Mitochondrial DNA Haplotype Frequencies Research Articles

Habitat fragmentation influences gene structure and gene differentiation among the Loxoblemmus aomoriensis populations in the Thousand Island Lake

Thousand Island Lake (TIL) is a fragmented landscape consisting of more than 1000 land-bridge islands isolated during reservoir formation. To evaluate the effects of fragmentation and island attributes on insect populations, we examined the genetic structure of Loxoblemmus aomoriensis, a species of cricket widely distributed in TIL, and compared genetic diversity between islands samples. Population genetic analyses was conducted based on mitochondrial DNA haplotype frequencies of 10 sample islands. By comparing three island attributes with population genetic diversity reveals that island area influenced population genetic diversity (r2 = 0.5094, p = 0.00204). Using Pairwise Fst values, we also found that long-distance isolation increased the genetic differentiation, while short-distance isolation can be offset by dispersal. These results indicate that fragmentation can impact populations on a genetic level.

Genetic structure of a Japanese brown frog (Rana japonica) population implies severe restriction of gene flow caused by recent urbanization in a satoyama landscape

Rapid urbanization is one of the major pressures on amphibian species. Elucidating changes in genetic structure will be useful in evaluating the effects of urbanization on amphibian populations. Our study focused on Rana japonica, which is common in complex agricultural landscapes known as satoyama, which are also under intense development pressure. We conducted landscape genetic analyses based on mitochondrial DNA haplotype frequencies of 13 breeding sites in a rapidly urbanizing area of Japan. We found several breeding sites had significantly higher Fst values, and we also identified the barriers to gene flow between these sites. Observation of past aerial photographs revealed that these barriers coincided with the construction of man-made structures in the last few decades, suggesting that urbanization has restricted gene flow in R. japonica. Our results show that landscape genetic approaches are useful in conservation planning where rapid habitat degradation has taken place.

Patterns of Genetic Variation Among Populations of the Asian Longhorned Beetle (Coleoptera: Cerambycidae) in China and Korea

Abstract Central to the study of invasive species is identifying source populations in their native ranges. Source populations of invasive species can provide important information about species life cycles, host use, and species-specific predators and parasites that could be deployed in a biological control program. The Asian longhorned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), is a serious invasive pest of urban forests in North America and Europe. We analyzed mitochondrial DNA haplotype frequencies and microsatellite allele frequencies to characterize phylogeographical patterns in potential source populations of A.. glabripennis. The data suggest that although there is evidence of genetic structure within and among populations in China, a substantial amount of genetic admixture has occurred. This admixture is probably due to recent reforestation efforts in China where beetles from previously isolated populations moved into new areas of abundant, susceptible, and stressed resources, leading to outbreak populations.

Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea

Abstract We investigated the genetic structure of blacktip shark (Carcharhinus limbatus) continental nurseries in the northwestern Atlantic Ocean, Gulf of Mexico, and Caribbean Sea using mitochondrial DNA control region sequences and eight nuclear microsatellite loci scored in neonate and young-of-the-year sharks. Significant structure was detected with both markers among nine nurseries (mitochondrial PhiST = 0.350, P < 0.001; nuclear PhiST = 0.007, P < 0.001) and sharks from the northwestern Atlantic, eastern Gulf of Mexico, western Gulf of Mexico, northern Yucatan, and Belize possessed significantly different mitochondrial DNA haplotype frequencies. Microsatellite differentiation was limited to comparisons involving northern Yucatan and Belize sharks with nuclear genetic homogeneity throughout the eastern Gulf of Mexico, western Gulf of Mexico, and northwestern Atlantic. Differences in the magnitude of maternal vs. biparental genetic differentiation support female philopatry to northwestern Atlantic, Gulf of Mexico, and Caribbean Sea natal nursery regions with higher levels of male-mediated gene flow. Philopatry has produced multiple reproductive stocks of this commercially important shark species throughout the range of this study.

Genetic load in marginal populations of Drosophila subobscura.

