Regional structure despite limited mtDNA sequence diversity found in the endangered Huchen, <Emphasis Type="Italic">Hucho hucho</Emphasis> (Linnaeus, 1758)

We evaluate the hypothesis of no geographic structure in the Huchen (Hucho hucho), a large, predatory salmonid endemic to the Danube basin. Forty-seven individuals sampled from throughout the Huchen’s native range were genetically characterized. Extremely limited sequence diversity across 1,800 bases of mtDNA (the complete control region and partial NADH-1 subunit) evidenced by four closely related mtDNA haplotypes was found. Nonetheless, the geographic distribution of mtDNA repeats (5–10, 82-bp long copies per individual) as well as allelic diversity across two microsatellite loci indicated large-scale geographic structure between the north-western (Austria and Slovenia) distribution area and eastern (Slovakia and Ukraine) or southern (Bosnia-Herzegovina and Montenegro) sample sites. An extremely slow rate of substitution for the H. hucho mtDNA is considered along with the alternative hypotheses to explain the limited mtDNA diversity. Considering the regional genetic structure implied by our data, we advocate restrictions on the transport of brood fish or yearlings across the range of the species distribution and sale of Huchen across international boundaries. Future genetic analysis to support local conservation and monitoring efforts must focus on developing a high-resolution screen that may be applied to identify hatchery versus naturally reproduced individuals in the wild.     

Plastidic trnFUUC pseudogenes in North American genus Boechera (Brassicaceae): mechanistic aspects of evolution

The origin and maintenance of a plastidic tandem repeat next to the TRNF (UUC) gene were analyzed in the genus BOECHERA in a phylogenetic context and were compared to published analogous examples that emerged in parallel in the Asteraceae and Juncaceae, respectively. Although we identified some features common to these taxonomic groups with respect to structure and origin of the region, obvious differences were encountered, which argue against a specific mechanism or evolutionary principle underlying the parallel origin and maintenance of the TRNF-tandem repeats in those families. In contrast to the situation in the Asteraceae, no reciprocal recombinant repeat types have been observed in the Brassicaceae. Forty copy types, classified into three groups, were isolated from 103 chloroplast haplotypes of BOECHERA and it was demonstrated that they are composed of four subregions of various origins. We discuss various mutation mechanisms such as DNA replication slippage, and inter- and intrachromosomal recombination which were reported to mediate variation in copy numbers and other types of observed sequence length polymorphism. It is shown that the observed molecular structure of the tandem repeat region did not fully fit the particular patterns expected under a scenario of evolution including any of the known mechanisms. Nevertheless, it appeared that intermolecular unequal crossing-over is most likely the driving force in the evolution of this tandem repeat. However, it remains to be explained, why no reciprocal recombinant copy types have been observed. The reconstructed phylogenetic relationships among copies reflected different evolutionary scenarios as follows: (1) A single and ancient origin of copies pre-dates the radiation of BOECHERA. (2) Parallel expansion and shortening of the tandem repeat within different BOECHERA lineages. (3) Conservation of the first copy, as it was the only one present in all chloroplast haplotypes.     

Mitochondrial DNA Length Variation and Heteroplasmy in Populations of White Sturgeon (Acipenser Transmontanus)

Southern blot analysis was used to quantify the extent of mtDNA D-loop length variation in two populations of white sturgeon, Acipenser transmontanus. Over 42% of individuals were heteroplasmic for up to six different mtDNA length variants attributable to varying copy numbers of an 82-bp repeat sequence. Chi-square analyses revealed that the frequencies of length genotypes and the incidence of heteroplasmy were significantly different between Fraser and Columbia River sturgeon populations but not between restriction site haplotypes. Heteroplasmic fish have, on average, higher copy number than homoplasmic fish. Forty-five of 101 homoplasmic individuals carry only a single copy of the repeat, while none of the 73 heteroplasmic fish has the single repeat as the predominant variant. On the basis of differences in frequency distributions of copy number within and between fish, we suggest that (1) heteroplasmy is maintained by high recurrent mutation of multiple copy genomes, favoring increased copy number and (2) the mutation pressure toward higher copy number heteroplasmy is partially offset by selection to reduced genome size and segregation to the homoplasmic condition.     

Genetic evidence of multiple matrilineal lineages of the channel catfish, Ictalurus punctatus in North America

Using mitochondrial DNA control region (mtDNA CR) sequence data the present study evaluates the genetic status of the wild populations of channel catfish, Ictalurus punctatus, in North America. A total of 584 individuals representing 56 drainages across its distributional range in the United States were collected. There were 105 mtDNA CR haplotypes defined by 51 variable sites. Phylogenetic analyses have revealed the existence of six distinct matrilineal genetic lineages of channel catfish in the United States. Four of these lineages were restricted to southeast Gulf Coast, a region that never glaciated during the Pleistocene. While samples from the Mississippi river and its tributaries represent a single genetic lineage, samples from the southeast Atlantic coastal plain drainages formed a unique lineage. Each lineage should be regarded as an evolutionarily significant unit/management unit and therefore separate management and conservation strategies should be undertaken in order to conserve the genetic resources.     

