Mitochondrial DNA Sequence Variation Research Articles

Genetic structure and demographic history of whiting Merlangius merlangus (Linnaeus, 1758) populations distributed in Turkey inferred from variation in mitochondrial DNA sequences

The genetic diversity, structure, and demographic history of the economically important and overfished Gadidae species Merlangius merlangus were investigated using the non-coding mitochondrial Control Region (CR) from five different sites in the Sea of Marmara and the Black Sea in Turkey. The populations of M. merlangus were found to be genetically diverse, with 14 haplotypes and 15 polymorphic regions. The overall haploid diversity was 0.910 ± 0.024, and the nucleotide diversity was 0.003± 0.0003. Genetic distances between populations varied between 0.13% and 8.02%, while genetic distances within M. merlangus populations varied between 0.09% and 0.42%. Principle Coordinates Analysis showed that Marmara, Black Sea, and Karadeniz Ereğli populations were clearly separated. Pairwise FST values varied from 0.12 to 0.69, highlighting high genetic variation among populations. The Black Sea and Marmara lineages of M. merlangus diverged from the North Sea lineage 1.65 (1.08-2.29) mya, whereas the separation between the Atlantic lineage occurred about 0.84 (0.51-1.2) mya. The recent expansion of the whiting population was identified through neutrality tests and mismatch distribution analyses. This study provides important insight into the genetic structure, conservation, and management of this species.

Molecular systematic analysis demonstrates that the threatened southern bell frog, Litoria raniformis (Anura: Pelodryadidae) of eastern Australia, comprises two sub-species

In south-eastern Australia, the pelodryadid Litoria aurea Group (sensu Tyler & Davies 1978) comprises three species: Litoria aurea (Lesson, 1829), Litoria raniformis (Keferstein, 1867), and Litoria castanea (Steindachner, 1867). All three species have been subject to declines over recent decades and taxonomic uncertainty persists among populations on the tablelands in New South Wales. We address the systematics of the Group by analysing mitochondrial and nuclear DNA sequences to assess divergence in the Litoria raniformis from across its current range in New South Wales (NSW), Victoria, South Australia (SA) and Tasmania. We also included samples of Litoria castanea from a recently rediscovered population in the southern tablelands of NSW. Our phylogenetic and population genetic analyses show that Litoria raniformis comprises northern and southern lineages, showing deep mitochondrial DNA sequence divergence (7% net average sequence divergence) and can be diagnosed by fixed allelic differences at more than 4,000 SNP loci. Samples of the northern lineage were collected from the Murray-Darling Basin while those of the southern lineage were collected from south-eastern South Australia, southern and south-eastern Victoria and Tasmania. Analysis of the morphology and bioacoustics did not unequivocally delineate the two lineages. The presence of a hybrid backcross individual in western Victoria at the northern margin of the southern lineage, leads us to assign sub-species status to the two lineages, L. r. raniformis for the northern lineage and L. r. major for the southern lineage. Our data do not unequivocally resolve the taxonomic status of L. castanea which will require molecular genetic analyses of museum vouchers from those parts of the range where L. castanea and L. raniformis are no longer extant. Our data also suggest that human mediated movement of frogs may have occurred over the past 50 years. Our genotyping of vouchers collected in the 1970s from the Mount Lofty Ranges in South Australia detected mitochondrial haplotypes of both sub-species and SNP analysis showed that a single Tasmanian specimen was a backcross with L. r. raniformis ancestry. Movement of L. r. raniformis into Tasmania and both sub-species into the Mount Lofty Ranges are not likely due to passive movements of animals through agricultural commerce, but due to the attractiveness of the species as pets and subsequent escapes or releases, potentially of the larval life stage.

Phylogenetic assessment of endangered and look‐alike Pigtoe species in a freshwater mussel diversity hotspot

The Green River in Kentucky in the eastern United States is a freshwater mussel biodiversity hotspot, with 71 known species. Among them, the endangered Pleurobema plenum coexists with other morphologically similar species in the genera Fusconaia and Pleurobema, known colloquially as "pigtoes." Identification of species in these genera is challenging even for mussel experts familiar with them. In our study, the correct identification of these species by experts ranged from 57% to 83%. We delineated taxonomic boundaries among seven species and tested for cryptic biodiversity among these look-alike mussels utilizing mitochondrial and nuclear DNA sequence variation. Phylogenetic analysis of combined (1215 bp) mitochondrial DNA cytochrome oxidase I (COI) and NADH dehydrogenase 1 (ND1) genes showed five well-diverged groups that included F.flava, F.subrotunda, P.cordatum, and P.plenum as distinct clades, with P.sintoxia and P.rubrum grouped into a single clade. While our mitochondrial DNA analyses did not distinguish P.sintoxia and P.rubrum as phylogenetically distinct species, the typical shell forms of these two nominal taxa are very distinct. Further phylogenetic analysis using nuclear ribosomal transcribed spacer region subunit I (ITS1) DNA sequences also showed that P.sintoxia and P.rubrum were not distinct lineages. No cryptic species were detected in the Fusconaia and Pleurobema samples analyzed from the Green River. The highest haplotype diversity (h), average number of nucleotide differences (k), and nucleotide diversity (π) were observed for F.subrotunda at both the COI (h=0.896, k=3.805, π=0.00808) and ND1 (h=0.984, k=6.595, π =0.00886) markers, with similarly high genetic diversity in the other taxa. Our results give managers confidence that cryptic taxa do not occur within or among these morphologically similar species in the Green River, and populations appear genetically diverse, indicative of large and healthy populations.

