Mitochondrial Control Region Sequences Research Articles

A Recent Stranding of Omura’s Whale (Balaenoptera omurai) in Western Australia

Omura's whale ( Balaenoptera omurai ), described in 2003, is a putatively rare rorqual species known mostly from waters in the lower latitudes of the Indo-Pacific. A small (5.68 m) baleen whale that stranded near Exmouth on the northwestern coast of Australia in March 2015 was initially thought to be a small Omura's whale (although unknown for the area) or a Bryde's whale ( B. brydei ). Morphological assessment showed the whale had a strongly falcate, steeply angled dorsal fin characteristic of Omura's whale and a slightly prominent single median ridge but was smaller in size than was typical for Omura's whale. Phylogenetic analysis of mitochondrial control region sequences from the whale against other reference baleen species showed our specimen nested within sequences from Omura's whale with high bootstrap support and was clearly separate from sequences of Bryde's whale, thus confirming the limited morphological identification of the specimen as Omura's whale. The carcass was in good condition with no obvious signs of trauma, and assessment revealed the animal was recently deceased. Lack of decomposition and no injury suggested it was likely to have been alive at the time of stranding and to have been occupying inshore waters prior to being washed ashore. Confirmation of an Omura's whale in Western Australian waters extends knowledge of its distribution southwards in the eastern Indian Ocean, suggesting further survey in these waters may provide more information on this poorly known species.

Genetic variation of mitochondrial sequence-hv2 in Vietnamese populations

HV1 and HV2, which located in control D-loop region of mitochondrial, are the hyper-variable parts of mitochondrial DNA (mtDNA). Therefore, these two sequences were often used for evolutional and forensic science. In order to determine the genetic variation of populations belong to Nam-A and Nam-Dao language systems, we sequenced and analyzed the mtDNA HV2 region of individuals from four ethic groups: Kinh, Muong, Ede and Jarai which represent for those language systems. Study subjects are peripheral blood of 169 individuals belonging to four populations: Kinh, Muong, Ede and Jarai. HV2 regions were sequenced by Sanger sequencing. As a result, the analyzed mitochondrial control region sequences could be assigned to 79 different haplogroups, with the dominant proportion of three haplogroups: R, B and F. Donors representing Kinh or Muong population revealed higher haplogroup composition variation in comparison with those affiliated with Jarai or Ede. In addition, it was indicated that the 4 populations shared the genetic analogy with other populations inhabited in Southeast Asia and South Asia.

Redrawing the map: mtDNA provides new insight into the distribution and diversity of short‐finned pilot whales in the Pacific Ocean

AbstractCorrelations between morphological and genetic data provide evidence to delineate species or evolutionarily significant units, which then become the units to conserve in management plans. Here, we examine the distribution and genetic differentiation of two morphotypes of short‐finned pilot whale (Globicephala macrorhynchus) in the Pacific Ocean. Mitochondrial control region sequences from 333 samples were combined with 152 previously published sequences to describe genetic variability globally and population structure in the Pacific. Although genetic variability is low, we found strong differentiation at both broad and local levels across the Pacific. Based on genetics, two types are distributed throughout the Pacific, one predominantly in the eastern Pacific and the other in the western and central Pacific. In the eastern Pacific Ocean, no correlation was found between distribution and sea surface temperature. The two types have broad latitudinal ranges, suggesting their distributions are likely driven by more complex factors, such as prey distribution, rather than sea surface temperature.

Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir

The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.

Identification of wild tilapia species in the main rivers of south China using mitochondrial control region sequence and morphology

Tilapias are now the most common alien fish in the rivers of South China and the dominant species in many sites. However, wild tilapia species have not been well-characterized or studied systematically. In this study, mitochondrial DNA control regions (mtDNA CR) and morphological characteristics were used to identify invasive tilapia species. Using mtDNA CR sequence, we identified Oreochromis niloticus, Tilapia zillii, Oreochromis aureus, Sarotherodon galilaeus, and hybrids of Oreochromis mossambicus and O. niloticus in the rivers of South China, and characterized their morphological features. Of the 5 species, O. niloticus and T. zillii were the most abundant in the rivers of South China. Furthermore, the distribution of O. niloticus may be related to their large numbers in the aquaculture industry, and the explosion of T. zillii invasion may be related to their strong capacity for environmental adaptation. These findings are beneficial for identifying wild tilapia populations and for the specific control of invasive tilapia species.

Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera)

Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus.

Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations.

Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA, all individuals were assigned to their respective species with >0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3 and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011-0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.