Identifying Source Populations and Genetic Structure for Savannah Elephants in Human-Dominated Landscapes and Protected Areas in the Kenya-Tanzania Borderlands

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.     

Mitochondrial genome diversity in soybean: repeats and rearrangements

Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.     

Molecular phylogeny of Philippine freshwater sardines based on mitochondrial DNA analysis

The commercially important Sardinella species (family Clupeidae or herrings) usually thrive in marine environments. An exception is Sardinella tawilis of Taal Lake, Batangas, Philippines, the only known freshwater sardine. This species is believed to have immigrated from Balayan Bay to the lake when it was formed in the course of volcanic eruptions some 240 years ago. To determine the relationship of S. tawilis to the marine species S. albella, S. fimbriata, and S. longiceps from the Balayan Bay we sequenced 358 bp of the cytochrome b gene and the mitochondrial control region. The cytochrome b gene was highly conserved and contained little phylogenetic information. The control region sequences, however, demonstrated two highly diversified main haplotypes grouping S. tawilis with S. albella, as shown by maximum parsimony and neighbor-joining analysis. The haplotypes are characterized by the presence of an 81 bp indel and up to eight 35 bp tandem repeat elements. The repeat copy number varied within individuals of S. tawilis and S. albella, thus showing heteroplasmy in these two species only. The analysis of two subpopulations of S. tawilis revealed restricted substitutions that may indicate the beginning of genetic differentiation of the two subpopulations.     

Length Variation in Mitochondrial DNA of the Minnow Cyprinella Spiloptera

Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation.     

Structure and Conservation of Tandem Repeats in the Mitochondrial DNA Control Region of the Least Brook Lamprey (<Emphasis Type="Italic">Lampetra aepyptera</Emphasis>)

Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution, function, and phylogenetic distribution. We report phylogenetic and geographic patterns of variation of control region repeat sequence and number in a nonparasitic lamprey, Lampetra aepyptera. A survey of populations from throughout the species’ range revealed remarkably low repeat sequence polymorphism but some interpopulation variation in repeat number. The high sequence similarity extended to repeats observed in other species in the genus Lampetra and other lamprey genera. The very low levels of variation suggest a high copy turnover. Our data are consistent with the illegitimate elongation model of repeat gain and loss and further suggest that repeat change occurs at internal copies. However, the limited variation across some species of lamprey suggests that functional constraints may further limit variation.     

Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences.

Halobacterium-halobium NRC-1 harbors a 200-kb plasmid, pNRC100, which contains a cluster of genes for synthesis of buoyant gas-filled vesicles. Physical mapping of pNRC100 by using pulsed-field gel electrophoresis showed the presence of a large (35 to 38-kb) inverted repeat (IR) sequence. Inversion isomers of pNRC100 were demonstrated by Southern hybridization analysis using two restriction enzymes, AflII and SfiI, that cut asymmetrically within the intervening small single-copy region and the large single-copy region, respectively, but not within the large IRs. No inversion isomers were observed for a deletion derivative of pNRC100 lacking one IR, which suggests that both copies are required for inversion to occur. Additionally, the identities and approximate positions of 17 insertion sequences (IS) in pNRC100 were determined by Southern hybridization and limited nucleotide sequence analysis across the IS element-target site junctions: ISH2, a 0.5-kb element, was found in four copies; ISH3, a 1.4-kb heterogeneous family of elements, was present in seven copies; ISH8, a 1.4-kb element, was found in five copies; and ISH50, a 1.0-kb element, was present in a single copy. The large IRs terminated at an ISH2 element at one end and an ISH3 element at the other end. pNRC100 is similar in structure to chloroplast and mitochondrial genomes, which contain large IRs and other large halobacterial and prokaryotic plasmids that are reservoirs of IS elements but lack the large IRs.     

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos)

Two sections of the control region and the genes coding for NADH dehydrogenase sub-units 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.     

Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian,European, and North American populations

To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.     

Transferability of microsatellite loci from Cervidae species to the endangered Brazilian marsh deer, Blastocerus dichotomus

Blastocerus dichotomus, the marsh deer, is the largest Brazilian Cervidae species. The species is endangered because of hunting and loss of its natural habitat, i.e., flood plain areas, because of hydroelectric power station construction and agricultural land expansion. In the present study, we tested 38 microsatellite loci from four Cervidae species: Odocoileus virginianus (7), Rangifer tarandus (17), Capreolus capreolus (7), and Mazama bororo (7). Eleven loci showed clear amplification, opening a new perspective for the generation of fundamental population genetic data for devising conservation strategies for B. dichotomus.     

