Mitochondrial DNA Control Region Sequences Research Articles

Mitochondrial DNA Profiling to Combat the Illegal Trade in Tortoiseshell Products

Hawksbill turtles (Eretmochelys imbricata) are exploited for their beautiful shell known as tortoiseshell or bekko, making them extremely vulnerable in the illegal global trade of tortoiseshell products. In this study, we developed an effective, standardized method using a commercially available kit to extract DNA and obtain informative mitochondrial DNA (mtDNA) control region sequences (~800 bp) from hawksbill turtle products in order to trace the sample back to a likely stock origin. We also sequenced additional skin samples from nesting beaches of Milman Island, Australia and Arnavon Island, Solomon Islands to add to the baseline data for hawksbill turtles in the Indo-Pacific. Our results indicate that nine of the 13 tortoiseshell products obtained from Papua New Guinea and Solomon Islands were from turtles with haplotypes found primarily at the Solomon Islands rookery and did not match those from nesting populations in Australia or SE Asia, with the exception of one haplotype also found in 3% of turtles at Milman Island. We also found that 23% of the market samples have haplotypes only documented in foraging populations, which illustrates the urgent need for more extensive sampling of rookeries to fill gaps in the reference baseline database. Nevertheless, our study results demonstrate an effective methodology for obtaining DNA of sufficient quantity and quality from hawksbill turtle products.

West Asian colonisation of topmouth gudgeon, Pseudorasbora parva (Teleostei: Gobionidae): Genetic admixture at the crossroad of Europe and east Asia

Abstract Iran is a major freshwater fish diversity hotspot in the Middle East, and is an important zoogeographical area in west Asia, acting as the crossroads and dispersal corridor between several major biogeographical realms of the world. The topmouth gudgeon, Pseudorasbora parva was first recorded in Iran on 6 May 1991 in the Caspian Sea basin and is now widely distributed across the country. Despite widespread distribution in the Iranian inland waters, its invasion history and genetic background remain unknown. Here, based on the mitochondrial DNA control region (806 bp) sequence variation of 161 P. parva samples collected from 15 Iranian localities and additional sites in Europe and Asia, as well as a cytochrome c oxidase subunit I barcode database (615 bp) including 166 novel and archived sequences, we characterised the pattern of genetic diversity and its colonisation history in Iran. Our results show the presence of three matrilineal haplotypes in Iran belonging to two distinct lineages: (1) a widespread lineage with a common haplotype found throughout the country and one exclusive haplotype confined to the Mashkid basin, whose origin can be traced back to a single introduction of a small number of propagules from Japan and corresponded to the Iranian introduction of P. parva in the late 1980s; (2) a Chinese lineage represented by a single haplotype found in the Shafarood River of the Caspian Sea basin but also translocated to central Iran, penetrated recently to northern Iran through natural dispersal from Azerbaijan as an extension of the European wave of invasion. At the global scale, there is less genetic diversity in west Asia than in Europe and the Asian native range. At the local scale, estimates of genetic diversity in Iranian P. parva populations are extremely low but the Caspian Sea and Esfahan basins gained higher diversities from admixture of highly divergent Japanese and Chinese lineages. Our phylogenetic and species delimitation analyses also suggest the existence of multiple putative species in the native range of P. parva and stress the need of an integrative taxonomical approach based on additional morphological and nuclear DNA data.

Genetic population structure of the fiddler crab <i>Austruca lactea</i> (De Haan, 1835) based on mitochondrial DNA control region sequences

Genetic population structure of the fiddler crab <i>Austruca lactea</i> (De Haan, 1835) based on mitochondrial DNA control region sequences

Phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) in relation to the tectonic events and Quaternary climatic oscillations in the Shaluli Mountains Region

The tectonic events and Quaternary climatic oscillations in the Shaluli Mountains (the margin of the southeastern Tibetan Plateau) had an extensive effect on the genetic structure and distribution patterns of this region’s terrestrial fauna and flora. It is not yet clear whether similar mechanisms influence this region’s fish fauna. Schizopygopsis malacanthus is limited to high-elevation rivers and lakes, and exhibits distinct adaptations to the mountains of, and near to, the Qinghai-Tibet Plateau (QTP). Therefore, this species is a good candidate for investigating patterns of genetic variation resulting from palaeoenvironmental fluctuations in the Shaluli Mountains (China). Here, we used microsatellite and mitochondrial DNA control region sequences to analyze six populations of S. malacanthus collected from the Jinsha and Yalong River drainages. Genealogical analyses identified four maternal lineages and perhaps even four putative species, of which the Ouqu River lineage played a pivotal role during the course of the species’ evolution. Two lineages from the Yalong River drainage did not cluster together, whereas those from different drainages grouped together, suggesting tectonic event impacts that possibly altered regional river drainages have been highly influential in population connectivity and gene flow. Population genetic analysis indicated that the geographic barriers and this species preference for higher elevations both played key roles in the divergence of S. malacanthus populations. Demographic tests suggested large-scale spatial synchrony in population fluctuations of S. malacanthus, accompanying dramatic Pleistocene climatic oscillations. It appears that palaeoenvironmental changes in the Shaluli Mountains influenced the distribution and evolution of studied S. malacanthus populations, which provide important information about the factors that influenced the phylogeographic history of this region’s fish fauna. Additionally, our study also has implications for ongoing conservation of this vulnerable fish.

Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan.

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782±0.079 to 0.982±0.015 and from 0.028±0.003 to 0.043±0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

Structure Analysis of Mitochondrial DNA Control Region Sequences and its Applications for the Study of Population Genetic Diversity of Acanthogobius ommaturus

Acanthogobius ommaturus, which belongs to the family Gobiidae, is a euryhaline, demersal fish widely distributed in coastal areas, harbors, and estuaries of China, the Korean Peninsula, and Japan. A genetic analysis based on identification of the structure of mitochondrial DNA control region was carried out in the present study. As a result, the conservative structure, including termination sequence region, central conservative region CSB-E and CSB-D, as well as conservative sequence region CSB-1, CSB-2, and CSB-3, was determined. A total of 32 polymorphic sites were identified and 33 haplotypes were defined, of which only 9 were shared haplotypes. A high level of haplotype diversity (h = 0.923 ± 0.018) and low nucleotide diversity (π = 0.003 ± 0.002) were detected. In general, the genetic differentiation among ten populations was at a medium level. There was a distinct single peak in the nucleotide mismatch distribution, which confirms that A. ommaturus populations have experienced recent expansion. In this study, the control region structure of A. ommaturus was similar to that of most marine fishes; however, the tandem repeat sequence and the CSB-F sequence were not detected. In addition, most of the genetic variation in the control region occurred in the high-variation region.

Phylogenetic analysis of marginal Asiatic black bears reveals a recent Iranian\u2013Himalayan divergence and has implications for taxonomy and conservation

A small population of Asiatic black bear—known as the Baluchistan black bear—survives in the western limit of the species’ range in Iran, where the species is rare, difficult to monitor and occupy an atypical habitat with extreme environmental conditions. Through the use of noninvasively collected samples, we analyzed mitochondrial DNA control region sequences to evaluate the phylogenetic relationships and divergence time between the Baluchistan Iranian black bear population and other Asian populations. Phylogenetic analyses indicate that Baluchistan and Nepalese (Himalayan) populations are monophyletic, with their divergence time estimated at circa 120 thousand years ago. The results reveal the low level of mitochondrial DNA variability in this small and marginal population, as is the case for many bear populations living in areas with similar conditions. The divergence time between the populations from Iran and Nepal dates to the Late Pleistocene, pointing to a transitional period between colder (glacial) and warmer (interglacial) conditions that allowed forests to expand and opened new habitats to population expansions. Pending further genetic and morphological corroboration, these preliminary results suggest that all Baluchistan and Himalayan (Nepalese) black bears might be considered as synonymous under the prior U. t. thibetanus trinomial (with gedrosianus just as junior synonym). Conservation efforts on this small and endangered population remain poor, and further measures are required to guarantee its long-term survival in Iran.

Mitochondrial DNA variation in the Italian Heavy Draught Horse.

BackgroundIn the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.MethodologyTo provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.ResultsAmong the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.

Genetic integrity and individual identification-based population size estimate of the endangered long-tailed goral, Naemorhedus caudatus from Seoraksan National Park in South Korea, based on a non-invasive genetic approach

ABSTRACT The long-tailed goral (also called the Amur goral) Naemorhedus caudatus (subfamily Caprinae), a vulnerable and protected species designated by IUCN and CITES, has sharply been declining in the population size and is now becoming critically endangered in South Korea. This species has been conserved as a natural monument by the Korean Cultural Heritage Administration since 1968. In this study, using 78 fecal DNA samples with a non-invasive genetic approach, we assessed the genetic integrity and individual identification-based population size for the goral population from Seoraksan National Park representing the largest wild population in Korea. Using the successfully isolated 38 fecal DNA, phylogeographic and population genetic analyses were performed with mitochondrial DNA control region (CR) sequences and nine microsatellite loci. We found seven CR haplotypes, of which five were unique to the Seoraksan population, considering previously determined haplotypes in Korean populations. The Seoraksan population showed higher haplotype diversity (0.777 ± 0.062) and mean number of alleles (4.67 ± 1.563) relative to southern populations in Korea reported from previous studies, with no signal of a population bottleneck. Microsatellite-based individual identification estimate based on probability of identity (PID) indicated a population size of ≥30 in this population. Altogether, we suggest that for future management efforts of this species in the Seoraksan National Park, conserving its genetic integrity as an ‘endemic’ lineage, and curbing a decrease in its number through mitigating habitat destruction might be key to secure the population for the long term.

