Mitochondrial Control Region Sequences Research Articles

Phylogeography Study of Ammodytes personatus in Northwestern Pacific: Pleistocene Isolation, Temperature and Current Conducted Secondary Contact

To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

Population subdivision and peripheral isolation in American badgers (Taxidea taxus) and implications for conservation planning in Canada

In Canada, three subspecies of American badgers ( Taxidea taxus (Schreber, 1777)) traditionally are identified; two of which are listed as endangered because of their restricted geographic range and low population sizes. To verify their subspecific designations and genetic insularity, we analyzed mitochondrial control region sequences within and among badger subspecies ( Taxidea taxus jacksoni Schantz, 1946, Taxidea taxus jeffersonii (Harlan, 1825), and Taxidea taxus taxus (Schreber, 1777)) from nine locations in Canada and bordering United States. Although subspecies designations were supported (a priori subspecific designations, n = 3, AMOVA: FST = 0.40, p < 0.001), insular populations also were found within subspecific ranges as shown by spatial analysis of molecular variation, which suggested that our sample set consisted of five genetic groups (FST = 0.39, p < 0.001). These five distinct groupings included the subdivision of T. t. jeffersonii on either side of the Selkirk Mountains, and of T. t. jacksoni in the western part of its range grouping more closely with T. t. taxus of Manitoba. These results indicate that endangered populations of badgers may be more segregated than previously identified using morphological characteristics as proxies for subspecific designation. These results have important implications for the conservation of badgers in Canada, particularly of the two endangered subspecies.

Identification and management of a single large population of wild dromedary camels

AbstractThe dromedary camel (Camelus dromedarius) is a significant invasive species in Australia. It is an unusual pest species that is of large body size with relatively low fecundity compared with other pest species. Camels are highly adapted to the arid regions that characterize a large proportion of Australia and occupy an almost completely undisturbed area of ≥3 million km2. They have no history of invasion elsewhere in the world. Despite this, their population has been expanding at approximately 80,000 camels per annum, with the most recent estimate of population size around 1,000,000 individuals. We employed a landscape‐genetic approach to evaluate the population structure and molecular ecology of Australian camels. We combined mitochondrial control region sequence (n = 209 animals) with 18 microsatellite markers to profile over 800 adult camels to identify the presence of a single panmictic population. We showed that demographically defined neighborhoods for wild camels are about 200 km; this value was supported by home range estimates. Distances greater than this display no pattern of isolation by distance across the Australian continent. The result is the largest single geographical population so far recorded for an invasive species in Australia. This pattern may be explained by the impressive and near‐nomadic dispersal pattern of camels, in combination with an unpredictable environment virtually devoid of barriers to movement and predatory suppression. Although it is technically feasible, the reality is that it would not be economically or politically viable to have continental eradication of wild camels in Australia because of the vast size and movement dynamics of the camel population. As such, we advocate a change away from an expensive solution to an intractable reduction program (that is almost entirely focused on protection of biological refugia) and moves to include cultural, economic, and biodiversity asset protection for the management of this most unorthodox of invasive species. © 2012 The Wildlife Society.

Mitochondrial and morphological variation of Tilapia zillii in Israel

BackgroundTilapia zillii is widespread in the East Levant inland aquatic systems as well as in artificial water reservoirs. In this study we explore the genetic and morphological variation of this widespread species, using mitochondrial control region sequences and meristic characters. We examine the hypothesis that T. zillii's population structure corresponds to the four Israeli aquatic systems.ResultsOut of seven natural water bodies, only two were found to possess genetically divergent populations of T. zillii. In addition to its presence in fish farms, the species was found in two artificial recreational ponds which were supposed to have been stocked only with other fish species. In these two artificial habitats, the haplotype frequencies diverged significantly from those of natural populations. Finally, fish from the Dead Sea springs of Ne'ot HaKikar appear to differ both genetically and morphologically from fish of the same aquatic system but not from fish of other water systems.ConclusionsOur results show that the population structure of T. zillii does not match the geography of the Israeli water-basins, with the exception of the Dead Sea and Kishon River, when considering natural populations only. The absence of a significant divergence between basins is discussed. Our results and observations suggest that the Ne'ot HaKikar Dead Sea population and those of artificial ponds could have originated from the "hitchhiking" of T. zillii, at the expense of some other cultivated tilapiine species.

