The complete mitochondrial DNA sequence of the harbor seal,Phoca vitulina

Summary The nucleotide sequence of the mitochondrial DNA (mtDNA) of the harbor seal, Phoca vitulina, was determined. The total length of the molecule was 16,826 bp. The organization of the coding regions of the molecule conforms with that of other mammals, but the control region is unusually long. A considerable portion of the control region is made up of short repeats with the motif GTACAC particularly frequent. The two rRNA genes and the 13 peptide-coding genes of the harbor seal, fin whale, cow, human, mouse, and rat were compared and the relationships between the different species assessed. At ordinal level the 12S rRNA gene and 7 out of the 13 peptide-coding genes yielded a congruent topological tree of the mtDNA relationship between the seal, cow, whale, human, and the rodents. In this tree the whale and the cow join first, and this clade is most closely related to the seal.Offprint requests to: Ú. Árnason     

Population genetic structure of the spotted seal Phoca largha along the Coast of Hokkaido,based on mitochondrial DNA sequences

Population genetic structure of the spotted seal, Phoca largha, along coastal regions of Hokkaido was investigated, using mitochondrial DNA (mtDNA) sequences. A 571-bp fragment of the mtDNA control region and adjacent threonine and proline transfer RNA genes was sequenced from 66 seals. We categorized all individuals into three groups considering sampling area and season: twenty-four seals from the Sea of Okhotsk in winter, 11 seals from the Sea of Okhotsk coast in fall, and 31 seals from the Sea of Japan coast in winter. From the 66 animals, 57 haplotypes were identified. Compared with the harbor seal sequence, all spotted seals examined shared two deletions in the control region, which distinguished between the two species. Forty-nine haplotypes were represented by a single individual, and haplotypes shared by more than two animals were generally restricted to same sampling-groups. Phylogenetic trees did not indicate clear geographic differences among the three groups. An Analysis of molecular variances (AMOVA) did not showed any significant population genetic structure in Hokkaido spotted seals (Phi(st )= -0.003). Our results showed a high level of diversity but no genetic structure, and did not deny the possibility that seals in the Okhotsk breeding concentration mainly stayed in the fall Okhotsk and also inhabited in the winter Sea of Japan.     

Phylogenetic relationships among the subfamily Coregoninae as revealed by mitochondrial DNA restriction analysis

Mitochondria1 DNA (mtDNA) restriction analysis was used to assess phylogenetic patterns among 21 taxa of the subfamily Coregoninae. The genus Prosopium formed a very distinct group differing by 10% (sequence divergence estimate) from other species. Coregonus and Stenodus species were closely related, diverging by sequence divergence estimates of less than 5.6%. These species split into two major sister groups. One comprised all 'true whitefish' (subgenus Coregonus ) and four cisco species (subgenus Leucichrhys ). The most distant species within this assemblage was the Acadian whitefish ( C. huntsmani ). The other group included all other cisco species and also the Inconnu ( Stenodus leucichthys ). These results supported a polyphyletic origin of the ciscoes, and did not support Stenodus as a sister taxon of the genus Coregonus . The levels of sequence divergence observed suggested that most extant coregonines radiated during the Pleistocene.     

Worldwide patterns of mitochondrial DNA differentiation in the harbor seal (Phoca vitulina)

The harbor seal (Phoca vitulina) has one of the broadest geographic distributions of any pinniped, stretching from the east Baltic, west across the Atlantic and Pacific Oceans to southern Japan. Although individuals may travel several hundred kilometers on annual feeding migrations, harbor seals are generally believed to be philopatric, returning to the same areas each year to breed. Consequently, seals from different areas are likely to be genetically differentiated, with levels of genetic divergence increasing with distance. Differentiation may also be caused by long-standing topographic barriers such as the polar sea ice. We analyzed samples of 227 harbor seals from 24 localities and defined 34 genotypes based on 435 bp of control region sequence. Phylogenetic analysis and analysis of molecular variance showed that populations in the Atlantic and Pacific Oceans and east and west coast populations of these oceans are significantly differentiated. Within these four regions, populations that are geographically farthest apart generally are the most differentiated and often do not share genotypes or differ in genotype frequency. The average corrected sequence divergence between populations in the Atlantic and Pacific Oceans is 3.28% +/- 0.38% and those among populations within each of these oceans are 0.75% +/- 0.69% and 1.19% +/- 0.65%, respectively. Our results suggest that harbor seals are regionally philopatric, on the scale of several hundred kilometers. However, genetic discontinuities may exist, even between neighboring populations such as those on the Scottish and east English coasts or the east and west Baltic. The mitochondrial data are consistent with an ancient isolation of populations in both oceans, due to the development of polar sea ice. In the Atlantic and Pacific, populations appear to have been colonized from west to east with the European populations showing the most recent common ancestry. We suggest the recent ancestry of European seal populations may reflect recolonization from Ice Age refugia after the last glaciation.      