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse.

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.

Effects of mitochondrial haplotype on pre-copulatory mating success in male fruit flies (Drosophila melanogaster).

While mitochondria have long been understood to be critical to cellular function, questions remain as to how genetic variation within mitochondria may underlie variation in general metrics of organismal function. To date, studies investigating links between mitochondrial genotype and phenotype have largely focused on differences in expression of genes and physiological and life-history traits across haplotypes. Mating display behaviours may also be sensitive to mitochondrial functionality and so may also be affected by sequence variation in mitochondrial DNA, with consequences for sexual selection and fitness. Here, we tested whether the pre-copulatory mating success of male fruit flies (Drosophila melanogaster) varies across six different mitochondrial haplotypes expressed alongside a common nuclear genetic background. We found a significant effect of mitochondrial haplotype on our measure of competitive mating success, driven largely by the relatively poor performance of males with one particular haplotype. This haplotype, termed 'Brownsville', has previously been shown to have complex and sex-specific effects, most notably including depressed fertility in males but not females. Our study extends this disproportionate effect on male reproductive success to pre-copulatory aspects of reproduction. Our results demonstrate that mutations in mitochondrial DNA can plausibly affect pre-copulatory mating success, with implications for future study into the subcellular underpinnings of such behaviours and the information they may communicate.

Integrative taxonomy documents two additional crypticErithacusspecies on the Canary Islands (Aves)

AbstractThe European RobinErithacus rubeculais currently treated as a single species with eight subspecies. A previous molecular study and new molecular, morphometric and bioacoustic data reported here strongly support the recognition of three species in this complex:E. rubecula(Europe, North Africa and Macaronesia except the central Canary Islands),E. superbus(Tenerife) and a recently described subspecies on Gran Canaria which we raise to species rank asE. marionae. The taxa on Tenerife and Gran Canaria have previously been lumped as a single taxon but differ from each other and fromE. rubeculain territorial songs,ticcalls,seepcalls and wing length. All three species are characterised by moderate to high levels of interspecific mitochondrial DNA sequence divergence (mean 4.2–4.8%). Phylogenetic analysis indicates thatE. marionaeis sister toE. superbus + E. rubecula. Recognition of Gran Canaria and Tenerife Robins as separate species adds two single‐island endemics to the Canary Islands avifauna.

Mitochondrial DNA haplogroup F confers genetic susceptibility to chronic HBV infection for the Yi nationality in Lijiang, China.

Mitochondria are essential for hepatitis B virus (HBV) infection. Moreover, the findings of our previous study indicate that host mitochondrial genetic factors are associated with chronic hepatitis B (CHB) for the Han Chinese. However, in terms of genetic heterogeneity, the impact of mitochondria on host susceptibility to HBV infection in ethnic minorities in China remains unclear. Here, a total of 7070 subjects who had visited the hospital between June 1, 2019, and April 31, 2020, were enrolled for seroprevalence of HBV infection investigation. A total of 220 individuals with CHB (CHBs) and 223 individuals with a trace of HBV infection (spontaneously recovered subjects, SRs) were analyzed for mitochondrial DNA (mtDNA) sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between CHBs and SRs. Among eight nationalities, Yi nationality patients had the highest HBsAg prevalence rate (27.9% [95% CI: 25.3%-30.5%]) and the lowest vaccination rate (4.9% [95% CI: 3.7%-6.2%]). After adjustment for age and gender, haplogroup F was a risk factor for CHB infection (P=0.049, OR=2.079, 95% CI=1.002-4.31), while D4 had a significant negative correlation with the HBeAg-positive rate (P=0.024, OR=0.215, 95% CI=0.057-0.816). Together with our previous study, the findings indicate that different nationalities have different genetic susceptibility to HBV infection.