Genetic Diversity in the Desert Warthog (Phacochoerus aethiopicus delameri) Population of Eastern Africa

Genetic variability is an important component in the ability of populations to evolve and adapt to changing environmental conditions and consequently for their long-term survival. Here we report the first description of both nuclear loci and mitochondrial control region sequence variability in a population of the desert warthog (Phacochoerus aethiopicus) sampled from 12 localities in its natural range in eastern Africa. From the total sample (30 individuals), at the six microsatellite loci that were analysed, a total of 43 alleles was observed averaging seven alleles per locus. Expected heterozygosity (HE) per locus was high, ranging from 0.53 to 0.87. At the mitochondrial loci, nucleotide diversity was low (π = 0.12%) with two unique haplotypes observed from the 19 individuals that amplified successfully. The diversity indices observed in the desert warthog are comparable to those previously reported for the closely related but widespread species, the common warthog (Phacochoerus africanus). These results suggest that the desert warthog is not genetically depauperate despite the rinderpest epidemic of the 1880s that eliminated it frommost of its natural range.

Mitochondrial DNA evidence for late Pleistocene population expansion of the white catfish, Ameiurus catus

Abstract Employing distance-based, maximum likelihood-based, and Bayesian coalescent methodologies and utilizing mitochondrial control region sequence data, the present study reports the importance of Pleistocene glacial epochs on the demographic expansion of the white catfish, Ameiurus catus . White catfish are endemic to the southeastern region of the United States, the region that had never glaciated during the Pleistocene epoch; however, compared to the present day meandering river patterns, the region did exhibit braided river patterns during the late Quaternary. The present study revealed the existence of two distinct matrilineal lineages of white catfish, southeast Gulf coast (SEGC) and southeast Atlantic coastal plains (SEACP), which are estimated to have diverged from their common ancestor approximately 0.71 (0.37–1.1) million years ago. Consistent with the results of the mismatch distribution and site frequency spectrum based summary statistics such as Fu's F, the Bayesian skyline plot (BSP) has also showed evidence for population expansion. The BSP showed two phase growth: a static phase until 0.2 million years, followed by a sudden population expansion thereafter, which is the time that coincides with the late Quaternary epoch. The changing patterns in drainage systems in response to the Quaternary climate change might have had a significant impact on the demographic expansion of white catfish.

Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages

Here we provide 129 complete mitochondrial control region sequences of indigenous Khoe-San individuals from Angola to contribute to the still underrepresented pool of data from Africa. The dataset consists of exclusively African lineages with a majority of Sub-Saharan haplogroups. The probability of a random match was calculated as 0.09. The data set comprises 21 haplotypes occurring more than once and 17 unique haplotypes. Upon publication, haplotypes were incorporated in the EMPOP database (www.empop.org; EMP00069) [1].

Genetic population structure of the Fire-bellied toad Bombina bombina in an area of high population density: implications for conservation

In this study, we report the genetic population structure of the Fire-bellied toad Bombina bombina in Brandenburg (East Germany) in the context of conservation. We analysed 298 samples originating from 11 populations in Brandenburg using mitochondrial control region sequences and six polymorphic microsatellite loci. For comparison, we included one population each from Poland and Ukraine into our analysis. Within Brandenburg, we detected a moderate variability in the mitochondrial control region (19 different haplotypes) and at microsatellite loci (9–12 alleles per locus). These polymorphisms revealed a clear population structure among toads in Brandenburg, despite a relatively high overall population density and the moderate size of single populations (100–2000 individuals). The overall genetic population structure is consistent with a postglacial colonization from South East-Europe and a subsequent population expansion. Based on genetic connectivity, we infer Management Units (MUs) as targets for conservation. Our genetic survey identified MUs, within which human infrastructure is currently preventing any genetic exchange. We also detect an unintentional translocation from South East to North West Brandenburg, presumably in the course of fish stocking activities. Provided suitable conservation measures are taken, Brandenburg should continue to harbor large populations of this critically endangered species.

Mitochondrial DNA control region variation in an autochthonous Basque population sample from the Basque Country

Mitochondrial control region (16024–576) sequences were generated from 106 samples from autochthonous Basques from the Autonomous Community of the Basque Country. It is especially important to generate mtDNA databases from isolated populations in order to maximize the power of discrimination of this molecular marker. It also represents a useful approach to carry out a more accurate haplogroup classification. This is the first database report of complete control region sequences in an autochthonous Basque population sample. Strict selection criteria of autochthonous individuals, automation of laboratory processing and independent reviews of the raw electropherograms ensure the high quality of these sequences and their utility as reference population data of the autochthonous Basque population.

Population genetic structure, coloration, and morphometrics of yellowhead jawfish Opistognathus aurifrons (Perciformes: Opistognathidae) in the Caribbean region

We investigated intraspecific variability in phenotype and population genetic structure of yellowhead jawfish Opistognathus aurifrons from 4 different locations in the Caribbean region: South Florida (USA), Bimini (Bahamas), St. Thomas (US Virgin Islands), and Aruba. Dis- criminant function analysis (DFA) of 9 melanistic traits in the head region resulted in clear separation between Bimini and the other 3 populations. South Florida, St. Thomas, and Aruba slightly overlapped in patterning, with St. Thomas forming the transition between South Florida and Aruba. DFA of 17 morphometric characters elucidated differentiation among the 4 populations with some overlap between populations. Analysis of concatenated cytochrome c oxidase subunit I (COI) and mitochondrial control region (mtCR) sequences revealed substantial differences among O. aurifrons populations (pairwise ΦST = 0.185�0.566), although there was a lack of reciprocal monophyly. Differences in patterning and morphometrics constituted different phenotypes that predominated in each location, with high levels of genetic differentiation between sampled populations. Bimini was most divergent in phenotype, while Aruba was most divergent in genetics. As such, variations in phenotype and genetics are not congruent for O. aurifrons investigated in this study.

Genetic Structure of Mongolian Gazelle (Procapra gutturosa): The Effect of Railroad and Demographic Change

The Mongolian gazelle (Procapra gutturosa) is a representative ungulate species of Mongolia that inhabits steppes. Their number and range decreased during the last century, and the population has been suffered from occasional demographic changes caused by human and environmental factors. During the summer of 2005, we obtained genetic samples from gazelle carcasses encountered along the international railroad between Russia and China, to examine genetic diversity and its changes in relation to historical demographic shifts. Gazelle genetic structure and diversity were investigated using mitochondrial control region sequence. In the phylogenetic analysis, we confirmed that there are two genetic groups unrelated to geographical location. We also showed the genetic structure of gazelles was unrelated to existence of the railroad. Based on the genetic diversity indices and demographic parameters, the population was suggested to have experienced demographic expansion historically, and effect of known demographic decline was not detected.

Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia

The saltwater crocodile is distributed throughout south-east Asia and Australia. In Australia, it is most abundant in the Northern Territory and Queensland, where it is sustainably farmed for its skins and meat. The aim of this study was to elucidate the relationships and genetic structure among saltwater crocodiles from the Northern Territory of Australia using mitochondrial control region sequences from 61 individuals, representing nine river basins and six of unknown origin, as well as published sequences from other regions. Eight mitochondrial control region haplotypes were identified among both published and novel sequences. Three of the haplotypes appear to be restricted to specimens from northern Australia, with a single haplotype being the most widely dispersed across all river basins. Although Analysis of Molecular Variance provides some support for differentiation among river basins, the frequency of shared haplotypes among these geographical units and median-joining network analysis do not support a clear genetic structure or phylogeographic pattern for saltwater crocodiles in the Northern Territory. The results of this study will assist in furthering our understanding of the genetic diversity of wild saltwater crocodile populations used for ranching in the Northern Territory, as well as providing a framework for assessing the origin of unknown specimens in the future.

