Mitochondrial DNA Variation in Goldfish Carassius auratus gibelio from Far Eastern Water Reservoirs

MtDNA variation of goldfish samples from several reservoirs of Southern Primorye was examined by RFLP analysis. High mtDNA polymorphism was found in the river populations but not in the lake ones. Considerable among-haplotype divergence was found within samples, which suggests periodic gene exchange between populations having long histories of independent evolution. The absence of substantial differences between clusters of mtDNA haplotypes indicates recurrent transfer from bisexual to gynogenetic reproduction mode and vice versa.     

山东荣成人群线粒体DNA多态性研究

人类线粒体DNA（mtDNA)COⅡ/tRNA^lys区有两个9－bp(CCCCCTCTA)的串联重复序列,此重复序列中一个重复单位的缺失,在亚态地区人群中很普遍。对210名山东荣成人的mtDNA COⅡ/tRNA^lys区的9-bp 缺失情况进行了检测,并从中随机选取95个样本,利用PCR－RFLP法对另外6个区进行了多态性分析,以确定其单位型。结果表明,荣成人9－bp缺失频率为12.4%,相对于已检测的中国其他群体,此缺失频率处于中等水平。同时多态性分析也表明在95个被检测对象中存在27种不同的单倍型。此外还发现了两个未报道过的新酶切位点,序列分析表明是由点突变造成的。     

Origin and differentiation of human mitochondrial DNA.

A recent study of mitochondrial DNA (mtDNA) polymorphism has generated much debate about modern human origins by proposing the existence of an "African Eve" living 200,000 years ago somewhere in Africa. In an attempt to synthesize information concerning human mtDNA genetic polymorphism, all available data on mtDNA RFLP have been gathered. A phylogeny of the mtDNA types found in 10 populations reveals that all types could have issued from a single common ancestral type. The distribution of shared types between continental groups indicates that caucasoid populations could be the closest to an ancestral population from which all other continental groups would have diverged. A partial phylogeny of the types found in five other populations also demonstrates that the myth of an African Eden was based on an incorrect "genealogical tree" of mtDNA types. Two measures of molecular diversity have been computed on all samples on the basis of mtDNA type frequencies, on one hand, and on the basis of the number of polymorphic sites in the samples, on the other. A large discrepancy is found between the two measures except in African populations; this suggests the existence of some differential selective mechanisms. The lapse of time necessary for creating the observed molecular diversity from an ancestral monomorphic population has been calculated and is found generally greater in Oriental and caucasoid populations. Implications concerning human mtDNA evolution are discussed.     

ANALYSIS OF MITOCHONDRIAL DNA POLYMORPHISMS AMONG CHANNEL ISLAND DEER MICE

Mitochondrial DNA (mtDNA) from 131 deer mice, Peromyscus maniculatus, collected on the eight California Channel Islands and from seven southern California mainland locations, was isolated and analyzed for restriction endonuclease fragment polymorphisms. A total of 26 mtDNA genotypes were distinguishable among the deer mice sampled. All of the island samples had mtDNA restriction-fragment patterns not found among the mainland samples. Distributions of specific restriction-fragment patterns provide evidence for at least four separate colonization events to the Channel Islands. The estimated percentage of sequence divergence between all mtDNA's in this study was less than 1%, suggesting that colonization of the islands occurred fairly recently, probably within the last 500,000 years. Levels of mtDNA heterogeneity were much lower within island populations than within mainland populations.     

Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in populations of deer mice (Peromyscus maniculatus)

We investigated a major geographic break in mitochondrial DNA (mtDNA) haplotypes in deer mice, Peromyscus maniculatus, by analysing spatial variation in a 491‐bp fragment of the mtDNA control region from 455 samples distributed across a north–south transect of 2000 km in Western North America. To determine whether the mtDNA break was reflected in the nuclear genome, we then compared spatial variation in 13 nuclear microsatellites of 95 individuals surrounding the mtDNA break. Using a canonical correlation analysis we found that nuclear genomic variation was not correlated with mtDNA differentiation. The contrasting patterns of variation in mtDNA and nuclear DNA are consistent with a hypothesis of historic genetic drift that occurred in isolated refugia combined with recent gene flow between the formerly isolated refugial populations. A Mantel test of genetic vs. geographic distance revealed that recent gene flow between deer mouse populations has been high. We conclude that past vicariant events associated with Pleistocene climate changes together with recent gene flow have created the observed intra‐specific cytonuclear discordance in Western North America.     