HereditasVolume 129, Issue 3 p. 283-286 Open Access Genetic Load in Marginal Populations of Drosophila Subobscura* Anssi Saura, Anssi Saura Department of Genetics, Umeå University, S-901 87 Umeå, SwedenSearch for more papers by this authorBo Johansson, Bo Johansson Department of Genetics, Umeå University, S-901 87 Umeå, SwedenSearch for more papers by this authorJuhani Lokki, Juhani Lokki Zoological Museum, FIN–00014 University of Helsinki, FinlandSearch for more papers by this authorMaija Kohonen–corish, Maija Kohonen–corish Cancer Genetics Laboratory, John Curtin School of Medical Research, The Australian National University, GPO BOX 334, Canberra ACT 2601, AustraliaSearch for more papers by this author Anssi Saura, Anssi Saura Department of Genetics, Umeå University, S-901 87 Umeå, SwedenSearch for more papers by this authorBo Johansson, Bo Johansson Department of Genetics, Umeå University, S-901 87 Umeå, SwedenSearch for more papers by this authorJuhani Lokki, Juhani Lokki Zoological Museum, FIN–00014 University of Helsinki, FinlandSearch for more papers by this authorMaija Kohonen–corish, Maija Kohonen–corish Cancer Genetics Laboratory, John Curtin School of Medical Research, The Australian National University, GPO BOX 334, Canberra ACT 2601, AustraliaSearch for more papers by this author First published: 06 May 2004 https://doi.org/10.1111/j.1601-5223.1998.00283.xCitations: 6 † * We dedicate this paper to Prof. Dr. Diether Sperlich of the University of Tübingen, Germany, in recognition to his inspiring leadership in the study of D. subobscura populations. AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL References Ayala FJ, Serra L and Prevosti A, (1989). A grand experiment in evolution: the Drosophila subobscura colonization of the Americas. Genome 31: 246– 255. Begon M, Krimbas CB and Loukas M, (1980). The genetics of D. subobscura populations. XV. Effective size of a natural population estimated by three independent methods. Heredity 45: 335– 350. Brussard PF, (1984). Geographic patterns and environmental gradients: the central–marginal model in Drosophila revisited. Ann. Rev. Ecol. Syst. 15: 25– 64. Desmet G, Nassimbeni P and Belli M, (1990). Transfer of radionuclides in natural and semi–natural environments. Elsevier, London & New York . Dobzhansky Th and Wright S, (1941). Genetics of natural populations. V. Relations between mutation rate and accumulation of lethals in populations of Drosophila pseudoobscura. Genetics 26: 23– 51. Dobzhansky Th, Hunter AS, Paviovsky O, Spassky B and Wallace B, (1963). Genetics of natural populations. XXXI. Genetics of an isolated marginal population of Drosophila pseudoobscura. Genetics 48: 91– 103. Garcia-Martinez J, Castro JA, Ramon M, Latorre A and Moyd A, (1998). Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura. Genetics 143: 1377– 1382. Gornostaev NG, (1993). New species and new records of Drosophilid flies Diptera Drosophilidae from Kazakhstan. Entomol. Rev. 71: 79– 82. Garcia-Corish M, Lokki J, Saura A and Sperlich D, (1985). The genetic load in a northern marginal population of Drosophila subobscura. Hereditas 102: 255– 258. Krimbas CB, (1992). Drosophila suboscura: Biology, genetics and inversion polymorphism. In: Inversion polymorphism in Drosophila (eds CB Krimbas and JR Powell) CRC Press, Boca Raton , p. 127– 220. Lakovaara S and Saura A, (1971). Genic variation in marginal populations of Drosophila subobscura. Hereditas 69: 77– 82. Latorre A, Hernandez C, Martinez D, Castro JA, Ramon M and Moya A, (1992). Population structure and mitochondrial DNA gene flow in Old World populations of Drosophila subobscura. Heredity 68: 15– 24. Loukas M, Krimbas CB and Sourdis J, (1979). The genetics of Drosophila subobscura populations. XII. A study of lethal allelism. Genetica 54: 197– 206. Mestres F, Pegueroles G, Prevosti A and Serra L, (1990). Colonization of America by D. subobscura: lethal genes and the problem of the 05 inversion. Evolution 44: 1564– 1568. Pfriem P and Sperlich D, (1982). Wild O chromosomes of Drosophila subobscura from different geographic regions have different effects on viability. Genetica 60: 49– 59. Saura A, Lakovaara S, Lokki J and Lankinen P, (1973). Genic variation in central and marginal populations of Drosophila subobscura. Hereditas 75: 33– 46. Saura A, Johansson B, Eriksson E and Kohonen-Corish M, (1990). Genetic load in northern populations of Drosophila subobscura. Hereditas 112: 283– 287. Sperlich D, Feuerbach-Mravlag H, Lange P, Michaelidis A and Penzos-Daponte A, (1977). Genetic load and viability distribution in central and marginal populations of Drosophila subobscura. Genetics 86: 835– 848. Townsend JI, (1952). Genetics of marginal populations of Drosophila willistoni. Evolution 6: 428– 442. Citing Literature Volume129, Issue3December 1998Pages 283-286 ReferencesRelatedInformation