Structure of the neocortex of the Baikal ringed seal (Pusa sibirica Gm.)]

The sulci and gyri of the neocortex, as well as cyto-, synaptoarchitectonics and neuronal composition of the sensomotor (brain area) have been studied in the Baikal ringed seal. The structure of the sulci and gyri have been found to be similar to that in carnivores. The following specific features have been revealed in the brain of this endemic species: a thick layer I, presence of giant pyramidal cells in the layer III, large mitochondria in the presynaptic parts and dendrites. The results obtained are discussed concerning adaptation to semiaqueous way of life and to diving.     

Phylogenetic relationships of sorghum taxa inferred from mitochondrial DNA restriction fragment analysis.

To elucidate the evolutionary history and affinity of sorghum species, 41 sorghum taxa were analyzed using variability in mitochondrial DNA. Analysis of species relationships at the molecular level can provide additional data to supplement the existing classification based on morphological characters and may also furnish unexpected but useful information. Total DNA extracted from each of the sorghum accessions was digested with each of five restriction enzymes, BamHI, HindIII, EcoRI, EcoRV, and XbaI, and probed with five mitochondrial DNAs cloned from Sorghumbicolor. A total of 180 restriction fragments was detected by the 25 probe-enzyme combinations. Forty-three fragment bands were phylogenetically informative. Multiple correspondence analysis was performed to visualize associations among the accessions and suggested that section Eusorghum species may be divided into four groups, with Sorghumlaxiflorum (section Heterosorghum) and Sorghumnitidum (section Parasorghum) appearing as outliers. A phylogenetic tree was assembled from mitochondrial restriction fragment data. The taxa analyzed formed three major groups comprising section Heterosorghum (group I), section Parasorghum (group II), and all accessions in section Eusorghum (group III). Group III is further divided into four groups: (i) two sweet sorghums and shattercane; (ii) Sorghumhalepense, Sorghummiliaceum, Sorghumhewisonii, Sorghumaethiopicum, Sorghumverticilliflorum, and S. bicolor, including Sorghumsudanense (sudangrass), the Chinese Kaoliangs, and a number of commercial sorghum inbreds from the U.S.A.; (iii) Sorghumpropinquum; and (iv) Sorghumarundinaceum, Sorghumniloticum, Sorghumalmum, Sorghumcontroversum, and the Chinese material C-401 and 5-27. Results indicate that the analysis of fragmented mitochondrial DNA was diagnostic and useful in sorghum phylogenetic and taxonomic research at the species, subspecies, and race levels, and can complement results from those analyses using nuclear ribosomal DNA and chloroplast DNA that effectively distinguish taxa at species and genus levels. Key words : Sorghum, mitochondrial DNA, phylogeny, restriction fragment.     

The origin and relationships of the pepino,Solanum muricatum (solanaceae): DNA restriction fragment evidence

The pepino (or pepino dulce:Solanum muricatum) is a domesticate, of interest because of its close relationship to tomatoes and potatoes, because it is enjoying increasing exposure in the international market, and because it is a cultigen with no known wild ancestor. Morphologically this South American native is a member of the Solanum sect. Basarthrum, and as such, is allied to a number of Andean wild species. Data from other studies are combined with results from restriction site analysis of chloroplast and nuclear ribosomal DNA to assay relationships and the potential origin of the pepino. The pepino may have existed in the wild previously and may be represented today only by the cultigen. However, if its ancestors are extant, three wild species—Solanum basendopogon (Perú),S. caripense (Costa Rica through Perú), S. tabanoense (Colombia and Ecuador)—emerge as most likely progenitors. Phylogenetic analyses of 61 accessions, including 27 of the pepino, dependent on chloroplast DNA (cpDNA) and nuclear ribosomal (rDNA) restriction site data show the pepino to be polymorphic, suggest independent origins for some of the cultivars, and most strongly supportS. tabanoense as the progenitor of the cultigen.Solanum caripense also may have been a direct ancestor of the pepino, or may have hybridized subsequent to its origin with the pepino to yield some of the haplotype variation. Similarly, S.cochoae may have hybridized with the pepino. There are no DNA characters supporting the involvement ofS. basendopogon in the origin.     