Temporal and spatial genetic variation in spawning grounds of European hake (Merluccius merluccius) in the Bay of Biscay

Polymorphism at five microsatellite loci were screened to determine the genetic variability and the temporal stability of population structure in natural populations of European hake (Merluccius merluccius, L.) within the Bay of Biscay. In addition, the control region (900 bp) and two protein coding genes (ATPase, subunits 6 and 8, 842 bp and a partial sequence of the ND1, 800 bp) of the mitochondrial DNA (mtDNA) were sequenced from geographically distant populations from the extremes of the species range. One hundred individuals from either side of a supposed stock boundary within the bay were collected in autumn 1997. This sampling strategy was repeated during hake spawning seasons in late spring of 1998 and 1999. Low levels of population subdivision were found between putative populations within years. Similarly, low levels of differentiation were found between autumn 1997 northern samples and spring 1998 southern samples which were collected 7 months later on spawning grounds. These results are discussed in relation to ecological, behavioural and oceanographic information. Sampling effects, which may influence these results, are also discussed. Theta (theta) estimates were significantly different from zero in every other pairwise comparison between geographical areas (north and south of the Bay of Biscay) and between years within the same area (P<0.05). Hierarchical analysis of molecular variance (AMOVA) does not confirm the temporal persistence of population structure. These results are discussed in relation to variance in reproductive success, and temporal spawning patterns, which may exist within the bay. mtDNA variability was very low between geographically distant samples from Norway and the Mediterranean Sea with only 10 variable sites found in a total of 2542 bp of mtDNA, these differences being exclusively in the D-loop.     

Population genetic structure of Bryde’s whales (<Emphasis Type="Italic">Balaenoptera brydei</Emphasis>) at the inter-oceanic and trans-equatorial levels

Bryde’s whales (Balaenoptera brydei) differ from other typical baleen whale species because they are restricted to tropical and warm temperate waters in major oceans, and frequent trans-equatorial movement has been suggested for the species. We tested this hypothesis by analyzing genetic variation at 17 microsatellite loci (N = 508) and 299 bp of mitochondrial DNA (mtDNA) control region sequences (N = 472) in individuals obtained from the western North Pacific, South Pacific, and eastern Indian Ocean. Combined use of microsatellite and mtDNA markers allowed us to distinguish between contemporary gene flow and ancestral polymorphism and to describe sex-specific philopatry. A high level of genetic diversity was found within the samples. Both nuclear and mtDNA markers displayed similar population structure, indicating a lack of sex-specific philopatry. Spatial structuring was detected using both frequency-based population parameters and individual-based Bayesian approaches. Whales in the samples from different oceanic regions came from genetically distinct populations with evidence of limited gene flow. We observed low mtDNA sequence divergence among populations and a lack of concordance between geographic and phylogenetic position of mtDNA haplotypes, suggesting recent separation of populations rather than frequent trans-equatorial and inter-oceanic movement. We conclude that current gene flow between Bryde’s whale populations is low and that effective management actions should treat them as separate entities to ensure continued existence of the species.     

Changes in Phenotype and Genotype of Austrian <Emphasis Type="BoldItalic">Salmo trutta</Emphasis> Populations during the Last Century

Synopsis We studied the phenotype and genotype of Austrian wild and hatchery Salmo trutta populations and compared with museum samples from the 19th century (1863--1909) using morphometric and genetic (RFLP of mtDNA) markers. We found significant differences between the populations from the 19th century, the current wild populations, and the hatchery populations in morphometric parameters (mainly shape of pectoral, ventral and anal fins) and the RFLP pattern of mtDNA. We could not find the typical phenotypes and genotypes from the 19th century in either of the current populations. This phenotypic and genotypic replacement is considered to be due to anthropogenic activities.     