Allozyme, mitochondrial-DNA, and morphometric variability indicate cryptic species of anchovy (Engraulis encrasicolus)

Previous surveys of population structure in the Atlantic-Mediterranean anchovy Engraulis encrasicolus L. have reported heterogeneity in morphology, allozyme frequencies, and mitochondrial DNA haplotype frequencies at a regional scale. In particular, two stocks of anchovy have been detected in the Adriatic Sea. In this paper, the available data is reviewed with the aim to relate genetic variation to geography at the widest possible geographical scale, for investigating the evolutionary mechanisms underlying stock structure in anchovy. Correspondence analysis of allozyme frequencies (24 samples, three polymorphic loci) compiled from the literature indicates three distinct entities in the Mediterranean Sea. Open-sea or oceanic anchovy populations are genetically different from inshore-water populations within a region (Nei's ^GST = 0.035–0.067), while broadscale geographical variation is weak for each of these two habitat-specific forms (^GST = 0.005–0.006). Mitochondrial-DNA haplotype frequencies support the distinction between an inshore form and an oceanic form (^GST = 0.067–0.107), with virtually no genetic differences among oceanic populations across the Gulf of Biscay, the western Mediterranean and the Ionian Sea (^GST = −0.001). If natural selection on marker loci is unimportant, these results indicate the occurrence of two parapatric, genetically distinct, habitat-specific forms that are widely distributed throughout the Mediterranean Sea. Persistent allele and haplotype-frequency differences between these forms indicate reproductive isolation and the presence of an E. encrasicolus species complex in the Mediterranean.

Genetic structure of Lake Magadi tilapia populations

The control region of the mitochondrial DNA haplotype frequencies were significantly different among the two separate lagoon populations of Oreochromis alcalicus grahami in Lake Magadi and of O. a. alcalicus from lake Natron, and DNA fingerprint similarity indices were significantly higher for intra-population comparisons of the two Magadi lagoon populations and the Lake Natron population than the inter-population similarity indices among these populations. A modified Fst measure indicated population sub-division and the phylogeographic partitioning of the VNTR fragments observed were unique to specific populations further indicating substantial genetic differentiation. The lagoon populations within Lake Magadi demonstrated the same degree of genetic differentiation as either of these populations did to the outgroup (the Lake Natron population). There appears to be limited gene flow between Lake Magadi tilapia populations and this population structure has important implications for protecting locally adapted populations within this unique ecosystem.

Genetic structure of Lake Magadi tilapia populations

The control region of the mitochondrial DNA haplotype frequencies were significantly different among the two separate lagoon populations of Oreochromis alcalicus grahami in Lake Magadi and of O. a. alcalicus from lake Natron, and DNA fingerprint similarity indices were significantly higher for intra‐population comparisons of the two Magadi lagoon populations and the Lake Natron population than the inter‐population similarity indices among these populations. A modified Fst measure indicated population sub‐division and the phylogeographic partitioning of the VNTR fragments observed were unique to specific populations further indicating substantial genetic differentiation. The lagoon populations within Lake Magadi demonstrated the same degree of genetic differentiation as either of these populations did to the outgroup (the Lake Natron population). There appears to be limited gene flow between Lake Magadi tilapia populations and this population structure has important implications for protecting locally adapted populations within this unique ecosystem.