A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand

Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using skin samples collected with a remote biopsy dart. Analysis of the molecular variance from mitochondrial DNA (mtDNA) control region sequences (n = 193) showed considerable differentiation among populations (F(ST) = 0.17, Phi(ST) = 0.21, P < 0.001) suggesting little or no female gene flow or interchange. All 3 populations showed higher mtDNA diversity than expected given their small population sizes and isolation. To explain the source of this variation, 22 control region haplotypes from New Zealand were compared with 108 haplotypes worldwide representing 586 individuals from 19 populations and including both inshore and offshore ecotypes as described in the Western North Atlantic. All haplotypes found in the Pacific, regardless of population habitat use (i.e., coastal or pelagic), are more divergent from populations described as inshore ecotype in the Western North Atlantic than from populations described as offshore ecotype. Analysis of gene flow indicated long-distance dispersal among coastal and pelagic populations worldwide (except for those haplotypes described as inshore ecotype in the Western North Atlantic), suggesting that these populations are interconnected on an evolutionary timescale. This finding suggests that habitat specialization has occurred independently in different ocean basins, perhaps with Tursiops aduncus filling the ecological niche of the inshore ecotype in some coastal regions of the Indian and Western Pacific Oceans.     

Spatial heterogeneity of mitochondrial DNA and allozymes among populations of white-tailed deer and mule deer.

A white-tailed deer (Odocoileus virginianus) population in northeastern Minnesota and a mule deer (O. hemionus) population in the Bridger Mountains Montana, have previously been shown to be spatially subdivided into contiguous subpopulations. We assessed the degree of genetic differentiation among subpopulations and tested the hypothesis that differentiation will be greater for mitochondrial DNA (mtDNA) than for nuclear-encoded allozymes. Differentiation of the white-tailed deer subpopulations was significant for two allozyme loci but not for mtDNA, and the overall degree of differentiation was low. Gene flow, recent founding of the subpopulations, and polygamous breeding structure may all have contributed to this pattern. Greater differentiation was evident among disjunct populations than between the contiguous subpopulations of white-tailed deer. The contiguous mule deer subpopulations were significantly differentiated for mtDNA and one allozyme locus. Differentiation was greater for mtDNA than for allozymes. These results are consistent with demographic data that indicate mule deer males disperse more than do females. Disjunct mule deer populations may be similar or dramatically different in mtDNA haplotype frequencies that do not necessarily vary with geographic distance. Current and historical gene flow and breeding structure will influence population genetic patterns.     

Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei

Characterization of mitochondrial genomes from individual Thaumamermis cosgrovei nematodes, obligate parasites of the isopod Armadillidium vulgare, revealed that numerous mtDNA haplotypes, ranging in size from 19 to 34 kb, are maintained in several spatially separated isopod populations. The magnitude and frequency of conspecific mtDNA size variation is unprecedented among all studied size-polymorphic metazoan mitochondrial genomes. To understand the molecular basis of this hypervariation, complete nucleotide sequences of two T. cosgrovei mtDNA haplotypes were determined. A hypervariable segment, residing between the atp6 and rrnL genes, contributes exclusively to T. cosgrovei mtDNA size variation. Within this region, mtDNA coding genes and putative nonfunctional sequences have accumulated substitutions and are duplicated and rearranged to varying extents. Hypervariation at this level has enabled a first insight into the life history of T. cosgrovei. In five A. vulgare hosts infected with multiple nematodes, four carried nematodes with identical mtDNA haplotypes, suggesting that hosts may become infected by ingesting a recently hatched egg clutch or become parasitized by individuals from the same brood prior to dispersal of siblings within the soil.     

Mitochondrial DNA variation in natural populations of the mushroom Agaricus bisporus

We investigated the patterns of mitochondrial DNA variation in the global population of the commercial mushroom Agaricus bisporus . Through the analysis of RFLP's among 441 isolates from nine countries in North America and Eurasia, we found a total of 140 mtDNA haplotypes. Based on population genetic analysis, there are four genetically distinct natural populations in this species, found in coastal California, desert California, France and Alberta (Canada). While 134 of the 140 mtDNA haplotypes were unique to single geographical regions, two mtDNA haplotypes, mt001 and mt002, were found in almost every population surveyed. These two mtDNA haplotypes also predominate among cultivars used throughout the world for at least the last two decades. These two mtDNA haplotypes are more similar to the cosmopolitan groups of mtDNA haplotypes than to the indigeneous clusters of mtDNA haplotypes from the two Californian regions.