mtDNA Haplotype Network Research Articles

Genetic variation of European mouflon depends on admixture of introduced individuals

In the early twentieth century, European mouflon was introduced in Croatia, while all introductions in Slovenia occurred in the 1950s and 1960s. Although majority of the introductions were historically documented, occasional cases involving individuals of unknown origin have likely contributed to a mixed genetic pool in established colonies. To understand the impact of past management and the potential founder effects on contemporary mouflon populations, we performed the first genetic study of the species in these two countries. Utilising next-generation sequencing of both mitochondrial control region (mtDNA CR) and major histocompatibility complex (MHC DRB exon 2), our study scrutinises the genetic diversity and structure of these populations. Additionally, the origins and genetic variability of mouflon in Croatia and Slovenia were compared with reference samples from Czech Republic, Sardinia (Italy), and Corsica (France). The mtDNA haplotype network showed that the majority of mouflon from Slovenia are closely related to mouflon from Sardinia, and only few shared the same haplotypes with mouflon from Croatia. Some mouflon from mainland Croatia share identical or closely related haplotypes with individuals from the initially established population in this country (on the Brijuni Archipelago), while others belong to a distinctly different cluster. We found five MHC alleles previously reported for mouflon in Europe, and genetic diversity was similar in both studied countries. We observed an excess of the Ovar-DRB1*07012/*07012 genotype, and only a few individuals exhibited the advantageous genotypes for parasite infection (Ovar-DRB1*0114 allele and Ovar-DRB1*0324/*0114 genotype). Genetic data showed that the population origins are generally in agreement with the written historical records, although we found signals of release of extra individuals into certain colonies.

Phenotypic and genetic variation of Triatoma costalimai (Hemiptera: Reduviidae).

INTRODUCTION: We aimed to study intraspecific variation in Triatoma costalimai, a potential vector of Chagas disease present in Brazil and Bolivia. METHODS: We analyzed phenotypic (connexivum color patterns, wing morphometrics) and genetic variation (16S mtDNA) of three Brazilian T. costalimai populations. We compared 16S sequences with those of putative Bolivian T. costalimai and its sister species, T. jatai. RESULTS: Brazilian populations had different connexivum color patterns and forewing shapes. A 16S mtDNA haplotype network showed a clear separation of Brazilian T. costalimai from both T. jatai and Bolivian T. costalimai. CONCLUSIONS: We report considerable variability in T. costalimai populations.

Genetic diversity and inferred dispersal history of the Schlegel’s Japanese Gecko (Gekko japonicus) in Northeast Asia based on population genetic analyses and paleo-species distribution modelling

To understand the genetic diversity and dispersal history of Schlegel’s Japanese gecko (Gekko japonicus), we performed genetic analyses and paleo-species distributional modelling. For the genetic analysis, we analyzed mitochondrial DNA (mtDNA) (cytochrome b [Cytb] and NADH dehydrogenase 2 [ND2]) and seven microsatellite loci of 353 individuals from 11 populations (2 east coast China, 4 west and central coast Japan and 5 Korea). For the paleo-species distribution modelling, we used 432 occurrence data points (125 China, 291 Japan and 16 Korea) over the Pleistocene and Holocene. China is inferred to be the source population, which had higher genetic diversity (mtDNA) and more private alleles (mtDNA) compared to Japanese and Korean populations. Differences between the three counties were very small in the mtDNA haplotype network despite some genetic structure among the three countries. Microsatellite analysis inferred that genetic exchange has actively occurred among the Chinese, Japanese and Korean populations. Suitable habitats in Japan should have been plentiful by the mid-Holocene, but have only recently become available in Korea. These results suggest that dispersal of G. japonicus occurred after the Holocene warming from the east coast of China to the west and central coasts of Japan and Korea, and gene flow is actively occurring among the three countries.