Evolutionary relationships of Gadopsis spp. inferred from restriction enzyme analysis of their mitochondrial DNA

Gadopsis marmoratus and G. bispinosus are the sole members of an endemic Australian genus of percoid fishes. At least nine mitochondrial genotypes, identified by site polymorphisms for seven restriction enzymes, were found among 50 individuals from the two species sampled during this study. Net divergence between G. marmoratus and G. bispinosus was 6.60%, or at least 12.65 mutations. Mean divergence within G. marmoratus was 5.98%, or at least 12.29 mutations. The southern and northern forms of G. marmoratus are monophyletic taxa and the amount of divergence between the two forms confirms that a detailed taxonomic study is necessary to review the status of G. marmoratus. Despite detailed phytogenies constructed from restriction enzyme analysis of mitochondrial DNA, the relationship between G. bispinosus and the northern and southern forms of G. marmoratus was not resolved.     

The evolutionary relationships of two families of cottoid fishes of Lake Baikal (East Siberia) as suggested by analysis of mitochondrial DNA

Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2–1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family. Correspondence to: S. Ja. Slobodyanuk     

Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis

The Hawaiian Drosophilidae are comprised of an estimated 1000 species, all arising from a single common ancestor in the last 25 million years. This group, because of its species diversity, marked sexual dimorphism and complex mating behavior, host plant specificity, and the well-known chronology of the Hawaiian Archipelago, is an excellent model system for evolutionary studies. Here we present a phylogeny of this group based on ~2.6 kb of mitochondrial DNA sequence. Our taxon sampling is the most extensive to date, with nearly 200 species representing all species groups and most subgroups from the larger clades. Our results suggest that the picture wing and modified mouthpart species, long believed to be derived within this radiation, may actually occupy a basal position in the phylogeny. The haleakale species group, in contrast, is strongly supported as sister to the AMC clade. We use the phylogenetic results to examine the evolution of two important ecological characters, the host family and type of substrate used for oviposition and larval development. Although both host and substrate transitions are common in the group, oviposition substrate is more conserved among species groups than host plant family. While the ancestral host plant family is equivocally reconstructed, our results suggest that the ancestor of this group may have used rotting bark as a primary oviposition substrate.     

Ovine mitochondrial DNA: restriction enzyme analysis, mapping and sequencing data

Restriction endonuclease fragment patterns of mitochondrial DNA (mtDNA) in sheep were analysed with 11 enzymes. Four breeds (Merinolandschaf, Rhoenschaf, Schwarzkoepfiges Fleischschaf and Skudde) of domestic sheep and European Mouflon were examined. A restriction map with 28 cleavage sites of seven enzymes was established. KpnI and PstI do not cut ovine mtDNA. Two EcoRI fragments of Merinolandschaf, Rhoenschaf and Mouflon each were cloned and partially sequenced. Intraspecific nucleotide sequence differences within 1.101 kb ranged from 0.09 to 0.27%. Hybridization analysis with a fragment of porcine mtDNA along with sequencing data from cloned fragments was used for orientation of the restriction map along the bovine sequence. Ovine mtDNA sequences encompassing parts of the Cyt.b-, ND5-, CoIII- and ATPase6 genes were compared with the corresponding sequences of the bovine mtDNA.     

辽东湾斑海豹MHC-DQB 基因的遗传多样性分析

本文从25 份斑海豹样本中获得141 bp 片段,发现21 个变异位点,定义了12 个MHC-DQB 等位基因,氨基酸变异率为25.5% 。等位基因之间的遗传距离范围是0. 0071 ～ 0.1064,平均值为0.0577,不同等位基因之间的碱基差异是1 ～ 15 bp,平均差异数为8 bp。与其他鳍足类动物对比后发现,斑海豹MHC-DQB 表现出较丰富的多态性。非同义替换率明显高于同义替换率,由此造成的氨基酸替换集中在肽结合位点PBR 附近,表明DQB 基因受到强烈的平衡选择作用。11 个样本出现多于两条等位基因的情况,推测存在基因重复现象。     

Phylogenetic relationships of the fox-like canids: mitochondrial DNA restriction fragment, site and cytochrome b sequence analyses

The fox-like canids include taxa from the genera Alopex, Otocyon, Fennecus, Urocyon and Vulpes . Previous morphological analysis indicated that species from the latter three genera are very similar and should be included in the same genus whereas Alopex and Otocyon are sufficiently different to be included in separate genera. Using phylogenetic methods, we analyse mitochondrial DNA (mtDNA) restriction fragment and restriction site data, and 402 bp of cytochrome b sequence variation in fox-like canids. Our results suggest that Alopex lagopus , the arctic fox, is actually a very close relative of the swift fox, a species in the genus Vulpes . Similarly, the fennec, Fennecus zerda is related to the co-existing desert species, the Blanford's fox, Vulpes cana . The grey fox, Urocyon cinereoargenteus , and the bat-eared fox, Otocyon megalotis , are not closely related to each other or to any of the sampled fox taxa. Our results indicate that desert adaptations have evolved independently at least twice in the Canidae, and that Pleistocene glaciations and character divergence may be important causes of morphological change in canids.     