Mitochondrial DNA control region variation in a population sample from Thailand

Mitochondrial DNA (mtDNA) control region sequences from hair samples of 213 individuals from Thailand were analyzed using Sanger sequencing. A total of 170 different haplotypes were identified, of which 146 occurred only once (unique haplotypes). The dataset showed a random match probability of 0.87% and a haplotype diversity of 0.9960. The samples were assigned to 85 different haplogroups with B5a, F1a1a, and M being the most frequent ones. Pairwise FST-values between this and other Southeast and East Asian populations revealed significant but relatively low differences, indicating a close relation. Heteroplasmic positions were observed in 12.2% of hair samples confirming the frequent appearance of heteroplasmic positions in hairs. This dataset will complement existing data as an mtDNA reference for forensic investigations.

A Genetic Assessment of Missouri's Lake Sturgeon after 30 Years of Restoration Releases

AbstractThe Lake Sturgeon Acipenser fulvescens is native to three major watersheds in the USA: the Great Lakes, Hudson Bay, and Mississippi River drainages. However, they have declined across much of their range due to overfishing, pollution, and major river alterations. After their near extirpation in Missouri, the Missouri Department of Conservation initiated a reintroduction program to restore the Lake Sturgeon in the state's largest waterways. From 1984 to 2015, offspring originating from Lake Winnebago (1984–2001) and from upper Mississippi River tributaries (2004–2015) were reared in captivity and released into portions of the Mississippi and Missouri rivers. After 32 years of restorative releases, we screened Lake Sturgeon samples from the state of Missouri by using 11 microsatellite loci and mitochondrial DNA control region sequences. We examined overall genetic diversity and genetic structure of Lake Sturgeon captured in the Mississippi and Missouri rivers for differences between rivers and among groups within rivers. We found high levels of genetic diversity within both rivers, with very little genetic differentiation between them. Higher‐than‐average relatedness within sample groups and heterozygote excess were consistent with the pattern expected from stocked fish and suggested that closely related fish may have aggregated at stocking sites. We detected two genetic groups in Missouri, reflecting the change in stock source. Haplotypes that may be unique to the Mississippi and Ohio River systems were observed at very low frequencies. Though largely the product of stocking, reproductively mature Lake Sturgeon will likely have sufficient genetic diversity and will have experienced selection pressures in Missouri's large rivers, making them the most appropriate source for further supplementation if it is deemed necessary. We recommend continued research and monitoring of reproductive habits and preservation of multiple spawning sites to continue the long path toward a self‐sustaining Lake Sturgeon population in Missouri's waters.

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.

Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

AbstractAimDetermine the evolutionary origin of the heretofore poorly characterized contemporary Great White Shark (GWS; Carcharodon carcharias) of the Mediterranean Sea, using phylogenetic and dispersal vicariance analyses to trace back its global palaeo‐migration pattern.LocationMediterranean Sea.TaxonCarcharodon carcharias.MethodsWe have built the largest mitochondrial DNA control region (CR) sequence dataset for the Mediterranean GWS from referenced historical jaws spanning the 19th and 20th centuries. Mediterranean and global GWS CR sequences were analysed for genetic diversity, phylogenetic relationships and divergence time. A Bayes factor approach was used to assess two scenarios of GWS lineage divergence and emergence of the Mediterranean GWS line using fossil records and palaeo‐geographical events for calibration of the molecular clock.ResultsThe results confirmed a closer evolutionary relationship between Mediterranean GWS and populations from Australia–New Zealand and the North‐eastern Pacific coast rather than populations from South African and North‐western Atlantic. The Mediterranean GWS lineage showed the lowest genetic diversity at the global level, indicating its recent evolutionary origin. An evaluation of various divergence scenarios determined the Mediterranean GWS lineage most likely appeared some 3.23 million years ago by way dispersal/vicariance from Australian/Pacific palaeo‐populations.Main conclusionBased on the fossil records, phylogeographic patterns and divergence time, we revealed that the Mediterranean GWS population originated in the Pliocene following the Messinian Salinity Crisis. Colonization of the Mediterranean by GWS likely occurred via an eastward palaeo‐migration of Australian/eastern Pacific elements through the Central American Seaway, before the complete closure of the Isthmus of Panama. This Pliocene origin scenario contrasts with a previously proposed scenario in which Australian GWS colonized the Mediterranean via antipodean northward migration resulting from navigational errors from South Africa during Quaternary climatic oscillations.

Evidence for divergence between sympatric stone charr and Dolly Varden along unique environmental gradients in Kamchatka

Here, we describe the biological and ecological differences between partially anadromous Dolly Varden and riverine stone charr distributed in the Kamchatka River middle course. Endemic stone charr, being the ambush predator, is defined by the accelerated growth and prolonged lifespan, robust body, and large mouth, as well as specific marble coloration since an early age. The significant restriction in gene flow between the stone charr and benthos-eating Dolly Varden was supported by an allelic distribution of eight microsatellite loci. Herewith, the identity of mitochondrial DNA control region and intron sequences of growth hormone and metallothionein genes confirms a relatively recent diversification of the groups within the single basin. We suggest the key role of the specific environment for reproduction isolation of stone charr. It occupies coniferous taiga zone with dark-colored water, whereas Dolly Varden spawns uppercourse in the zone of stunted, windblown forest. Conifer litter decomposition products could drive natural selection of stone charr via metabolism acceleration and resistance to toxicants. The metabolic difference could promote piscivory and development of the specific morphological peculiarities of the stone charr. Therefore, we present the first evidence in favor of trophic-based sympatric diversification in a river basin at high latitudes.

Genetic structure and population dynamics of the silver pheasant (Lophuranycthemera) in southern China

In southern China, the silver pheasant (Lophura nycthemera) is a widespread species due to complex topography and sufficient habitats and food resources. We investigated the microsatellite and mitochondrial DNA control region sequence of 115 individuals from 7 locations in China to study population dynamics of the silver pheasant during the Pleistocene. The neutrality test and mismatch distribution analyses showed that population expansion began in the interglacial period (76,053 years ago), and the latest common ancestor appeared approximately 970,300 years ago. Most populations exhibited a high level of genetic diversity as well as gene flow. Results of phylogenetic trees and network and STRUCTURE analyses provided insights into the weak population structure of this species. The weak phylogeographic and complex historical expansion population of the silver pheasant during the interglacial period could probably be related to its complex topography and the sufficient amount of suitable habitats and food resources in southern China.

Identification of a novel hybrid zone within the black-footed rock-wallaby (

It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.

The mitochondrial DNA control region sequences from the Chinese Miao population of southeastern China

Background: Miao people are an officially recognised ethnic group living in southwest China, but have seldom been studied genetically, especially with respect to mtDNA data.Aim: To investigate the sequences and haplogroups of the mtDNA control region in a typical Miao population, with the aim of providing a good start for the expansion of the East Asian mtDNA reference database for forensic DNA analysis.Subjects and methods: We analysed 203 Miao individuals, looking at mtDNA control region sequences. We calculated and illustrated the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Miao and six other worldwide populations to explore genetic polymorphisms and population relationships.Results: We observed 121 haplotypes with corresponding frequencies ranging from 0.0049 to 0.0690 in the Miao population. All the samples were assigned to 71 different haplogroups. The haplotype diversity and the random match probability were estimated to be 0.9844 and 0.0204, respectively. The pairwise Fst values and associated p values among seven populations suggest that the Miao population has significant differences to the other six populations, and is relatively isolated compared with them.Conclusions: Our results suggest that frequency estimates for mtDNA haplotypes in Miao ethnic groups should be determined independently rather than being pooled with other populations.

Distinct Patterns of Genetic Connectivity Found for Two Frugivorous Bat Species in Mesoamerica

Sturnira parvidens and Sturnira hondurensis are two frugivorous bat species distributed throughout the Mesoamerican region. Sturnira parvidens inhabits tropical lowland forests and S. hondurensis montane cloud forests. Their populations are respectively separated by the intervening highlands or lowlands. We used mitochondrial DNA control region sequences to compare genetic structure among the populations of these two species in the region of the Gulf of Mexico. We also measured genetic connectivity among their populations and assessed the distribution model for each species. We found high genetic diversity in both species: the FST comparisons values were low to high in S. hondurensis and low in S. parvidens. For S. hondurensis, we found isolation by landscape resistance (IBR) where the highland habitat heterogeneity may have restricted gene flow among the populations of the Sierra Madre Oriental, Sierra de Los Tuxtlas, Chiapas and Guatemala. For S. parvidens, the isolation is explained by geographic distance rather than by landscape heterogeneity.

Genetic landscape of the mitochondrial DNA control region in South African populations

A high-quality dataset of the mitochondrial DNA control region sequences was generated with Sanger and next-generation sequencing. The study was aimed at characterizing the maternal genetic ancestry and analyzing the haplogroup distribution of 246 individuals residing in South Africa. The study presents mtDNA sequences in South Africa for forensic applications.

Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales

The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89–1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.