Spatio-temporal genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin, Uganda: implications for genetic control trials in malaria endemic regions

BackgroundUnderstanding population genetic structure in the malaria vector Anopheles gambiae (s.s.) is crucial to inform genetic control and manage insecticide resistance. Unfortunately, species characteristics such as high nucleotide diversity, large effective population size, recent range expansion, and high dispersal ability complicate the inference of genetic structure across its range in sub-Saharan Africa. The ocean, along with the Great Rift Valley, is one of the few recognized barriers to gene flow in this species, but the effect of inland lakes, which could be useful sites for initial testing of genetic control strategies, is relatively understudied. Here we examine Lake Victoria as a barrier between the Ugandan mainland and the Ssese Islands, which lie up to 60 km offshore. We use mitochondrial DNA (mtDNA) from populations sampled in 2002, 2012 and 2015, and perform Bayesian cluster analysis on mtDNA combined with microsatellite data previously generated from the same 2002 mosquito DNA samples.ResultsHierarchical analysis of molecular variance and Bayesian clustering support significant differentiation between the mainland and lacustrine islands. In an mtDNA haplotype network constructed from this and previous data, haplotypes are shared even between localities separated by the Rift Valley, a result that more likely reflects retention of shared ancestral polymorphism than contemporary gene flow.ConclusionsThe relative genetic isolation of An. gambiae on the Ssese Islands, their small size, level terrain and ease of access from the mainland, the relative simplicity of the vectorial system, and the prevalence of malaria, are all attributes that recommend these islands as possible sites for the testing of genetic control strategies.

Genetic variation and phylogeographic structure of the cotton aphid, Aphis gossypii, based on mitochondrial DNA and microsatellite markers

Aphis gossypii, one of the most important agricultural pests in the world, can cause serious economic losses in the main crop-producing areas. To clarify issues such as the genetic differentiation, genetic structure, and demographic history of A. gossypii populations, we used 10 nuclear microsatellite loci (SSR) and two mitochondrial gene sequences (COI and Cytb) to investigate genetic diversity and population structure of A. gossypii populations that were collected from 33 sampling sites in China from different climatic zones. SSR and mtDNA data suggested low to moderate levels of genetic diversity. A star-shaped network of mtDNA haplotypes indicated that the maternal ancestor of China cotton aphids likely originated in Xinjiang. The POPTREE, STRUCTURE and principal coordinate analysis (PCoA) revealed two genetic clusters: an eastern and a western region group. Isolation by distance (IBD) results showed a positive correlation between geographic distance and genetic distance in the vast eastern region but not in the western region. Neutrality testing and mismatch distribution analysis provided strong evidence for a recent rapid expansion in most populations. Genetic bottleneck was not detected in A. gossypii populations of China. The present work can help us to develop strategies for managing this pest.

Evolutionary and natural history of the turtle frog, Myobatrachus gouldii, a bizarre myobatrachid frog in the southwestern Australian biodiversity hotspot.

Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter. In contrast, Myobatrachus is distributed widely throughout SWA over multiple climatic zones, but little is known of its population structure, geographic variation in morphology, or reproduction. We generated molecular and morphological data to test for genetic and morphological variation, and to assess whether substrate specialisation in this species may have led to phylogeographic structuring similar to that of other plant and animal taxa in SWA. We assembled sequence data for one mitochondrial and four nuclear DNA loci (3628 base pairs) for 42 turtle frogs sampled throughout their range. Likelihood phylogenetic analyses revealed shallow phylogeographic structure in the mtDNA locus (up to 3.3% genetic distance) and little variation in three of the four nDNA loci. The mtDNA haplotype network suggests five geographically allopatric groups, with no shared haplotypes between regions. These geographic patterns are congruent with several other SWA species, with genetic groups restricted to major hydrological divisions, the Swan Coastal Plain, and the Darling Scarp. The geographically structured genetic groups showed no evidence of significant morphological differentiation (242 individuals), and there was little sexual size dimorphism, but subtle differences in reproductive traits suggest more opportunistic breeding in lower rainfall zones. Call data were compared to sister genera Metacrinia and Arenophryne and found to be highly conservative across the three genera. Like many taxa in SWA, topographic variation and Plio-Pleistocene arid fluctuations likely were historic drivers of diversification in M. gouldii.

Phylogeography of endangered Dendrobium moniliforme in East Asia based on mitochondrial DNA sequence variations