Temporal stability and spatial divergence of mitochondrial DNA haplotype frequencies in red drum ( Sciaenops ocellatus ) from coastal regions of the western Atlantic Ocean and Gulf of Mexico

Restriction-site variation in mitochondrial (mt) DNA was assayed among 1675 red drum (Sciaenops ocellatus Linnaeus) sampled from 20 localities along the southeastern coast of the USA (western Atlantic) and the Gulf of Mexico (Gulf). Up to four consecutive year-classes (cohorts) were sampled at most localities. Nucleotide-sequence divergence among 170 mtDNA haplotypes identified ranged (in percentage) from 0.184 to 1.913, with a mean (±SD) of 0.887 ± 0.300. Comparisons of mtDNA haplotype frequencies across year-classes within localities were non-significant, indicating temporal stability of breeding components within localities. Significant heterogeneity in mtDNA haplotype frequencies was found across all localities, between (pooled) samples from the western Atlantic and the Gulf, and among geographically spaced, regional groupings in the Gulf. Genetic divergence between subpopulations of red drum in the western Atlantic and Gulf follows a pattern exhibited in other marine fishes, and probably stems from physical (historical environmental heterogeneity, absence of suitable habitat, and current patterns) and, perhaps, behavioral factors. Genetic differences among red drum in the Gulf appear to be due largely to an isolation-by-distance effect that is attributable to behavioral factors. The latter may include female philopatry to natal bays or estuaries, limited offshore (coastwise) movement of females relative to their natal bay or estuary, or both. Genetic divergence among red drum in the Gulf occurs despite high gene flow (estimated as the number of genetic effective migrants in an island mode). Conservation and management of red drum should be based on the premise that strategies for a given bay or estuary will impact geographically proximal bays or estuaries more than distal ones. Trajectories of correlograms in spatial autocorrelation analysis suggest a geographic neighborhood size, relative to genetic migration of red drum from a bay or estuary, of roughly 500 to 600 km.

Genetic Differentiation of Sockeye Salmon Subpopulations from a Geologically Young Alaskan Lake System

The Tustumena Lake drainage in southcentral Alaska is glacially turbid and geologically young (<2,000 years old). Previous field studies identified at least three subpopulations of sockeye salmon Oncorhynchus nerka at Tustumena Lake, based on the distribution and timing of spawners. The subpopulations included early-run salmon that spawned in six clearwater tributaries of the lake (mid August), lake shoreline spawners (late August), and late-run fish that spawned in the lakeˈs outlet, the Kasilof River (late September). Our objective was to determine the degree of genetic differentiation among these subpopulations based on restriction enzyme analyses of the cytochrome b gene of mitochondrial DNA and analyses of four polymorphic allozyme loci. Mitochondrial DNA haplotype frequencies for outlet-spawning sockeye salmon differed significantly from those of all other subpopulations. The most common (36%) haplotype in the outlet subpopulation did not occur elsewhere, thus suggesting little or no gene flow between outlet spawners and other spatially close subpopulations at Tustumena Lake. Allele frequencies at two allozyme loci also indicated a degree of differentiation of the outlet subpopulation from the shoreline and tributary subpopulations. Allele frequencies for three tributary subpopulations were temporally stable over approximately 20 years (based on a comparison to previously published results) despite initiation of a hatchery program in two of the tributaries during the intervening period. Collectively, our results are consistent with the hypothesis that significant genetic differentiation has occurred within the Tustumena Lake drainage since deglaciation approximately 2,000 years ago.

Stability of Allozyme and Mitochondrial DNA Markers among Three Year-Classes of Lake Trout Propagated from Seneca Lake, New York

Lake trout Salvelinus namaycush representing three year-classes (1988, 1989, and 1990) of gametes collected from adults captured in Seneca Lake, New York, were examined for allelic variation at 18 polymorphic loci and for mitochondrial DNA (mtDNA) haplotype variation, mtDNA was digested with the four restriction endonucleases Ava I, Bam H I, Hin f I, and Taq I. Analysis of allelic frequencies among these three year-classes of the Seneca strain and a previously analyzed collection (1983 year-class, also a wild egg taken from Seneca Lake) indicated temporal heterogeneity (P < 0.01) at three loci: two for proline dipeptidase (PEPD-1,2*) and one for malic enzyme (NADP+) (mMEP-1*). However, cluster analysis of genetic distances demonstrated that all four Seneca Lake samples exhibited a much lower level of differentiation than observed among other strains stocked into Lake Ontario. Mitochondrial DNA haplotype frequencies were not significantly different among the 1988, 1989, and 1990 year-class samples, which supported the conclusion of genetic similarity among Seneca strain samples. Allozyme differences among Seneca collections did not significantly affect estimates by mixed-stock analysis (MSA) of parental strain contributions to a mixture of wild fry from Lake Ontario. Based on these results, data from the four year-classes could be pooled and used as Seneca strain baseline data for future MSA estimates.