mtDNA Genome Sequences Research Articles

On the persistence and detectability of ancient Beothuk mitochondrial DNA genomes in living First Nations peoples

Claims have long been made as to the survival to the present day of descendants of the Newfoundland Beothuk, a group generally accepted to have become extinct with the death of the last known member, Shanawdithit, in 1829. Interest has recently been revived by the availability of commercial genetic testing, which some claim can assign living individuals to specific Native American groups. We compare complete mitogenome sequences (16569 bp) from aDNA of eight distinct Beothuk lineages, including Shanawdithit’s uncle Nonosabasut and his wife Demasduit, with three Newfoundland Mi’kmaq lineages and 21 other living Native Americans drawn from GenBank. A Newfoundland Mi’kmaq lineage in Haplogroup A is more similar to three Native Americans (1–3 SNPs) than to the most closely related Beothuk (24 SNPs). Nonosabasut in Haplogroup X is identical to a non-Beothuk Native American. Demasduit in Haplogroup C differs from three other Native Americans by 1–4 substitutions. Within a 2168 bp region of the HVS sequences available from living Mi’kmaq of the Miawpukek First Nation in Newfoundland, lineages in Haplogroups C, X, and A differ by 1, 4, and 8 substitutions, from the most similar Beothuk, and are more similar to other Native Americans. MtDNA genome sequences in living persons identical or similar to those of Beothuk do not necessarily indicate Beothuk ancestry. Mi’kmaq lineages cannot at this time be associated with any Beothuk lineages more closely than those of other Native Americans.

New insights from Thailand into the maternal genetic history of Mainland Southeast Asia

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA genomes from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the expansion of TK people through MSEA, although there is also some support for gene flow between central Thai and native Austroasiatic speaking Mon and Khmer. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.

MT-ND5 Mutation Exhibits Highly Variable Neurological Manifestations at Low Mutant Load

Mutations in the m.13094T>C MT-ND5 gene have been previously described in three cases of Leigh Syndrome (LS). In this retrospective, international cohort study we identified 20 clinically affected individuals (13 families) and four asymptomatic carriers. Ten patients were deceased at the time of analysis (median age of death was 10years (range: 5·4months−37years, IQR=17·9years). Nine patients manifested with LS, one with mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS), and one with Leber hereditary optic neuropathy. The remaining nine patients presented with either overlapping syndromes or isolated neurological symptoms. Mitochondrial respiratory chain activity analysis was normal in five out of ten muscle biopsies. We confirmed maternal inheritance in six families, and demonstrated marked variability in tissue segregation, and phenotypic expression at relatively low blood mutant loads. Neuropathological studies of two patients manifesting with LS/MELAS showed prominent capillary proliferation, microvacuolation and severe neuronal cell loss in the brainstem and cerebellum, with conspicuous absence of basal ganglia involvement. These findings suggest that whole mtDNA genome sequencing should be considered in patients with suspected mitochondrial disease presenting with complex neurological manifestations, which would identify over 300 known pathogenic variants including the m.13094T>C.

Ancient mitochondrial genomes reveal the demographic history and phylogeography of the extinct, enigmatic thylacine (Thylacinus cynocephalus)

AbstractAimThe Tasmanian tiger, or thylacine, is an infamous example of a recent human‐mediated extinction. Confined to the island of Tasmania in historical times, thylacines were hunted to extinction <150 years after European arrival. Thylacines were also once widespread across the Australian mainland, but became extinct there c. 3,200 years before present (bp). Very little is known about thylacine biology and population history; the cause of the thylacines extirpation from the mainland is still debated and the reasons for its survival in Tasmania into the 20th century are unclear. In this study, we investigate the thylacine's phylogeography and demographic history leading up to their extinction on both the mainland and Tasmania to gain insight into this enigmatic species.LocationSouthern Australia.MethodsWe generated 51 new thylacine mitochondrial DNA (mtDNA) genome sequences from sub‐fossil remains and historical museum specimens, and analysed them to reconstruct the species’ phylogeography and demographic history.ResultsWe found evidence that thylacines had contracted into separate eastern and western populations prior to the Last Glacial Maximum (c. 25,000 yr bp), and that the ancient western population was larger and more genetically diverse than the historical Tasmanian population. At the time of European arrival in c. 1800 CE, Tasmanian thylacines had limited mtDNA diversity, possibly resulting from a bottleneck event broadly coincident with an El Niño‐Southern Oscillation (ENSO) associated climate event, although we find some indication that the population was expanding during the late Holocene.Main ConclusionsThe timing of this putative expansion, in concert with a climate event, suggests that climate change had an influence on thylacine population dynamics. Given that ENSO effects are known to have been more severe on mainland Australia, we suggest that climate change, in synergy with other drivers, is likely to have contributed to the thylacine mainland extinction.

AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data

The feasibility of generating mitochondrial DNA (mtDNA) data has expanded considerably with the advent of next-generation sequencing (NGS), specifically in the generation of entire mtDNA genome (mitogenome) sequences. However, the analysis of these data has emerged as the greatest challenge to implementation in forensics. To address this need, a custom toolkit for use in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed through a collaborative effort between the Armed Forces Medical Examiner System − Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics. The AFDIL-QIAGEN mtDNA Expert, or AQME, generates an editable mtDNA profile that employs forensic conventions and includes the interpretation range required for mtDNA data reporting. AQME also integrates an mtDNA haplogroup estimate into the analysis workflow, which provides the analyst with phylogenetic nomenclature guidance and a profile quality check without the use of an external tool. Supplemental AQME outputs such as nucleotide-per-position metrics, configurable export files, and an audit trail are produced to assist the analyst during review. AQME is applied to standard CLC outputs and thus can be incorporated into any mtDNA bioinformatics pipeline within CLC regardless of sample type, library preparation or NGS platform.An evaluation of AQME was performed to demonstrate its functionality and reliability for the analysis of mitogenome NGS data. The study analyzed Illumina mitogenome data from 21 samples (including associated controls) of varying quality and sample preparations with the AQME toolkit. A total of 211 tool edits were automatically applied to 130 of the 698 total variants reported in an effort to adhere to forensic nomenclature. Although additional manual edits were required for three samples, supplemental tools such as mtDNA haplogroup estimation assisted in identifying and guiding these necessary modifications to the AQME-generated profile. Along with profile generation, AQME reported accurate haplogroups for 18 of the 19 samples analyzed. The single errant haplogroup assignment, although phylogenetically close, identified a bug that only affects partial mitogenome data. Future adjustments to AQME’s haplogrouping tool will address this bug as well as enhance the overall scoring strategy to better refine and automate haplogroup assignments. As NGS enables broader use of the mtDNA locus in forensics, the availability of AQME and other forensic-focused mtDNA analysis tools will ease the transition and further support mitogenome analysis within routine casework. Toward this end, the AFMES-AFDIL has utilized the AQME toolbox in conjunction with the CLC Genomics Workbench to successfully validate and implement two NGS mitogenome methods.

Mitogenomic diversity in Russians and Poles

Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved – about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered. While European populations showed a low, but statistically significant level of between-population differentiation (Fst=0.66%, p=0), Russians demonstrate lack of between-population differences (Fst=0.22%, p=0.15). Results of the Bayesian skyline analysis of Russian mitogenomes demonstrate not only post-Last Glacial Maximum expansion, but also rapid population growth starting from about 4.3kya (95% CI: 2.9–5.8kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists.

Erratum to: Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages.

The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion.

English

AbstractMitochondrial DNA sequences have been used extensively for studies of phylogeny, biogeography, and systematics in a vast array of taxa. In crayfish, the most widely used mitochondrial sequences are from the genes 16S ribosomal RNA, 12S ribosomal RNA, and cytochrome oxidase I. Other regions might perform well for certain questions, and entire mtDNA genome sequences might be very useful for phylogenetic studies, but these uses are curtailed by lack of sequence information. The complete mitochondrial genome from an individual of Orconectes cf. ozarkae (Williams) was sequenced, assembled, and annotated. The circular genome was 15,815 base pairs in length, and included the complement of 37 genes expected for metazoans, two ribosomal RNA genes, thirteen protein coding genes, and 22 tRNA genes. The gene order is equivalent to other species of crayfish from the family Cambaridae.

Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai\u2013Kadai languages

The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion.

Improvement in detection of minor alleles in next generation sequencing by base quality recalibration.

BackgroundMinor allele detection in very high coverage sequence data (>1000X) has many applications such as detecting mtDNA heteroplasmy, somatic mutations in cancer or tumors, SNP calling in pool sequencing, etc., where reads with low frequency are not necessarily sequence error but may instead convey biological information. However, the suitability of common base quality recalibration tools for such applications has not been investigated in detail.ResultsWe show that the widely used tool GATK BaseRecalibration has several limitations in minor allele detection. First, GATK IndelRealignment fails to work if the sequence coverage is above a certain level since it then becomes computationally infeasible. Second, the accuracy of the base quality largely depends on the database of known SNPs as the control, which limits the ability of de novo minor allele detection. Third, GATK reduces the base quality of sequence errors at the cost of reducing scores for true minor alleles. To overcome these limitations, we present a novel approach called SEGREG, which applies segmented regression to control sequences (e.g. phiX174 DNA) spiked into a sequencing run. Based on simulations SEGREG improves both the accuracy of base quality scores and the detection of minor alleles. We further investigate sequence error and recalibration parameters by applying a Logarithm Likelihood Ratio (LLR) approach to SEGREG recalibrated base quality scores for phiX174 DNA sequenced to very high coverage, and for mtDNA genome sequences previously analyzed for heteroplasmic variants.ConclusionsOur results suggest that SEGREG improves base recalibration without suffering the limitations discussed above, and the LLR approach benefits from SEGREG in identifying more true minor alleles, while avoiding false positives from sequencing error.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2463-2) contains supplementary material, which is available to authorized users.

