Variation In mtDNA Control Region Research Articles

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin.

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Phylogenetic relationship and variation of alarm call traits of populations of red-cheeked ground squirrels (Spermophilus erythrogenys sensu lato) suggest taxonomic delineation.

Distribution area and taxonomic borders within the species complex Spermophilus erythrogenys sensu lato remain questionable. Early evidence suggests that red-cheeked ground squirrels of Southeast Kazakhstan are remarkably different in terms of the acoustic structure of their alarm calls from the red-cheeked ground squirrels of the Kurgan region in Russia. In this study, we analyzed the differences in the acoustic structure of the alarm call and mitochondrial DNA (complete control region, 1005-1006 bp and complete cytochrome b gene, 1140 bp) in 3 populations of red-cheeked ground squirrels (Tara, Altyn-Emel and Balkhash), all located within areas isolated by geographical barriers in Southeast Kazakhstan. We found that the alarm call variables were similar between the 3 study populations and differed by the maximum fundamental frequency (8.46 ± 0.75 kHz) from the values (5.62 ± 0.06 kHz) reported for the red-cheeked ground squirrels from the Kurgan region of Russia. Variation in mtDNA control region was only 3% and variation in cytochrome b gene was only 2.5%. Phylogenetic trees based on cytochrome b gene polymorphism of 44 individuals from the study area and adjacent territories indicated 3 clades with high (98-100%) bootstrap support: "intermedius," "brevicauda" and "iliensis"). We conclude that the 3 study populations in Southeast Kazakhstan belong to the clade intermedius and suggest a taxonomical revision of the species complex Spermophilus erythrogenys sensu lato, including analyses of nuclear DNA and alarm calls for populations of the brevicauda and iliensis clades.

Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region

Sequence analysis of the mitochondrial DNA (mtDNA) control region can provide forensically useful information, particularly in challenging samples where autosomal DNA profiling fails. Sub-division of the 1122-bp region into shorter PCR fragments improves data recovery, and such fragments can be analysed together via massively parallel sequencing (MPS). Here, we generate mtDNA data using the prototype PowerSeq™ Auto/Mito/Y System (Promega) MPS assay, in which a single PCR reaction amplifies ten overlapping amplicons of the control region, in a set of 101 highly diverse samples representing most major clades of the mtDNA phylogeny. The overlapping multiplex design leads to non-uniform coverage in the regions of overlap, where it is further increased by short amplicons generated alongside the intended products. Primer sequences in targeted amplification libraries are a potential source of reference sequence bias and thus should be removed, but the proprietary nature of the primers in commercial kits necessitates an alternative approach that minimises data loss: here, we introduce the bioinformatic selection of sequencing reads spanning putative primer sites (Overarching Read Enrichment Option, OREO). While OREO performs well in mitigating the effects of primer sequences at the ends of sequence reads, we still find evidence of the internalisation of primer-derived sequences by overlap extension, which may compromise the ability to call variants or to measure heteroplasmy in primer-binding regions. The commercially available PowerSeq™ CRM Nested System design prevents primer internalisation, as shown in a reanalysis of a subset of 57 samples that contain possible heteroplasmies. In combination with OREO, the CRM Nested kit mitigates reference sequence bias, allowing heteroplasmic variants to be estimated down to a 5% threshold. Provided appropriate steps are taken in data processing, single-reaction multiplex assays represent robust tools to analyse mtDNA control region variation. The OREO approach will allow users to bypass the effects of unknown primer sequences in any single-reaction tiled multiplex and eliminate primer-derived bias in overlapping amplicon sequencing studies, in both forensic and non-forensic settings.

The phylogeography of coho salmon based on mtDNA control region variation: Asian populations descend from the Beringian Refugium

The phylogeography of coho salmon based on mtDNA control region variation: Asian populations descend from the Beringian Refugium

Genetic structure analysis of mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region sequence.

The genetic relationships of mantis shrimp Oratosquilla oratoria between the coastal waters of China and Japan were not well studied. To reveal the genetic differentiation and genetic structure among populations, we collected populations of mantis shrimp O. oratoria from the coastal waters of China and Japan to analyze the mtDNA control region variation. A total of 309 individuals of O. oratoria were collected from 13 localities (11 from China and 2 from Japan) and a segment of mitochondrial DNA control region was sequenced. Three hundred nine haplotypes were defined, yielding a very high haplotype diversity and nucleotide diversity. Two lineages of O. oratoria were revealed and displayed strong differences in the geographical distribution. In the coastal waters of China, the geographic distribution of the two lineages was completely separated by the Yangtze River estuary; however, the lineages showed geographic sympatry in two populations from Japan. Based on the lineage distribution, three groups were defined. There was no significant genetic differentiation among the populations within the three groups, indicating high gene flow within each group. Significant and negative values for Tajima D and Fu's Fs tests, and mismatch distributions for two lineages indicated population expansion. The present result confirmed that the freshwater outflow from the Yangtze River formed a physical barrier and affected gene exchange. The different distribution patterns of the two lineages in coastal waters of China and Japan indicated that the larvae of O. oratoria were transferred from China to the coastal waters of Japan with a one-way gene flow.

MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa

BackgroundThe current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/’hoansi, !Xun, /Gui+//Gana, Khwe, ≠Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record.ResultsThe most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/’hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: ≠Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages.ConclusionsOn the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.

Preliminary Study on Microsatellite and Mitochondrial DNA Variation of the Stone MartenMartes foinain Bulgaria

In Europe, distribution of many animal species has been severely restricted to small refugia during the last glacial period. The Balkan Peninsula including Bulgaria has been identified as one of the three main glacial refugia (Randi 2007). To know biogeographical history in Europe, molecualr phylogeographical studies about various European mammal species have been performed: for example, the least weasel Mustela nivalis by the mitochondrial DNA (mtDNA) control region and cytochrome b (Lebarbenchon et al. 2010), the ground squirrel Spermophilus citellus by cytochrome b (Krystufek et al. 2009), the yellow-necked fieldmouse Apodemus flavicollis and the woodmouse A. sylvaticus by cytochrome b (Michaux et al. 2005), the brown bear Ursus arctos by mtDNA control region (Taberlet and Bouvet 1994; Taberlet et al. 1998) and the hedgehogs Erinaceus europaeus and E. concolor by cytochorome b (Santucci et al. 1998). These studies commonly show that distribution of European species was influenced by climate changes in the Quaternary glaciations, and they survived in different ways (Michaux et al. 2005). Studies on the genetic diversity of mammals in Bulgaria as part of the Balkan Peninsula provides further insights to understanding of biogeographical history from the last glacial maximum (LGM) to present in south Europe. The stone marten Martes foina is a medium-sized carnivore of the family Mustelidae, and is distributed from Spain and Portugal in the west, through central and southern Europe, the Middle East, and central Asia, extending as far east as the Altai and Tien Shan Mountains and northwest China (Abramov et al. 2006). This species prefers more open areas than other martens (Sacchi and Meriggi 1995). Its habitat preferences vary in different parts of its range. Martes foina is typically found in deciduous forests, forest edges and open rocky hillsides. In some areas, however, M. foina also inhabits suburban and urban areas, with rare woods (Tikhonov et al. 2008). Because the Balkan Peninsula is one of the southern limit of distribution of M. foina, the analysis of its Balkan population would contribute to further understanding of refugia and phylogeography in Europe. Whereas there have been some phylogenetic studies about the family Mustelidae including M. foina (Marmi et al. 2003; Li et al. 2011) and a microsatellite variation study of M. foina in southern Portugal (Basto et al. 2010), no population genetic studies about this species in Bulgaria have been reported. In the present study, to know the population structure and phylogeography of the Bulgarian population of M. foina, we studied its microsatellite polymorphisms and mtDNA control region variation, and then discuss the genetic diversity in the population.

The south-eastern house mouse Mus musculus castaneus (Rodentia: Muridae) is a polytypic subspecies

Accurate knowledge of the biogeographic history and precise characterization of the genetic make-up of a taxon are essential to investigate speciation processes and achieve sound evolutionary comparisons. A case in point is the house mouse Mus musculus and its three parapatric subspecies, which have become a model for such studies. However, although Mus musculus domesticus and Mus musculus musculus constitute genetically well-characterized homogeneous entities, the case of Mus musculus castaneus remains poorly documented. Using mtDNA control region variation in a sample of 402 individuals, covering much of the distribution range of this subspecies, we identify four haplogroups that show largely non-overlapping geographic distributions. They appear to have undergone post-Neolithic expansions, presumably through commensalism with humans, but exhibit a much more ancient divergence. These results point towards a strong past subdivision and a vicariant origin of the different haplogroups, with each retaining a subfraction of the total variability. The genomic consequences of this spatial heterogeneity on the present taxonomic partition will have to be appraised, and may challenge the use of this subspecies as a single entity in evolutionary studies. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

Genetic architecture of trout from Albania as revealed by mtDNA control region variation.

To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean – Adriatic – marmoratus haplotypes, which were further delimited into three subdivisions of Mediterranean, marmoratus, and a previously non-described formation of four Adriatic haplotypes (Balkan cluster). Haplotypes of the Balkan cluster and the other Adriatic haplotypes, do not represent a contiguous haplotype lineage and appear not to be closely related, indicating independent arrivals into the Adriatic drainage and suggesting successive colonization events. Despite the presence of marmoratus haplotypes in Albania, no marbled phenotype was found, confirming previously reported findings that there is no association between this phenotype and marmoratus haplotypes.