Belonging to the genus Dendrobium of Orchidaceae, Dendrobium moniliforme is an endangered species with disjunct distribution in East Asia, possessing significant medicinal value. To investigate its phylogeography, this study compared sequences of two mitochondrial DNA (mtDNA) fragments (nad 1/b-c and nad 7/2-3) from 143 samples of 18 natural populations of D. moniliforme almost covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. As a result, a total of 30 mtDNA haplotypes were identified in these populations which revealed high levels of haplotype diversity (H d = 0.8733) and total genetic diversity (H T = 0.8886). Additionally, G ST value being significantly lower (0.451) than N ST value (0.722) (P < 0.05) indicated the presence of strong phylogeographic structure in these populations, and the network of mtDNA haplotypes showed that all haplotypes were divided into two clades (A and B). Haplotype overlap was observed among several D. moniliforme population groups in mainland China, suggesting the occurrence of ongoing and/or historical gene flow among them. No common haplotypes were shared by D. moniliforme populations from mainland China and the CKJ Islands (representing Taiwan [China], South Korea, and Japan collectively), pointing to their allopatric evolution in the two regions. Moreover, mismatch distribution analysis and neutral test of mtDNA data rejected the population expansion model. According to the mtDNA-based results, we infer that multiple refugia for D. moniliforme existed in the SJFR of East Asia during the Quaternary glacial period.

Genetic structure of Parnassius mnemosyne (Lepidoptera: Papilionidae) populations in the Carpathian Basin

The pattern of genetic variation in a butterfly species depends on the past history of the given species and also on recent evolutionary processes affecting its populations. The aim of the present study was (i) to analyse the enzyme polymorphism in the Clouded Apollo populations of the Carpathian Basin to reveal the contemporary pattern of their genetic differentiation and (ii) to compare it with an expanded mitochondrial DNA (mtDNA) haplotype network of the SE European populations. Allozyme polymorphism was analysed in 22 populations of four geographic regions: Transdanubian (TM) and North Hungarian Mountains (NM), Koros (KOR) and Bereg–Apuseni–East Carpathian regions (BEAC). The results of the Bayesian clustering analyses based on allozymes supported the presence of three main genetic lineages in the Carpathian Basin: One was typical for TM, another was characteristic for NM and the third cluster was predominant in KOR. The populations of BEAC harboured a mixture of two clusters. The mtDNA haplotype network suggested a fairly similar distribution: The peri-Alpine clade together with the West Balkan clade was detected in TM, while the East Balkan clade occurred in NM, partly in TR and in the two eastern regions of the Basin (KOR and BAEC). The incongruities between the results of the mtDNA and allozyme studies can be explained by the different timescales represented by the two markers. The mtDNA haplotype network provided strong evidence concerning the existence of two Balkan lineages, which probably formed a ‘zone of admixture’ in the Transdanubian and North Hungarian Mountains. The possibility of Last Glacial survival of Parnassius mnemosyne in the Carpathian Basin and the conservation implications of these results are discussed.

Identification of a Rare Gecko from North Island New Zealand, and Genetic Assessment of Its Probable Origin: A Novel Mainland Conservation Priority?

Abstract The largest extant New Zealand gecko, Hoplodactylus duvaucelii (Duvaucel's Gecko), is a nocturnal, viviparous species of conservation concern. Hoplodactylus duvaucelii, once widespread throughout New Zealand, is now confined to offshore islands, the majority of which are free from all introduced mammalian predators (mice, rats, cats, mustelids, brushtail possums). A single H. duvaucelii, caught within a fenced reserve on North Island in 2010 was genotyped to determine whether it represents a recent introduction or a previously unknown native relict population. Genotypes from seven nuclear loci and a minimum spanning network of mtDNA haplotypes revealed two clusters representing southern (Cook Strait) and northern island populations. This genetic structure is concordant with variation between these two groups observed in body size, color pattern, and scalation. The mainland specimen was found to possess a mixture of morphological character states typical of northern and southern island populations...

Is black coat color in wolves of Iran an evidence of admixed ancestry with dogs?

Melanism is not considered a typical characteristic in wolves of Iran and dark wolves are believed to have originated from crossbreeding with dogs. Such hybrid individuals can be identified with the combined use of genetic and morphological markers. We analyzed two black wolves using a 544 base pairs (bp) fragment of the mtDNA control region and 15 microsatellite loci in comparison with 28 dogs, 28 wolves, and four known hybrids. The artificial neural networks (ANNs) method was applied to microsatellite data to separate genetically differentiated samples of wolves, dogs, and hybrids, and to determine the correct class for the black specimens. Individual assignments based on ANNs showed that black samples were genetically closer to wolves. Also, in the neighbor-joining network of mtDNA haplotypes, wolves and dogs were separated, with the dark specimens located in the wolf branch as two separate haplotypes. Furthermore, we compared 20 craniometrical characters of the two black individuals with 14 other wolves. The results showed that craniometrical measures of the two black wolves fall within the range of wolf skulls. We found no trace of recent hybridization with free-ranging dogs in the two black wolves. Dark coat color might be the result of a natural combination of alleles in the coat-color-determining gene, mutation in the K locus due to past hybridization with free-ranging dogs, or the effect of ecological factors and adaption to habitat conditions.