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck.

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.

The mitochondrial genome of Murina huttoni rubella (Chiroptera: Vespertilionidae) from China

Murina huttoni rubella is a common Murina species in China, with a medium forearm length and reddish brown hairs. In this study, based on a male M. h. rubella individual from Jiangxi, China, its complete mitochondrial genome was sequenced and analyzed. The genome is 16,707 bp in length, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and a control region. The composition and arrangement of genes are similar to other bats. Phylogenetic trees that covered all released complete mitochondrial genome of bats were constructed using Bayesian Inference and maximum likelihood methods. Both phylogenetic results showed that M. h. rubella and M. ussuriensis have closer phylogenetic relationship. The complete mtDNA genome sequence of M. h. rubella would provide valuable information for solving taxonomic and phylogenetic problem in future.

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus).

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on “fast ice” attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40 ~ 60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.

Complete mitochondrial genome of Schizothorax nukiangensis Tsao (Cyprinidae: Schizothorax)

In this work, we reported the complete mitochondrial genome sequence of the Schizothorax nukiangensis Tsao for the first time. The complete mtDNA genome sequence of S. nukiangensis Tsao was 16 585 bp in length, which contains 22 transfer RNA genes, 2 rRNA genes, 13 protein-coding genes, an origin of light-strand replication (OL) and a control region (D-Loop). The overall base composition of the mitogenome was calculated to be 29.6% for A, 27.0% for C, 17.9% for G and 25.5% for T. The complete mitogenome of the S. nukiangensis Tsao can provide an important data set for further studies on population history, molecular systematics, phylogeography and stock assessment.

The complete mitochondrial genome of Schizothorax yunnanensis paoshanensis (Cyprinidae: Schizothorax)

In this study, the complete mitochondrial DNA (mtDNA) sequence of Schizothorax yunnanensis paoshanensis is determined for the first time. The complete mtDNA genome sequence of S. yunnanensis paoshanensis is 16,585 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and a putative control region (D-loop region). The gene order of S. yunnanensis paoshanensis mtDNA is identical to most of the vertebrate mtDNAs. The complete mitogenome sequence information of S. yunnanensis paoshanensis can provide useful data for further studies on molecular systematics, taxonomic status and conservation genetics.

The mitochondrial genome of Spualiobarbus curriculus of Pearl River

Spualiobarbus curriculus is an important economic species in China. In this study, the complete mitochondrial genome of S. curriculus collected from three parts of Pearl River is cloned and analyzed. The complete sequence includes 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a D-loop region. The composition of nucleic acid is calculated and it is similar to the known S. curriculus mtDNA. The diversities of sequences and the phylogenetic tree approve that there is high similarity with the one of Yangtze, but there is geographic differences between the sequences. The complete mtDNA genome sequence would contribute to studying phylogenetics in S. curriculus and gemplasm protection of aquatic animal in Pearl River.

The complete mitochondrial genome of the Onychostoma gerlachi (Cypriniformes, Cyprinidae)

Onychostoma gerlachi, which belongs to the genus Onychostoma (Cypriniformes, Cyprinidae), is an economic fish that inhabits the flowing freshwater in south of China. The complete mitochondrial genome of O. gerlachi was determined to be 16,601 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. It includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding control region (D-loop). The overall base composition of O. gerlachi is 31.38% for A, 24.24% for T, 28.29% for C and 16.09% for G, with a slight AT bias of 55.62%. The complete mtDNA genome sequence of O. gerlachi obtained in this study provides fundamental data for studying genetic diversity and phylogenetics on this species.

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.

Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations

Heteroplasmy in human mtDNA may play a role in cancer, other diseases, and aging, but patterns of heteroplasmy variation across different tissues have not been thoroughly investigated. Here, we analyzed complete mtDNA genome sequences at ∼3,500× average coverage from each of 12 tissues obtained at autopsy from each of 152 individuals. We identified 4,577 heteroplasmies (with an alternative allele frequency of at least 0.5%) at 393 positions across the mtDNA genome. Surprisingly, different nucleotide positions (nps) exhibit high frequencies of heteroplasmy in different tissues, and, moreover, heteroplasmy is strongly dependent on the specific consensus allele at an np. All of these tissue-related and allele-related heteroplasmies show a significant age-related accumulation, suggesting positive selection for specific alleles at specific positions in specific tissues. We also find a highly significant excess of liver-specific heteroplasmies involving nonsynonymous changes, most of which are predicted to have an impact on protein function. This apparent positive selection for reduced mitochondrial function in the liver may reflect selection to decrease damaging byproducts of liver mitochondrial metabolism (i.e., "survival of the slowest"). Overall, our results provide compelling evidence for positive selection acting on some somatic mtDNA mutations.

Maternal ancestry and population history from whole mitochondrial genomes.

MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations.