Patterns Of mtDNA Variation Research Articles

Pattern of mtDNA variation in three populations from São Tomé e Príncipe.

We have analysed the matrilineal genetic composition of three self-reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS-I) and II (HVS-II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y-chromosome STRs. In addition, the crossing of mtDNA and Y-STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio-historical interactions among the groups.

Mitochondrial DNA Variation in the South American Grasshopper <I>Dichroplus elongatus</I> (Orthoptera: Acrididae)

Dichroplus elongatus (Giglio-Tos) is a phytophagous grasshopper widely distributed in Argentina. In the current work, the genetic variation and phylogeography of this species was studied with mtDNA techniques. In total, 171 individuals from northwestern (Las Yungas province) and eastern (Espinal and Pampeana provinces) Argentina populations were analyzed using restriction fragment-length polymorphism. The number of substitutions per site between pairs of haplotypes ranged from 0.65 to 3.84%. The neighbor-joining phenogram yielded two main groups; one clusters together the haplotypes restricted to the east and the other the haplotypes restricted to the northwestern region. Phylogenetic consensus unrooted tree among mtDNA haplotypes allowed us to propose the ancestral haplotype, which occupies the central position of the network. The unweighted pair-group method with arithmetic average dendrogram from nucleotide divergence among populations showed that populations are roughly grouped according to their geographic distribution. There was a significant heterogeneity of the mtDNA distribution when populations from all three biogeographic provinces were compared. The distribution patterns of mtDNA variation observed in D. elongatus may be explained by isolation by distance when referring to the main biogeographic provinces. In Las Yungas and Pampeana provinces, ecological factors seem to have contributed to the genetic differentiation among populations.

Genetic Evidence for the Proto-Austronesian Homeland in Asia: mtDNA and Nuclear DNA Variation in Taiwanese Aboriginal Tribes

Previous studies of mtDNA variation in indigenous Taiwanese populations have suggested that they held an ancestral position in the spread of mtDNAs throughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995), but the question of an absolute proto-Austronesian homeland remains. To search for Asian roots for indigenous Taiwanese populations, 28 mtDNAs representative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwan) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Alu insertion loci were analyzed, to determine if the pattern of mtDNA variation is concordant with nuclear DNA variation. Tribal groups shared considerable mtDNA sequence identity (P>.90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs with a 9-bp deletion have considerable mainland-Asian diversity and have spread to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any other populations, but these shared types were widely dispersed geographically throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overall, the results suggest that the Taiwanese have temporally deep roots, probably in central or south China, and have been isolated from other Asian populations in recent history.

Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat,Eonycteris spelaea

The fruit bat,Eonycteris spelaea, occurs from India through the Philippines to the southeast limit of its distribution in the Lesser Sunda islands of Indonesia. Mitochondrial DNA (mtDNA) variation was examined in IndonesianE. spelaeaisland populations by amplification of the D-loop and digestion with restriction endonucleases. In addition, microgeographic variation was assessed by investigation of three cave populations within one island. A total of 24 genotypes, comprising two broad clades, was detected. The pattern of mtDNA variation reflects the colonization history ofE. spelaeawith estimates of haplotype and sequence diversity highest in the older western populations and lowest at the eastern periphery of the species» distribution. These findings may also be associated with an environmental cline from west to east. There is also evidence that genetic distance between populations reflects geographic relationships, especially historical connectedness, as measured by Pleistocene sea-crossing distances. At the microgeographic level, cave populations were heterogeneous and composed of diverse lineages suggesting restricted local interchange.

Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea

Abstract The fruit bat, Eonycteris spelaea , occurs from India through the Philippines to the southeast limit of its distribution in the Lesser Sunda islands of Indonesia. Mitochondrial DNA (mtDNA) variation was examined in Indonesian E. spelaea island populations by amplification of the D-loop and digestion with restriction endonucleases. In addition, microgeographic variation was assessed by investigation of three cave populations within one island. A total of 24 genotypes, comprising two broad clades, was detected. The pattern of mtDNA variation reflects the colonization history of E. spelaea with estimates of haplotype and sequence diversity highest in the older western populations and lowest at the eastern periphery of the species» distribution. These findings may also be associated with an environmental cline from west to east. There is also evidence that genetic distance between populations reflects geographic relationships, especially historical connectedness, as measured by Pleistocene sea-crossing distances. At the microgeographic level, cave populations were heterogeneous and composed of diverse lineages suggesting restricted local interchange.

Patterns of mtDNA variation in Hawaiian freshwater fishes: the phylogeographic consequences of amphidromy.

MtDNA sequencing was used to assess the phylogeographic structure of four species of Hawaiian freshwater fishes: Lentipes concolor, Stenogobius hawaiiensis, Sicyopterus stimpsoni, and Awaous guamensis. Samples of each species were collected from streams on the northeast side of Kauai, Maui, Molokai, Oahu, and Hawaii. We sequenced segments from both coding and noncoding regions (638-1391 bp) in each species. Sequence analysis uncovered genetic variability in these fishes but no evidence of strong geographic structure among island populations. This result is most readily explained by the fishes' larval marine life stage (amphidromy), which likely facilitates gene flow among island populations. By constraining genetic differentiation among populations, amphidromy may impede speciation in these fishes, possibly explaining why the Hawaiian freshwater fish fauna is depauperate compared to other species-rich Hawaiian faunas. It may also provide them with a kind of evolutionary flexibility atypical of other, more isolated island faunas and allow natural restocking to occur in streams that have been restored to suitable conditions. Comparisons of restriction site and sequence data suggested similar population genetic conclusions for all species except S. stimpsoni, for which the restriction site data is questioned.

Phylogeography, population structure and dispersal patterns of the beluga whale Delphinapterus leucas in the western Nearctic revealed by mitochondrial DNA

The recent evolutionary history, population structure and movement patterns of beluga whales in the western Nearctic were inferred from an analysis of mitochondrial DNA control region sequence variation of 324 whales from 32 locations representing five summer concentration areas in Alaska and north‐west Canada. Phylogenetic relationships among haplotypes were inferred from parsimonious networks, and genetic subdivision was examined using haplotypic frequency‐based indices and an analysis of variance method modified for use with interhaplotypic distance data. MtDNA relationships were characterized by a series of star‐like phylogenies which, when viewed in conjunction with information on haplotype frequency and distribution, suggested a rapid radiation of beluga whales into the western Nearctic following the Pleistocene, and an early divergence of the Beaufort Sea from the Chukchi and Bering Seas subpopulations. Overall nucleotide diversity was low (0.51%) yet all major summering concentrations were significantly differentiated (ΦST= 0.33) from one another. Stratification of samples by gender and age from the three northernmost subpopulations suggested that female cohorts from neighbouring subpopulations were more differentiated than males. Further stratification of adult animals by age revealed that older adults were substantially less subdivided among locations than younger adults, particularly for males, suggesting that dispersal, although limited, is biased toward older adult males. Overall, the patterns of mtDNA variation in beluga whales indicated that the summering concentrations are demographically, if not phyletically distinct. Population structure appears to be maintained primarily by natal homing behaviour, while asymmetries in dispersal may be associated with the type of mating system.

MULTIPLE MODES OF SPECIATION INVOLVED IN THE PARALLEL EVOLUTION OF SYMPATRIC MORPHOTYPES OF LAKE WHITEFISH (COREGONUS CLUPEAFORMIS, SALMONIDAE).

We performed a phylogenetic analysis of mtDNA variation among seven sympatric pairs of dwarf and normal morphotypes of whitefish from northern Québec and the St. John River drainage to address three questions relevant to understanding their radiation. Are all sympatric pairs reproductively isolated? Do phylogenetic analyses confirm that sympatric whitefish morphotypes found in eastern North America represent the outcome of polyphyletic evolutionary events? If so, did all sympatric pairs from the St. John River drainage originate from the same scenario of allopatric divergence and secondary contact? The hypothesis of genetic differentiation was supported for all sympatric pairs from the St. John River drainage, whereas lack of mtDNA diversity precluded any test of reproductive isolation for northern Québec populations. Patterns of mtDNA variation confirmed that dwarf and normal morphotypes evolved in parallel among independent, yet closely related, lineages, thus providing indirect evidence for the role of natural selection in promoting phenotypic radiation in whitefish. Patterns of mtDNA diversity among sympatric pairs of the St. John River indicated a complex picture of whitefish evolution that implied sympatric divergence and multiple allopatric divergence/secondary contact events on a small geographic scale. These results suggests that ecological opportunities, namely trophic niche availability, may promote population divergence in whitefish.

Applications of mitochondrial DNA analysis in conservation: a critical review

AbstractPatterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) ‘gene conservation’ ‐ the identification and management of genetic diversity, and (ii) ‘molecular ecology’ ‐ the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time‐frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long‐term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within‐population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short‐term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource‐intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long‐term planning and short‐term execution of species recovery plans.

HISTORICAL BIOGEOGRAPHY AND CONTEMPORARY PATTERNS OF MITOCHONDRIAL DNA VARIATION IN WHITE-TAILED DEER FROM THE SOUTHEASTERN UNITED STATES.

Mitochondrial DNA (mtDNA) was used to characterize patterns of geographic variation among white-tailed deer (Odocoileus virginianus) populations in the southeastern United States. Fifteen restriction enzymes were employed to survey and map 99 restriction sites in 142 deer from 18 localities in five southeastern states. Phylogenetic analysis revealed three primary groups of haplotypes: (1) southern Florida and the Florida Keys, (2) the remainder of peninsular Florida northward to South Carolina, and (3) the Florida panhandle westward to Mississippi. Geographical heterogeneity in haplotype frequencies suggests that stochastic lineage sorting or isolation by distance are not important determinates of mtDNA differentiation among deer populations. The pattern of mtDNA variation in white-tailed deer is concordant spatially with those observed in unrelated taxa suggesting the common influence of historical biogeographic events. The data (1) support previous hypotheses that relate contemporary patterns of intraspecific phylogeography in northern Florida to the physiogeographic history of the region; and (2) suggest that genetic differentiation in southern Florida may be attributable to episodes of Pleistocene dispersal. Despite potentially high vagility and human intervention, ecological and demographic characteristics of deer have effectively preserved the historical pattern of intraspecific mtDNA differentiation.

Mitochondrial DNA polymorphisms in subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel, and its peripheral isolates.

Patterns of mitochondrial DNA (mtDNA) variation were examined in 133 mole-rats constituting all four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of the Spalax ehrenbergi superspecies in Israel, as well as the peripheral isolates of 2n = 60. In the main range of the complex, a total of 28 mtDNA haplotypes were found in 64 mole-rats, with most haplotypes being unique to either a single chromosomal species or population. mtDNA divergence increased from low to high diploid number in a north-to-south direction in Israel. Overall levels of mtDNA diversity were unexpectedly the highest in the 2n = 60, the youngest species of the complex. The mtDNA haplotypes can be separated into two major groups, 2n = 52-54 and 2n = 58-60, and a phylogenetic analysis for each group revealed evidence of a few haplotypes not sorted by diploid number. The overall patterns of mtDNA divergence seen within and among the four chromosomal species are consistent with the parapatric mode of speciation as suggested from previous studies of allozyme and DNA hybridization. In a separate data set the patterns of mtDNA variation were examined across the main geographic range and across peripheral semi-isolates and isolates of the 2n = 60 chromosomal species. Fifteen haplotypes were found in 69 mole-rats. High levels of mtDNA diversity characterized the main range, semi-isolated, and even some desert isolated populations. The peripheral isolates contain much mtDNA diversity, including novel haplotypes.

MtDNA polymorphisms: evolutionary significance in adaptation and speciation of subterranean mole rats

Patterns of mtDNA diversity in subterranean mole rats of the Spalax ehrenbergi superspecies (2n = 52, 54, 58 and 60) were previously studied in the main ranges of the four chromosomal species, and specifically in the 2n = 60 species and its peripheral steppe semi-isolates and desert isolates. In the present study we correlated mtDNA diversity indices, nucleon diversity, h, and nucleotide divergence, π, with physical (climatic), biotic (parasites) and biological (genetical, morphological, physiological and behavioural) factors, showing that mtDNA diversity is structured ecogeographically and biologically. The following significant correlations of mtDNA diversity were indicated with: (i) climatic heterogeneity and unpredictability; (ii) levels of ecto- and endoparasites; and (iii) biological diversities, primarily with physiological diversity associated with the energy budget. Small steppe semi-isolates and desert isolates harbour high levels of mtDNA haplotype diversity, some novel, which may be a prerequisite for future speciation events. We conclude that the ecogeographical and biological correlates, as well as the maintenance of mtDNA polymorphisms in small isolated populations, strongly suggest that mtDNA diversity is not neutral. Diversifying natural selection appears to be an important differentiating factor of mtDNA diversity in the twin evolutionary processes of adaptive radiation and active speciation. We suggest critical experiments to substantiate our conclusions and highlight the contribution of mtDNA diversity to fitness, i.e. to the biological function of mtDNA diversity in the evolutionary process.

Variation in Mitochondrial DNA and the Biogeographic History of Woodrats (Neotoma) of the Eastern United States