Mitochondrial DNA variation in populations of the chum salmon Oncorhynchus keta (Walbaum) from rivers of the Prymorye and Sakhalin

Mitochondrial DNA (mtDNA) variation was studied using restriction fragment length polymorphism (RFLP) in chum salmon populations from three rivers in southern Primorye and one river in Sakhalin Island. Significant differences were detected between the samples from Primorye and Sakhalin Island. No differences were found between the samples from the rivers of Primorye, which can be explained by a high rate of gene flow due to transplantation of spawn from one river to another. The effect of fish breeding on the chum salmon populations correlated with the indices of haplotype and nucleotide diversity (h and pi, respectively). The lowest diversity was found in the completely artificial population from the Ryazanovka River; the highest, in natural populations from the Narva and Naiba rivers. Frequencies of haplotypes in consecutive generations were significantly different, which confirms the effects of genetic drift on the small-size chum salmon populations of Primorye.     

Evolution of human mitochondrial DNA: Evidence for departure from a pure neutral model of populations at equilibrium

Summary Human mitochondrial DNA (mtDNA) data from 18 populations have been carefully reexamined. A phylogeny of 77 mtDNA types found among the 1389 individuals analyzed for restriction fragment length polymorphisms (RFLPs) was established using the parsimony principle and compared to a UPGMA tree of the 18 populations. Both analyses agreed in separating African samples from the other populations, though the mtDNA type phylogeny suggested close relations between Africans and other continental groups. Conformity of observed mtDNA type frequency distributions with the infinite allele model was studied for 31 human populations. Several Oriental and Caucasoid populations were found to be overly homogeneous, generally due to an elevated frequency of one particular type. Contrastingly, all African samples conformed to the neutral model of populations at equilibrium and presented more diversified distributions. This suggested that part of the apparent African divergence was due to heterogeneous evolutionary processes and confirmed that some diversity reducing factors were at work in Caucasoids and Orientals. Several nonexclusive hypotheses accounting for the rejection of the neutrality tests were discussed. Alternative hypotheses concerning modern human emergence were also reviewed in the light of present results.     

Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in China, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of China. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.     

An evaluation of introgression of Atlantic coast striped bass mitochondrial DNA in a Gulf of Mexico population using formalin-preserved museum collections

Striped bass Morone saxatilis populations in drainages along the Gulf of Mexico coast (Gulf) were depleted in the 1950s and 1960s, probably because of anthropogenic influences. It is believed that only the Apalachicola-Chattahoochee-Flint (A-C-F) river system continually supported a naturally reproducing population of Gulf lineage. Striped bass juveniles of Atlantic coast (Atlantic) ancestry were introduced to restore population abundances in the A-C-F from the late 1960s to the mid 1970s and in many other Gulf rivers from the 1960s to the present. We previously identified mtDNA polymorphisms that were unique to ? 60% of striped bass from the A-C-F and which confirmed the continued successful natural reproduction of striped bass of Gulf maternal ancestry within the system. However, the genetic relatedness of the extant A-C-F population to ‘pure’ Gulf striped bass was not addressed. In this study, we determined the frequency of a diagnostic mtDNA XbaI polymorphism in samples of ‘pure’ Gulf striped bass that were collected from the A-C-F prior to the introduction of Atlantic fish, that were obtained from museum collections, and that were originally preserved in formalin. PCR primers were developed that allowed for amplification of a 191-bp mtDNA fragment that contained the diagnostic XbaI restriction site. Using RFLP and direct sequence analyses of the PCR amplicons, we found no significant differences in mtDNA XbaI genotype frequencies between the archived samples and extant A-C-F samples collected over a 15-year period. This indicates that significant maternally mediated introgression of Atlantic mtDNA genomes into the A-C-F gene pool has not occurred. Additionally, we found no evidence of the unique Gulf mtDNA genotype in striped bass from extant populations in Texas, Louisiana and the Mississippi River. These results highlight the importance of the A-C-F as a repository of striped bass to restore extirpated Gulf populations and the potential use of museum collections in retrospective population studies.     

Effects of Wolbachia on mtDNA variation in two fire ant species

Wolbachia are endosymbiotic bacteria that infect arthropods. As they are maternally transmitted, the spread of Wolbachia variants within host populations may affect host mtDNA evolution. We sequenced a portion of the mitochondrial cytochrome oxidase I gene from numerous individuals of two Wolbachia-infected fire ant species, Solenopsis invicta and S. richteri, to determine how these bacteria influence patterns of mtDNA variation. As predicted, there was a strong association between Wolbachia strain and host mtDNA lineage within and between these fire ant species. However, there was no consistent association between the presence of Wolbachia and a reduction in mtDNA diversity. Moreover, patterns of mtDNA variation within Wolbachia-infected populations did not differ consistently from neutral expectations, despite our prediction that strong positive selection acting on Wolbachia influences the evolutionary dynamics of other cytoplasmic genomes. Specifically, while values of Tajima's D consistently were less than zero for all six samples of fire ants harbouring Wolbachia, MacDonald-Kreitman tests suggested that the patterns of variation were different from those expected under neutrality in only two of the samples. We conclude that these neutrality tests do not unambiguously reveal a clear effect of Wolbachia infection on patterns of mtDNA variation and substitution in fire ants. Finally, consistent with an earlier study, our data revealed the presence of two divergent mtDNA haplotype lineages and Wolbachia strains within S. invicta. Recognition of these two lineages has important consequences for interpreting patterns of mtDNA evolution and genetic differentiation between conspecific social forms of this species.     

Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L. complex)

Genetic variation at 47 protein loci was investigated in 16 wild brown trout populations from the Pô basin and three major domesticated stocks used for stocking this area. Twenty-four loci were polymorphic and large frequency differences were found at 15 of them. The most significant allozyme variations were congruent with the mtDNA sequence polymorphism previously observed in the same samples. We confirmed the occurrence of two parapatric incipient species, Salmo marmoratus and S. trutta fario , previously identified by morphological traits. These two species were fixed or nearly fixed for alternate alleles at eight loci (Nei's standard genetic distance = 0.16–0.18), but introgression was detected between adjacent samples of the two forms. Divergence levels at both mtDNA and nuclear loci suggested that the differentiation between S. marmoratus and S. trutta fario started between 3 and 1 million years before present. Variation at protein loci and mtDNA supported the hypothesis that the third species found in this area, S. carpio (an endemic population of the lake Garda) was issued from a recent hybridization of the two first species. Finally, we showed that three of the major Italian fish-farm strains originated from the Atlantic side and displayed substantial genetic differences with the natural populations of the Pô basin. Most of these populations were contaminated by stocking with introgression rate ranging from 0 to 70% and measures of protection and restoration of the rich genetic diversity present in this area should be urgently applied.     

Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication

Mitochondrial DNA (mtDNA) diversity in European and Asian pigs was assessed using 1536 samples representing 45 European and 21 Chinese breeds. Diagnostic nucleotide differences in the cytochrome b (Cytb) gene between the European and Asian mtDNA variants were determined by pyrosequencing as a rapid screening method. Subsequently, 637bp of the hypervariable control region was sequenced to further characterize mtDNA diversity. All sequences belonged to the D1 and D2 clusters of pig mtDNA originating from ancestral wild boar populations in Europe and Asia, respectively. The average frequency of Asian mtDNA haplotypes was 29% across European breeds, but varied from 0 to 100% within individual breeds. A neighbour-joining (NJ) tree of control region sequences showed that European and Asian haplotypes form distinct clusters consistent with the independent domestication of pigs in Asia and Europe. The Asian haplotypes found in the European pigs were identical or closely related to those found in domestic pigs from Southeast China. The star-like pattern detected by network analysis for both the European and Asian haplotypes was consistent with a previous demographic expansion. Mismatch analysis supported this notion and suggested that the expansion was initiated before domestication.     

Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences

Shortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 10(1) to 10(4), but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty-nine mtDNA nucleotide-substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2-5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide-substitution haplotypes and length-variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once-glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five-region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units.     

Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in China, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of China. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.     

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.     

Collation of data on the ploidy levels and mitochondrial DNA phylogenetic lineages in the silver crucian carp Carassius auratus gibelio from Far Eastern and Central Asian populations

The distribution of the diploid and triploid forms and the correspondence between ploidy and mitochondrial DNA (mtDNA) phylogenetic lineages of the silver crucian carp have been studied in Far Eastern water bodies and the Syr Darya River. Both diploid and triploid forms have been found in large river systems (the Amur, Suifun, Tumangan, and Syr Darya river basins). Only the diploid form has been detected in lakes of Bol'shoi Pelis Island (Peter the Great Bay of the Sea of Japan), Sakhalin Island, and the Kamchatka River basin (the Kamchatka Peninsula). It has been confirmed that there are two mtDNA phylogroups in the silver crucian carp in the area studied. Both mtDNA phylogenetic lineages are present in the Suifun and Tumangan river basins. Only one mtDNA phylogroup (characteristic of the gynogenetic form) has been detected in two samples from the Amur River and in the Syr Darya population. The other mtDNA phylogroup is predominant in insular populations and in Kamchatka. The gynogenetic form carries only mtDNA phylogroup I, whereas both phylogroups have been found in diploid bisexual fish. The existence of only two mtDNA phylogroups substantially differing from each other indicates that the gynogenetic form has emerged from the diploid form only once and evolved independently for a long time after that. The absence of haplotypes transitional between the two mtDNA phylogroups suggests that the secondary contact between the gynogenetic and bisexual forms in continental populations occurred within recent historical time. The obtained data confirm that genetic (though asymmetric) exchange between the two forms is possible, which explains the high morphological and, probably, genetic similarity between them.     

Collation of data on the ploidy levels and mitochondrial DNA phylogenetic lineages in the silver crucian carp <Emphasis Type="Italic">Carassius auratus gibelio</Emphasis> from Far Eastern and Central Asian populations

The distribution of the diploid and triploid forms and the correspondence between ploidy and mitochondrial DNA (mtDNA) phylogenetic lineages of the silver crucian carp have been studied in Far Eastern water bodies and the Syr Darya River. Both diploid and triploid forms have been found in large river systems (the Amur, Suifun, Tumangan, and Syr Darya river basins). Only the diploid form has been detected in lakes of Bol’shoi Pelis Island (Peter the Great Bay of the Sea of Japan), Sakhalin Island, and the Kamchatka River basin (the Kamchatka Peninsula). It has been confirmed that there are two mtDNA phylogroups in the silver crucian carp in the area studied. Both mtDNA phylogenetic lineages are present in the Suifun and Tumangan river basins. Only one mtDNA phylogroup (characteristic of the gynogenetic form) has been detected in two samples from the Amur River and in the Syr Darya population. The other mtDNA phylogroup is predominant in insular populations and in Kamchatka. The gynogenetic form carries only mtDNA phylogroup I, whereas both phylogroups have been found in diploid bisexual fish. The existence of only two mtDNA phylogroups substantially differing from each other indicates that the gynogenetic form has emerged from the diploid form only once and evolved independently for a long time after that. The absence of haplotypes transitional between the two mtDNA phylogroups suggests that the secondary contact between the gynogenetic and bisexual forms in continental populations occurred within recent historical time. The obtained data confirm that genetic (though asymmetric) exchange between the two forms is possible, which explains the high morphological and, probably, genetic similarity between them.