum) subdivision signals were not erased for P. minutus during the LGM. Middle Pleistocene glaciations yielded isolated and differently evolving sets of populations. In contrast to the case for most other taxa, only the northern Atlantic group contributed to the post‐glacial recolonization. The historical demography of Mediterranean sand gobies was influenced mainly by Middle Pleistocene glaciations, in contrast to that of the Atlantic populations, which was shaped by Late Pleistocene expansions.     

Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data

Aim To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis. Location Representative samples of all four Sarda species collected world‐wide were analysed. Methods Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring. Results Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected. Main conclusions The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.     

A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus

The evolution, taxonomy and conservation of the genus Equuswere investigated by examining the mitochondrial DNA sequences of thecontrol region and 12S rRNA gene. The phylogenetic analysis of thesesequences provides further evidence that the deepest node in thephylogeny of the extant species is a divergence between twolineages; one leading to the ancestor of modern horses (E.ferus, domestic and przewalskii) and the other to thezebra and ass ancestor, with the later speciation events of the zebrasand asses occurring either as one or more rapid radiations, or withextensive secondary contact after speciation. Examination of the geneticdiversity within species suggested that two of the E. hemionussubspecies (E. h. onager and E. h. kulan) onlyrecently diverged, and perhaps, are insufficiently different to beclassified as separate subspecies. The genetic divergence betweendomestic and wild forms of E. ferus (horse) and E.africanus (African ass) was no greater than expected within anequid species. In E. burchelli (plains zebra) there was anindication of mtDNA divergence between populations increasing withdistance. The implications of these results for equid conservation arediscussed and recommendations are made for conservation action.     

A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus)

Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographic events by examining mitochondrial DNA (mtDNA) restriction fragment length and cytochrome b sequence polymorphism among north Pacific and Arctic, north-western Atlantic (north-eastern North American), and north-eastern Atlantic (European) regional forms of the boreal smelt, genus Osmerus. Our analyses also assessed whether the regional forms within this ‘species complex’: (i) represent a single widely distributed and polytypic species, or is composed of three geographically distinct species, and (ii) resulted from a single split from north Pacific ancestral Osmerus or two independent Pacific-Atlantic divergences. MtDNA sequence divergence estimates among forms ranged from 5.6–8.9% and from 6.1–8.5% based on restriction fragment and 300 base pairs of cytochrome b sequencing, respectively. Divergence within forms averaged less than 0.5% for fragment analysis and no differences were detected from sequence analysis. Provisional dating of lineage separations in Osmerus based on our sequence divergence estimates suggested a mid-Pliocene to early Pleistocene time frame for diversification among the forms. These estimated lineage separation dates support the idea that geological events in ‘Beringia’ and the surrounding trans-Arctic area (e.g. opening of the Bering Seaway, Pleistocene glacial advances), occurring over a similar time frame, have influenced radiation in Osmerus. Phenetic and parsimony analyses of the sequence divergence estimates and of sequence polymorphisms suggested that the north Pacific/Arctic form and the northwestern Atlantic form shared a common ancestor more recently than either has with the north-eastern Atlantic form, thus supporting the hypothesis that the species complex has arisen from two independent Pacific-Atlantic divergences probably beginning during the mid-Pliocene.