?Genetic variation in 114 woodrats (Neotoma) from 33 locations in the eastern and central United States was examined using analysis of mitochondrial DNA (mtDNA) restriction sites. Results indicate that three major lineages of Neotoma floridana (southern, western, and northern) diverged in the early Pleistocene. The southern lineage exhibits substantial mtDNA variability and population structure. The pattern of mtDNA variation in the southern lineage suggests that vicariance events, including the insularization of Florida, have been important determinants of geographic variation. The low levels of sequence variation within the northern and western lineages indicate that woodrat populations in these areas are probably the result of relatively recent (Holocene) range expansions. These conclusions are not entirely consistent with the current taxonomy of eastern woodrats and suggest that taxonomic revision is warranted. [Mitochondrial DNA; biogeography; phylogeography; cladistics; phylogenetics; Neotoma.] The geographic distribution and genetic structure of contemporary populations are determined both by current ecology and by historical patterns of vicariance and dis? persal. The availability of DNA restriction site and sequence data has focused atten? tion on the use of gene genealogies (es? pecially mitochondrial DNA [mtDNA] ge? nealogies) to clarify recent patterns of gene flow and historical patterns of population subdivision and genetic differentiation. Empirical studies of the distribution of mtDNA haplotypes in the context of ex? plicit mtDNA phylogenies have demon? strated the value of this approach (e.g., Ber? mingham and Avise, 1986; Cann et al., 1987; Baker et al., 1990; Riddle and Honeycutt, 1990). The study of the relationship be? tween genealogy and geography has been termed intraspecific phylogeography (Avise et al., 1987; Avise, 1989). Analysis of animal mtDNA can be a powerful tool in the identification of phylogeographic patterns. Not only is mtDNA variation easily assessed (because of high copy number, small genome size, and sim? ple sequence organization), but maternal inheritance and apparent absence of re? combination simplify interpretation of mtDNA phylogenies (which are equiva? lent to maternal genealogies). In mammals, sequence differences appear to accumulate faster in mtDNA than in many single-copy nuclear genes (Wilson et al., 1985; Moritz et al., 1987), allowing discrimination of lin? eages that have diverged from one another relatively recently. However, because mtDNA is a set of completely linked mark? ers and because of lineage sorting (from polymorphic ancestors) and differential in? trogression, an mtDNA genealogy is not necessarily an accurate representation of organismal phylogeny (Avise et al., 1987; Harrison, 1989). We examined phylogeographic varia? tion of mtDNA haplotypes in woodrats of the eastern United States (Neotoma pon? dana) to gain insights into the recent pop? ulation history of this widespread rodent species. Our observations and conclusions are relevant to issues surrounding conser? vation and management of woodrat pop? ulations, which have experienced signifi? cant declines in several northern states. 3 Present address: Department of Forest Science, Oregon State University, Hatfield Marine Science Center, Newport, Oregon 97365, USA.

The material ancestry and approximate age of parthenogenetic species of Caucasian rock lizards (Lacerta: Lacertidae)

Restriction enzymes were used to assay variation among mitochondrial DNAs from parthenogenetic and sexual species of Lacerta. This permitted identification of the sexual species that acted as the maternal parent of the various hybrid-parthenogenetic lineages. Lacerta mixta was the maternal parent for both L. dahli and L. armeniaca, L. valentini was the maternal parent for L. uzzelli, and L. raddei was the maternal parent of L. rostombekovi. The maternal ancestry of L. unisexualis is not as clear. The sample of L. nairensis was very similar to one from a population of L. raddei and either species could be the maternal parent of L. unisexualis. The parthenogenetic species all had very low nucleotide diversity in absolute terms and in comparison to their sexual relatives. The close similarity between mtDNAs from the parthenogenetic species and their respective sexual maternal ancestor species provides strong evidence for the recent origin of the parthenogens. The low diversity of the parthenogens indicates that few females were involved in their origins; the maternal parents of L. dahli and L. armeniaca could have come from a single population. The patterns of mtDNA variation in Lacerta are very similar to those in Cnemidophorus and Heteronotia, establishing recent and geographically restricted origins as a general feature of parthenogenetic lizards.

MITOCHONDRIAL-DNA VARIATION IN THE CRESTED NEWT SUPERSPECIES: LIMITED CYTOPLASMIC GENE FLOW AMONG SPECIES.

The crested newt has a widespread European distribution and encompasses four taxa recently elevated to full species: Triturus cristatus, T. carnifex, T. dobrogicus, and T. karelini. These are distinct on morphological, chromosomal, and isozymic grounds and have fairly sharp transition zones. A widespread survey (12 countries, 49 geographic sites, 210 individuals) of mtDNA variation (20-27 restriction enzyme sites mapped per individual) was made in order to 1) correlate mtDNA variation with morphological features defining the species, 2) determine the degree of differentiation within and among species, and 3) detect any introgression among species. The mtDNAs of these species were clearly differentiated (d = 3.9-7.1%). Additionally, geographic structuring was observed within T. carnifex and T. karelini, each displaying two divergent mitochondrial genome types (d = 3.5% and 4.7%, respectively). The other two (more northerly distributed) species were genetically homogeneous over most (T. cristatus) or all (T. dobrogicus) of their ranges. In the case of T. cristatus, one may infer bottlenecking as a result of Pleistocene glaciation events. This may also apply in part to T. dobrogicus, but high population connectedness and gene flow in this lowland river species may alone be sufficient for homogenization of mtDNA. Patterns of mtDNA variation were largely concordant with morphology; some interspecific mitochondrial gene flow was observed, but only close to or in the transition zones. Analyses of mapped restriction-site data by UPGMA and parsimony methods (using the closely related T. marmoratus as an outgroup) produce very similar dendrograms. The levels of divergence found concur with the systematics of the group, but the differentiation within T. carnifex and T. karelini is notable.