Phylogenetic relationships of turfgrasses as revealed by restriction fragment analysis of chloroplast DNA

Chloroplast DNAs (cpDNAs) were analyzed in order to clarify the phylogenetic relationships among turfgrasses. Physical maps of cpDNAs from Agrostis stolonifera and Zoysia japonica, which are representative species of cool (C3 type) and warm (C4 type) season turfgrasses, respectively, were constructed with four restriction enzymes, i.e., PstI, SalI, SacI, and XhoI. The genome structures of these cpDNAs were found to be similar to each other in terms of genome size and gene orders, showing thereby a similarity to other grass cpDNAs. CpDNAs of 5 species of cool season turfgrasses and 6 species of warm season turfgrasses as well as four species of cereals, distributed among 14 genera of Gramineae, were digested with PstI, XhoI, and BamHI, and their restriction fragment patterns were compared. Their genome sizes were estimated to be 135–140 kbp. Each species showed characteristic RFLP patterns. On the basis of the frequency of commonly shared fragments, a dendrogram showing the phylogenetic relationships among their cpDNAs was constructed. This dendrogram shows that turfgrasses can be divided into three major groups; these correspond to the subfamilies. Cool and warm season turfgrasses are clearly distinguishable from each other, and the latter can be further classified into two subgroups that correspond to Eragrostoideae and Panicoideae. Our classification of turfgrasses and cereals by RFLP analysis of cpDNA agreed in principal with their conventional taxonomy, except for the location of Festuca and Lolium.Contribution no. 101 from the Kihara Institute for Biological Research, Yokohama City University, Yokohama 232, Japan     

Testing the homozygosity of Baikal seal using data on genetic variability of proteins

Interspecies genetic variability of Baikal seal was studied for 22 proteins encoded by 24 loci. Genetic variants have been detected in transferrin (TfA = 0.96; TfB = 0.04), postalbumin (PaA = 0.130; PaB = 0.870) and "slow" carboxylesterase (CrE-6A = 0.98; CrE-6B = 0.02). Low genetic variability is characteristic of species as well as of many other representatives of Pinnipedia order.     

Genetic relationships among the shads (Alosa) revealed by mitochondrial DNA analysis

We surveyed restriction site differences in mitochondrial DNA. (mtDNA) among five species of shad ( Alosa ) from North America and Europe. Allis shad, Alosa alosa and twaite shad, Alosa fallax shared two divergent genotype groups, suggesting that the two forms are either a single species, or are distinct species that have hybridized. Phenetic and cladistic analyses of the relationships among the mitochondrial genotypes defined two groups of shad, corresponding to the subgenera, Alosa and Pomolobus . The mean estimated sequence divergence between the mtDNAs of these two groups of shad was 6.5%. Taken in conjunction with fossil data, this divergence estimate suggests that the rate of mtDNA divergence between the two subgenera has been almost 10-fold lower than the 'conventional' clock calibration for mtDNA.     

The lipid composition of serum lipoproteins in the harbour seal, Phoca vitulina

The density profile of serum lipoproteins and their lipid composition was studied in 12 adult, female harbour seals. The animals were sampled after an approximate 20 hr fast. The density profile of lipoproteins showed that the harbour seals displayed a distinct VLDL (density less than 1.006 g/ml) and HDL band (density about 1.125 g/ml), but no clear LDL band. There was a rather diffuse population of lipoproteins in the density range of 1.019-1.100 g/ml. Mean serum total cholesterol concentration was 5.7 mmol/l; about 60% of this cholesterol was located in the HDL fraction (density greater than 1.063 g/ml). The fasted seals were found to carry 4% of serum total lipids in chylomicrons. These lipoproteins consisted of 51% of triaclyglycerols (on the basis of total chylomicron lipids). The LDL (defined as heparin-manganese precipitable lipoproteins in VLDL and chylomicron-deficient serum) contained 49% of cholesterol and 43% of phospholipids (on the basis of total LDL lipids). The HDL (defined as heparin-manganese soluble lipoproteins in VLDL and chylomicron-deficient serum) contained 36% of cholesterol and 58% of phospholipids (on the basis of total HDL lipids).