High genetic variability of vagrant polar bears illustrates importance of population connectivity in fragmented sea ice habitats

Projections by the Intergovernmental Panel on Climate Change (IPCC) and sea ice forecasts suggest that Arctic sea ice will decline markedly in coming decades. Expected effects on the entire ecosystem include a contraction of suitable polar bear habitat into one or few refugia. Such large-scale habitat decline and fragmentation could lead to reduced genetic diversity. Here we compare genetic variability of four vagrant polar bears that reached Iceland with that in recognized subpopulations from across the range, examining 23 autosomal microsatellites, mitochondrial control region sequences and Y-chromosomal markers. The vagrants' genotypes grouped with different genetic clusters and showed similar genetic variability at autosomal microsatellites (expected heterozygosity, allelic richness, and individual heterozygosity) as individuals in recognized subpopulations. Each vagrant carried a different mitochondrial haplotype. A likely route for polar bears to reach Iceland is via Fram Strait, a major gateway for the physical exportation of sea ice from the Arctic basin. Vagrant polar bears on Iceland likely originated from more than one recognized subpopulation, and may have been caught in sea ice export during long-distance movements to the East Greenland area. Although their potentially diverse geographic origins might suggest that these vagrants encompass much higher genetic variability than vagrants or dispersers in other regions, the four Icelandic vagrants encompassed similar genetic variability as any four randomly picked individuals from a single subpopulation or from the entire sample. We suggest that this is a consequence of the low overall genetic variability and weak range-wide genetic structuring of polar bears – few dispersers can represent a large portion of the species' gene pool. As predicted by theory and our demographic simulations, continued gene flow will be necessary to counteract loss of genetic variability in increasingly fragmented Arctic habitats. Similar considerations will be important in the management of other taxa that utilize sea ice habitats.

Phylogeography of the common pandora Pagellus erythrinus in the central Mediterranean Sea: sympatric mitochondrial lineages and genetic homogeneity

ABSTRACTThe distribution of the genetic diversity and the population structure of Pagellus erythrinus were analysed using mitochondrial control region sequences and cytochrome b restriction profiles in a total of 128 and 508 individuals, respectively, that were collected from 15 sampling sites in the central Mediterranean Sea and from one site in the Atlantic Ocean. No population genetic structure was detected within the central Mediterranean and thus, the commonly recognized transition zones in the area do not seem to affect population connectivity. The comparison between the Mediterranean samples and the single Atlantic sample suggests weak differentiation between the two basins. Three mitochondrial lineages were identified, each including individuals from almost every sampling site. The haplotype and nucleotide diversity values, mismatch distribution and demographic parameters indicate that the sympatry of these lineages can be ascribed to a period of isolation followed by genetic divergence, population expansion and secondary contact, all of which are likely to be associated with climatic oscillations that occurred during the middle and late Pleistocene.

Population genetic structure of the European conger (Conger conger) in North East Atlantic and West Mediterranean Sea

Assessment of population genetic structure is crucial in species conservation and stock management. The use of multiple markers is recommended to obtain accurate studies. In this study, a panel of five microsatellite loci described for Conger myriaster was optimized for the European conger eel Conger conger. These are the first hypervariable nuclear loci employed for C. conger population study and have a high discrimination power. A total of 67 alleles were observed for Atlantic and Mediterranean samples with an average number of alleles per locus of 13.4 (range 4–24). Variation at these microsatellite loci was combined with mitochondrial control region sequences (395bp) to explore genetic structure of C. conger across the Cantabrian Sea (North East Atlantic ocean) and the West Mediterranean Sea. Overall, there is not total isolation between the Atlantic and the Mediterranean stocks, as previously suggested in other studies, but a subtle differentiation. Cross-species amplification of microsatellite loci in C. conger is hoped to encourage further population studies of this species and the development of new nuclear markers in order to provide scientific advice for the stock management.

Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya.

Phylogenetic relationships among and genetic variability within 60 goats from two different indigenous breeds in Narok and Isiolo counties in Kenya and 22 published goat samples were analysed using mitochondrial control region sequences. The results showed that there were 54 polymorphic sites in a 481-bp sequence and 29 haplotypes were determined. The mean haplotype diversity and nucleotide diversity were 0.981±0.006 and 0.019±0.001, respectively. The phylogenetic analysis in combination with goat haplogroup reference sequences from GenBank showed that all goat sequences were clustered into two haplogroups (A and G), of which haplogroup A was the commonest in the two populations. A very high percentage (99.90%) of the genetic variation was distributed within the regions, and a smaller percentage (0.10%) distributed among regions as revealed by the analysis of molecular variance (amova). This amova results showed that the divergence between regions was not statistically significant. We concluded that the high levels of intrapopulation diversity in Isiolo and Narok goats and the weak phylogeographic structuring suggested that there existed strong gene flow among goat populations probably caused by extensive transportation of goats in history.

Complete Mitochondrial Genomes of New Zealand's First Dogs.

Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia.

Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the Adriatic Sea.

Population histories depend on the interplay between exogeneous and endogeneous factors. In marine species, phylogeographic and demographic patterns are often shaped by sea level fluctuations, water currents and dispersal ability. Using mitochondrial control region sequences (n = 120), we infer phylogeographic structure and historic population size changes of a common littoral fish species, the black‐faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the north‐eastern Adriatic Sea. We find that Adriatic T. delaisi are differentiated from conspecific populations in the remaining Mediterranean, but display little phylogeographic structure within the Adriatic basin. The pattern is consistent with passive dispersal of planktonic larvae along cyclonic currents within the Adriatic Sea, but limited active dispersal of adults. Demographic reconstructions are consistent with recent population expansion, probably triggered by rising sea levels after the last glacial maximum (LGM). Placing the onset of population growth between the LGM and the warming of surface waters (18 000–13 000 years BP) and employing a novel expansion dating approach, we inferred a substitution rate of 2.61–3.61% per site per MY. Our study is one of only few existing investigations of the genetic structure of animals within the Adriatic basin and is the first to provide an estimate for mitochondrial control region substitution rates in blennioid fishes.

Molecular taxonomy and population structure of the rough-toothed dolphinSteno bredanensis(Cetartiodactyla: Delphinidae)

Several delphinid species have shown genetic population structure, both between and within ocean basins. We investigated genetic differentiation in the rough-toothed dolphin, Steno bredanensis, using mitochondrial control region sequences from several localities worldwide (N = 112). Preliminary analyses indicated high levels of genetic differentiation between the Atlantic and Pacific/Indian Oceans, which were further investigated using complete cytochrome b sequences and mitogenomes. Phylogenetic analyses were inconclusive about the existence of cryptic speciation in the genus Steno. Notwithstanding this result, analysis of molecular variance and Φ-statistics analyses revealed strong population differentiation not only between the Atlantic and Pacific, but also within the Atlantic, where three populations were detected: Caribbean, southeastern Brazil, and southern Brazil. We propose that these populations be considered management units for conservation purposes. Our results provide the first perspective on the worldwide genetic differentiation of S. bredanensis. © 2015 The Linnean Society of London

Developing a genetic baseline for the yellowtail amberjack species complex, Seriola lalandi sensu lato, to assess and preserve variation in wild populations of these globally important aquaculture species

Recent study suggest the globally distributed yellowtail amberjack, Seriola lalandi sensu lato, is a complex of three closely related species. Together, these and three other species of Seriola comprise an important component of global aquaculture production with an estimated annual value of $1.3 billion. As yellowtail aquaculture grows, the impact of unintentional releases on wild populations has become an increasingly important issue, particularly in light of international trade of hatchery seed. To create a genetic baseline, we examined spatial genetic structure in 260 specimens collected from seven locations over a wide geographical range using 15 nuclear microsatellites and mitochondrial control region sequences. Overall genetic differentiation among locations, as revealed by microsatellite data, was highly significant (FST = 0.085, DEST = 0.382, P < 0.001), and pairwise estimates of divergence derived from mitochondrial and microsatellite data support the presence of four significantly differentiated populations corresponding to the N.E. Pacific, N.W. Pacific, S. Pacific, and South Atlantic. Based on the genetic differentiation detected in this study, and recently published sequence data, these populations more accurately reflect the presence of at least three cryptic species of Seriola. Especially strong genetic differentiation between hemispheres indicates that the equatorial region is a significant dispersal barrier for yellowtail. This study represents the broadest geographic investigation of genetic population structure conducted, to date, for specimens of the S. lalandi complex.

Mitogenomic variation of Bangladesh Penaeus monodon (Decapoda, Panaeidae) and reassessment of its phylogeography in the Indo-West Pacific region

Large variation in the mtDNA control region (CR) in Penaeus monodon has been reported from the Indo-West Pacific region, characterizing three distinct lineages, A, B and C. This diversification has been explained by geographic barriers but may also be due to paralogous duplication events. Here we evaluate the diversity, origin and population patterns of this species in Bangladesh based on mtDNA, and reconsider the evidence for paralogous duplication. MtDNA variation revealed high diversity with almost all individuals carrying a unique haplotype, indicating a large effective population size and a single reproductive pool. The Bangladesh haplotypes cluster within lineage C, found mainly west of the Sunda Shelf. This lineage, which diverged from lineages A and B around 6.6 Mya, has diverged further into several lineages in the western Indian Ocean. Sequences of mitochondrial CR, 16S rRNA gene and a combined fragment of the 16S rRNA and tRNAVal genes from Bangladesh did not reveal any duplication or heteroplasmy. Further, phylogenies based on the three markers, including samples from different areas in the Indo-West Pacific region, support the occurrence of three distinct lineages. Thus, the variation in CR appears to result from segregation of orthologous variants rather than diversification following a paralogous duplication.

Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii) in China from Mitochondrial Control Region and Nuclear Intron Sequences.

Identifying the dispersal pathways of an invasive species is useful for adopting the appropriate strategies to prevent and control its spread. However, these processes are exceedingly complex. So, it is necessary to apply new technology and collect representative samples for analysis. This study used Approximate Bayesian Computation (ABC) in combination with traditional genetic tools to examine extensive sample data and historical records to infer the invasion history of the red swamp crayfish, Procambarus clarkii, in China. The sequences of the mitochondrial control region and the proPOx intron in the nuclear genome of samples from 37 sites (35 in China and one each in Japan and the USA) were analyzed. The results of combined scenarios testing and historical records revealed a much more complex invasion history in China than previously believed. P. clarkii was most likely originally introduced into China from Japan from an unsampled source, and the species then expanded its range primarily into the middle and lower reaches and, to a lesser extent, into the upper reaches of the Changjiang River in China. No transfer was observed from the upper reaches to the middle and lower reaches of the Changjiang River. Human-mediated jump dispersal was an important dispersal pathway for P. clarkii. The results provide a better understanding of the evolutionary scenarios involved in the rapid invasion of P. clarkii in China.

Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data

The large yellow croaker Larimichthys crocea is an important commercial marine fish species in China. However, information about the population structure of this species is limited. In the present study, mitochondrial DNA (mtDNA) control region was sequenced from four populations of the yellow croaker in the southern Yellow Sea, East China Sea and South China Sea to investigate the genetic structure of this species. A total of 54 haplotypes were detected among 62 individuals of large yellow croaker. High levels of population genetic diversity were observed. Among the four populations, the haplotype diversity was between 0.9895 ± 0.0193 (Xiamen) and 1.0000 ± 0.0524 (Lvsi, Zhoushan). The nucleotide diversity ranged from 0.0208 ± 0.0108 (Xuwen) to 0.0246 ± 0.0138 (Lvsi). The results of AMOVA detected no significant differences among populations. The conventional FST statistics were negative and insignificant values. These indicated lack of population genetic structure throughout the Yellow Sea, East China Sea and South China Sea, and random mixing of individuals among the samples. Biological characters of large yellow croaker and lack of physical barrier in the studied area could be the reasons for lack of genetic structure in this species.

Comparative pattern of genetic structure in two Mediterranean killifishes Aphanius fasciatus and Aphanius iberus inferred from both mitochondrial and nuclear data.

In this study, genetic variation was assessed in Aphanius fasciatus and Aphanius iberus characterized by similar ecological traits but with very different distribution ranges in the Mediterranean area. Five populations of A. iberus and five of A. fasciatus were analysed using five polymorphic microsatellite loci and partial mitochondrial control region (D-loop) sequences. Congruent results were found with both nuclear and mitochondrial molecular markers. The results showed that similar levels of genetic divergence, based on mitochondrial control region sequences, are present among populations of A. iberus and among populations of A. fasciatus despite the very different geographic distance existing among the examined populations of the two species (low geographic distance in A. iberus and high in A. fasciatus). A possible explanation could be that the populations of A. iberus were isolated for a longer time than the populations of A. fasciatus supporting the hypothesis that the split in the lineage leading to A. iberus is older than the split in the lineage leading to A. fasciatus. The possibility that the wide circum-Mediterranean distribution of A. fasciatus ensures the high connectivity of its populations, preventing, in some cases, local differentiation, however, cannot be ruled out.

Fish species substitution and misnaming in South Africa: An economic, safety and sustainability conundrum revisited

While fish species mislabelling has emerged as a global problem, the tracking of improvements or deteriorations in seafood trading practices is challenging without a consistent basis for monitoring. The aim of this study was to develop a robust, repeatable species authentication protocol that could be used to benchmark the current and future incidences of fish mislabelling in South Africa. Using this approach, 149 fish samples collected from restaurants and retailers in three provinces (KwaZulu-Natal, Western Cape and Gauteng) were identified using DNA barcoding, supplemented in certain cases with mitochondrial control region sequencing. Overall, 18% of samples were incorrectly described in terms of species, with similar misrepresentation rates in restaurants (18%) and retail outlets (19%). While there appears to be some improvement in the transparency of local seafood marketing compared to previous studies, the results remain of concern and signal the need for enhanced seafood labelling regulations, monitoring and law enforcement.