Mitochondrial control region sequences of the Czech Republic population and a comparison to other populations

The correct use of mitochondrial DNA (mtDNA) testing in the forensic context requires appropriate population databases to determine the relative rarity of the haplotype of the tested sample. The aim of this study was to evaluate the results of full HVRI and HVRII mtDNA sequences of 255 unrelated individuals and to compare the data to the previously published Czech and European population data The results indicate that the full control region sequencing can bring more precise population information that is useful for the comparison with other data sets and also for the forensic identification purposes.

Resolving the genetic structure of striped marlin,Kajikia audax, in the Pacific Ocean through spatial and temporal sampling of adult and immature fish

Spatial genetic structure in the highly migratory striped marlin ( Kajikia audax ) was examined using nuclear (microsatellite) and mitochondrial (control region sequences) DNA markers. While previous studies on striped marlin were limited by sampling design and sample size, this study employed a multiyear concurrent sampling scheme to collect tissue from seven locations representative of the species’ range in the Pacific: Japan, Hawaii, Southern California, Mexico, Central America, New Zealand, and Australia. Mature and immature specimens were analyzed separately to evaluate life-stage-specific population structure and movements. Microsatellite and sequence results revealed small but significant overall spatial subdivision (FST = 0.0145 and KST = 0.06995, respectively). Pairwise microsatellite analyses (n = 1199) revealed four groups: (1) Japan – Immature Hawaii – Southern California, (2) Mature Hawaii, (3) Mexico – Central America, and (4) Australia – New Zealand. Mitochondrial sequence analysis (n = 451) showed similar patterns; however, no significant differentiation was found between groups 1 and 2. This enhanced resolution of geographic genetic structure is important for understanding the complex migration patterns in this species. Moreover, the consistency among independent genetic studies on striped marlin provides strong support for management of at least three clearly delineated Pacific stocks.

Phylogeography of Anguilla marmorata (Teleostei: Anguilliformes) from the eastern Caroline Islands

Recent analyses of the tropical giant mottled eel Anguilla marmorata have suggested four to six populations within its Indo-Pacific distribution, including one represented by specimens from Guam, and that the population on Guam includes eels occurring in the eastern Caroline Islands based on morphological similarities. To test this hypothesis, sequences of the entire mitochondrial control region (mtCR) were obtained for 39 eels from Kosrae and Pohnpei, and compared to 267 previously sequenced haplotypes from across the Indo-Pacific Ocean. Results support recognition of two lineages distinctive for the eastern Caroline Islands and Guam, and the likelihood of an additional spawning area in the Indo-Pacific Ocean.

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

AbstractAim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor.Location The Indo‐Pacific region.Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences.Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (FST = 0.0174–0.0251, P < 0.05 for microsatellites; ΦST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence.Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.

Population genetic structure of Guizhou snub‐nosed monkeys (Rhinopithecus brelichi) as inferred from mitochondrial control region sequences, and comparison with R. roxellana and R. bieti

The Guizhou snub-nosed monkey (Rhinopithecus brelichi) is a primate species endemic to the Wuling Mountains in southern China. With a maximum of 800 wild animals, the species is endangered and one of the rarest Chinese primates. To assess the genetic diversity within R. brelichi and to analyze its genetic population structure, we collected fecal samples from the wild R. brelichi population and sequenced the hypervariable region I of the mitochondrial control region from 141 individuals. We compared our data with those from the two other Chinese snub-nosed species (R. roxellana, R. bieti) and reconstructed their phylogenetic relationships and divergence times. With only five haplotypes and a maximum of 25 polymorphic sites, R. brelichi shows the lowest genetic diversity in terms of haplotype diversity (h), nucleotide diversity (π), and average number of pairwise nucleotide differences (Π). The most recent common ancestor of R. brelichi lived ∼0.36 million years ago (Ma), thus more recently than those of R. roxellana (∼0.91 Ma) and R. bieti (∼1.33 Ma). Phylogenetic analysis and analysis of molecular variance revealed a clear and significant differentiation among the three Chinese snub-nosed monkey species. Population genetic analyses (Tajima's D, Fu's F(s) , and mismatch distribution) suggest a stable population size for R. brelichi. For the other two species, results point in the same direction, but population substructure possibly introduces some ambiguity. Because of the lower genetic variation, the smaller population size and the more restricted distribution, R. brelichi might be more vulnerable to environmental changes or climate oscillations than the other two Chinese snub-nosed monkey species. Am J Phys Anthropol, 2012. © 2011 Wiley Periodicals, Inc.

Genetic variation at mtDNA and microsatellite loci in Chinese longsnout catfish (Leiocassis longirostris)

Genetic variability and population structure of the Chinese longsnout catfish Leiocassis longirostris Günther in the Yangtze River was examined with mitochondrial control region sequences and nuclear microsatellite markers. A 705-bp segment of the mitochondrial DNA control region was sequenced from 132 samples, which identified a total of 61 haplotypes. The Chinese longsnout catfish in the Yangtze River was characterized with high haplotype diversity (h=0.9770±0.0041) but low nucleotide diversity (π=0.0081±0.0043). Median-joining network analysis revealed a star-shaped pattern and mismatch distribution analysis found a smooth unimodal distribution, which suggested that this species in the Yangtze River underwent a population expansion following bottlenecks and/or they originated from a small size of founding population. It was estimated that the possible time of population expansion was 139,000-435,000years before present, a time period in the middle Pleistocene. The analysis of molecular variance and phylogenetic reconstructions did not detect significant geographic structure between different river sections. This pattern of genetic variation was further evidenced with nuclear microsatellite markers. The genetic differentiation between above and below the Gezhouba Dam and Three Gorges Dam is very small at mitochondrial and nuclear levels, which suggested that these recently developed dams might have not significantly resulted in population genetic fragmentation in the Chinese longsnout catfish. However, the potential exacerbation of genetic structuring by the dams should not be overlooked in the future.

Prisoners in their habitat? Generalist dispersal by habitat specialists: a case study in southern water vole (Arvicola sapidus).

Habitat specialists inhabiting scarce and scattered habitat patches pose interesting questions related to dispersal such as how specialized terrestrial mammals do to colonize distant patches crossing hostile matrices. We assess dispersal patterns of the southern water vole (Arvicola sapidus), a habitat specialist whose habitat patches are distributed through less than 2% of the study area (overall 600 km2) and whose populations form a dynamic metapopulational network. We predict that individuals will require a high ability to move through the inhospitable matrix in order to avoid genetic and demographic isolations. Genotypes (N = 142) for 10 microsatellites and sequences of the whole mitochondrial Control Region (N = 47) from seven localities revealed a weak but significant genetic structure partially explained by geographic distance. None of the landscape models had a significant effect on genetic structure over that of the Euclidean distance alone and no evidence for efficient barriers to dispersal was found. Contemporary gene flow was not severely limited for A. sapidus as shown by high migration rates estimates (>10%) between non-neighbouring areas. Sex-biased dispersal tests did not support differences in dispersal rates, as shown by similar average axial parent-offspring distances, in close agreement with capture-mark-recapture estimates. As predicted, our results do not support any preferences of the species for specific landscape attributes on their dispersal pathways. Here, we combine field and molecular data to illustrate how a habitat specialist mammal might disperse like a habitat generalist, acquiring specific long-distance dispersal strategies as an adaptation to patchy, naturally fragmented, heterogeneous and unstable habitats.

Taxonomic recommendations for British birds: seventh report

Taxonomic recommendations for British birds: seventh report