The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia).

The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041–0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.

Mitochondrial DNA variation and reticulate evolution of the genus Abies

The sequences of three regions of mitochondrial DNA (mtDNA) of a total length of 5226 bp were used to study the phylogeography of the genus Abies. The mtDNA haplotype network, comprising 36 studied Abies taxa, consisted of two branches: the first represented all American species plus two Asian, and the second included the remaining Eurasian species. Within these clusters, the haplotypes formed nine major groups, generally corresponding to the clades of the previously obtained phylogeny based on chloroplast DNA (cpDNA), but the relationships of these groups were significantly different: species assignment to the particular mtDNA haplotype group was more in line with its geographical distribution. In addition, the mtDNA haplotype network contains cycles indicating the recombination. It is assumed that the incongruence of cpDNA and mtDNA phylogenies is caused by the introgression capture of alien mtDNA during species hybridization and thus contains information about past migrations. The cases of incongruence of mitochondrial and chloroplast DNA suggesting a migration of Abies between Asia and North America are discussed.

Genetic Divergence and Effective Size among Lane Snapper in U.S. Waters of the Western Atlantic Ocean

AbstractPopulation structure of lane snapper Lutjanus synagris in U.S. waters in the northern Caribbean Sea was assessed using nuclear‐encoded microsatellites and mitochondrial DNA (mtDNA) from samples from four localities in the U.S. Caribbean and one locality in the Florida Keys. Significant heterogeneity was detected for both allele and genotype distributions (microsatellites) and for haplotype distribution (mtDNA). Pairwise comparisons revealed that fish in the Florida Keys differed significantly from fish in the U.S. Caribbean with respect to both microsatellites and mtDNA. A parsimony network of mtDNA haplotypes was consistent with division of the five sample localities into two distinct populations. Genetic diversity at both microsatellites and mtDNA was greater among fish from the Florida Keys. The average, long‐term migration rate from the U.S. Caribbean westward to the Florida Keys was approximately 1.75‐fold greater than the reverse, suggesting that the elevated genetic variability among fish from the Florida Keys reflects the westward movement of alleles as a function of westward‐flowing surface currents in the region. Bayesian coalescent analysis (microsatellites) indicated that each of the two populations has experienced a 10‐fold decline in effective population size (Ne). Estimates of long‐term effective size, generated using a coalescent, maximum‐likelihood method, were 1,671.9 (Florida Keys) and 2,923.2 (U.S. Caribbean). Estimates of contemporaneous effective size, generated using a linkage‐disequilibrium approach with minor alleles (those with frequencies of 0.02 or less) being excluded, were 275.6 (Florida Keys) and 668.9 (U.S. Caribbean) and differed significantly from one another. Because the samples contained mixed cohorts, the short‐term estimates reflect the effective number of breeders (Nb) that produced the cohort(s) from which the samples were taken. The difference between the long‐term and short‐term estimates of Ne (or Nb) suggests that the declines in the effective size of both populations are relatively recent and that management concern over lane snapper in the Florida Keys is justified.Received July 23, 2010; accepted December 14, 2010

Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout ( Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y-marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish.

Mitochondrial DNA genetic differentiation of the muksun Coregonus muksun (Pallas) and related Siberian species of Coregonus (Coredonidae, Salmoniformes)

Restriction enzyme analysis of the mitochondrial DNA (mtDNA) fragment encoding subunit 1 of the NADH dehydrogenase complex (ND-1) amplified via polymerase chain reaction (PCR) has been used to obtain data on genetic differentiation of muksun Coregonus muksun (Pallas) populations. Population polymorphism with respect to the restriction sites of 18 endonucleases has been described. It has been demonstrated that the muksun is genetically related to the pidschian C. pidschian (Gmelin), its sympatric species in Siberian waters. Analysis of the median network of mtDNA haplotypes has shown that haplotypes of muksun from various Siberian basins form a common group with haplotypes of pidschian of the Arctic Ocean basin, some frequent haplotypes been found in both forms. This raises the question as to the validity of the muksun as a species. Differences within this group of haplotypes are much smaller than those typical of species of the genus Coregonus. The possibility of a hybrid origin of the muksun from a pidschian-like ancestor and species of the cisco-peled (C. sardinella-C. peled) complex is discussed.