Presence of unexpected phylogenetic lineages of brown trout Salmo trutta L. in Gacka River, Croatia

This study provides the first analysis of mtDNA control region variation of brown trout samples from the Gacka River, in order to assess their phylogenetic lineage affliation and address the question of the origin of phylogenetic haplotypes in the river. Aligned sequences from 21 individuals were sorted into two haplotypes. Based on the 334 bp fragment at the 50'end of the control region, 14 fish were assigned to the Danubian lineage (67%) and seven were assigned to the AT lineage (33%). All fish assigned to the Danubian lineage revealed just one haplotype: Da2 (M97975). The same was observed within the AT lineage-assigned fish, where only one haplotype, At1 (M97969), was found.The prevalence of Danubian haplotype and no finding of Adriatic haplotype imply an autochthonous status of the Danubian haplotype in Gacka River.

Mitochondrial DNA geneflow indicates preferred usage of the Levant Corridor over the Horn of Africa passageway

Both the Levantine Corridor and the Horn of Africa route have figured prominently in early hominid migrations from Africa to Eurasia. To gauge the importance of these two African-Asian thoroughfares in the demic movements of modern man, we surveyed the mtDNA control region variation and coding polymorphisms of 739 individuals representing ten African and Middle Eastern populations. Two of these collections, Egypt and Yemen, are geographically close to the Levant and Horn of Africa, respectively. In this analysis, we uncover genetic evidence for the preferential use of the Levantine Corridor in the Upper Paleolithic to Neolithic dispersals of haplogroups H, J*, N1b, and T1, in contrast to an overwhelming preference in favor of the Horn of Africa for the intercontinental expansion of M1 during the Middle to Upper Paleolithic. Furthermore, we also observed a higher frequency of sub-Saharan mtDNA compared to NRY lineages in the Middle Eastern collections, a pattern also seen in previous studies. In short, the results of this study suggest that several migratory episodes of maternal lineages occurred across the African-Asian corridors since the first African exodus of modern Homo sapiens sapiens.

Low genetic diversity in the Endangered Crested Ibis Nipponia nippon and implications for conservation

Crested Ibis Nipponia nippon is an Endangered species that has experienced a severe but short-lived population bottleneck in recent years. Only one wild population and two captive populations exist in China today, all of which were probably initiated from two breeding pairs rediscovered in 1981. This paper represents the first study of the genetic diversity of Crested Ibis by analysing sequence variation of a fragment spanning domains II and III of the mitochondrial DNA (mtDNA) control region of both wild and captive populations. Two haplotypes were identified in both wild and captive populations, and the captive population had a bias towards haplotype 1. The species as a whole demonstrated an extremely low level of genetic diversity, with a haplotype diversity and nucleotide diversity of 0.386 ± 0.074 and 0.069% ± 0.013%, respectively. Despite the rapid increase in numbers of birds under intensive management, the paucity of genetic diversity remains a real threat to the species. The mtDNA control region variations detected in the present study could provide significant information additional to the studbook data of Crested Ibis; therefore we suggest that special attention be paid to individuals with haplotype 2 when considering captive breeding management. Overall, great care should be taken in the selection of reintroduction sites for this rare bird, as species with low genetic diversity are thought to be more limited in their ability to tolerate a wide range of environmental extremes and diseases.

Lack of mtDNA control region variation in Hainan Eld's deer: Consequence of a recent population bottleneck?

We find no genetic variation at 550bp of mtDNA control region among 55 Hainan Eld's deer in an island population that has suffered recent population contractions. Congeneric species show high levels of variation at this locus. We use a simulation approach to test the likelihood of various bottleneck scenarios, and show, in the context of what is known about the recent demographic history of this population, that there are credible scenarios for a bottleneck driven by hunting pressure in the 1960s that could account for the lack of variation at this locus.

Length variation in mtDNA control region in hatchery stocks of European sea bass subjected to acclimation experiments

Length polymorphism of the mtDNA control region was analysed in samples from the sea bass Dicentrarchus labrax before and after acclimation to freshwater. Acclimation trials were repeated twice for two samples originating from the same broodstock. DNA amplification of 221 individuals made it possible to detect 40 different D-loop length variants and a mean level of gene diversity (/c!) of 0.850. Out of 52 scored distinct genotypes, 18 were homoplasmic and the remaining ones were heteroplasmic for up to four variants. Shifts in frequencies between starting and acclimated samples in the same direction of the same genotypes in both years were not observed. Patterns of mtDNA control region variation were compared to previous allozymic and RAPD studies carried out on the same samples. While variation found in the allozyme alleles and the RAPD markers in replicate experiments revealed differential survival of the genotypes, stochastic processes, such as genetic drift, explained the observed variation of mtDNA control region. Very high levels of genotype diversity were observed within each sample, ranging from 0.77 to 0.97. This high diversity associated with the maternal inheritance of mtDNA makes this molecular marker especially suitable for studies in aquaculture genetics, when the allozyme studies fail to reveal genetic variation or when the identification of progeny based on the mother's contribution is relevant. © Inra/Elsevier, Paris

Length variation in mtDNA control region in hatchery stocks of European sea bass subjected to acclimation experiments

Length variation in mtDNA control region in hatchery stocks of European sea bass subjected to acclimation experiments