Population structure, phylogeography and demographic history of Tenualosa ilisha populations in the Indian Ocean region inferred from mitochondrial DNA sequence variation

Understanding evolutionary processes reshaping the genetic structure in the context of environmental changes is an important component of sustainable management for the fisheries resources. In this study, we analyzed mitochondrial control region sequence to reveal population structure, phylogeography and demographic history of six populations of hilsa shad (Tenualosa ilisha) in the Indian Ocean regions (Andaman Sea, Bay of Bengal, Arabian Sea and Persian Gulf). High haplotype diversity was found in all of the populations of T. ilisha. The Analysis of Molecular Variance and FST comparisons revealed high level of genetic variation and divergence between populations of the Bay of Bengal and Arabian Sea. Four cryptic genetic barriers were found for the studied populations of T. ilisha, and the highest degree of population divergence was found between the Western Indian Ocean (Arabian Sea and Persian Gulf) and Eastern Indian Ocean (Andaman Sea and Bay of Bengal) regions based on the Voronoï tessellation of BARRIER analysis. The gene flow analysis detected almost no migration between Eastern and Western part of the Indian Ocean regions. Besides, one-way migration was found from Pakistan of Arabian Sea to Kuwait population of Persian Gulf. Demographic history of population expansion and long stable population varied for different populations of hilsa shad. Distinct cryptic genetic barriers, limited gene flows and complex evolutionary process resulted in a significant population genetic and phylogeographic structure, and intricate demographic histories of T. ilisha populations. Further, the study provided valuable insights for conserving and managing of this fishery resource in its broad geographical coverage.

Neither cardiac mitochondrial DNA variation nor copy number contribute to congenital heart disease risk

The well-established manifestation of mitochondrial mutations in functional cardiac disease (e.g., mitochondrial cardiomyopathy) prompted the hypothesis that mitochondrial DNA (mtDNA) sequence and/or copy number (mtDNAcn) variation contribute to cardiac defects in congenital heart disease (CHD). MtDNAcns were calculated and rare, non-synonymous mtDNA mutations were identified in 1,837 CHD-affected proband-parent trios, 116 CHD-affected singletons, and 114 paired cardiovascular tissue/blood samples. The variant allele fraction (VAF) of heteroplasmic variants in mitochondrial RNA from 257 CHD cardiovascular tissue samples was also calculated. On average, mtDNA from blood had 0.14 rare variants and 52.9 mtDNA copies per nuclear genome per proband. No variation with parental age at proband birth or CHD-affected proband age was seen. mtDNAcns in valve/vessel tissue (320 ± 70) were lower than in atrial tissue (1,080 ± 320, p = 6.8E−21), which were lower than in ventricle tissue (1,340 ± 280, p = 1.4E−4). The frequency of rare variants in CHD-affected individual DNA was indistinguishable from the frequency in an unaffected cohort, and proband mtDNAcns did not vary from those of CHD cohort parents. In both the CHD and the comparison cohorts, mtDNAcns were significantly correlated between mother-child, father-child, and mother-father. mtDNAcns among people with European (mean = 52.0), African (53.0), and Asian haplogroups (53.5) were calculated and were significantly different for European and Asian haplogroups (p = 2.6E−3). Variant heteroplasmic fraction (HF) in blood correlated well with paired cardiovascular tissue HF (r = 0.975) and RNA VAF (r = 0.953), which suggests blood HF is a reasonable proxy for HF in heart tissue. We conclude that mtDNA mutations and mtDNAcns are unlikely to contribute significantly to CHD risk.

The role of mtDNA haplogroups on metabolic features in narcolepsy type 1

Narcolepsy type 1 (NT1) is due to selective loss of hypocretin (hcrt)-producing-neurons. Hcrt is a neuropeptide regulating the sleep/wake cycle, as well as feeding behavior. A subset of NT1 patients become overweight/obese, with a dysmetabolic phenotype. We hypothesized that mitochondrial DNA (mtDNA) sequence variation might contribute to the metabolic features in NT1 and we undertook an exploratory survey of mtDNA haplogroups in a cohort of well-characterized patients.We studied 246 NT1 Italian patients, fully defined for their metabolic features, including obesity, hypertension, low HDL, hypertriglyceridemia and hyperglycemia. For haplogroup assignment, the mtDNA control region was sequenced in combination with an assessment of diagnostic markers in the coding region.NT1 patients displayed the same mtDNA haplogroups (H, HV, J, K, T, U) frequency as those reported in the general Italian population. The majority of NT1 patients (64%) were overweight: amongst these, 35% were obese, 48% had low HDL cholesterol levels, and 31% had hypertriglyceridemia.We identified an association between haplogroups J, K and hypertriglyceridemia (P = 0.03, 61.5% and 61.5%, respectively vs. 31.3% of the whole sample) and after correction for age and sex, we observed a reduction of these associations (OR = 3.65, 95%CI = 0.76–17.5, p = 0.106 and 1.73, 0.52–5.69, p = 0.368, respectively). The low HDL level showed a trend for association with haplogroup J (P = 0.09, 83.3% vs. 47.4% of the whole sample) and after correction we observed an OR = 6.73, 95%CI = 0.65–69.9, p = 0.110.Our study provides the first indication that mtDNA haplogroups J and K can modulate metabolic features of NT1 patients, linking mtDNA variation to the dysmetabolic phenotype in NT1.

Mitochondrial DNA sequence variation and risk of glioma

BackgroundMalignant gliomas are the most common primary adult brain tumors, with a poor prognosis and ill-defined etiology. Mitochondrial DNA (mtDNA) sequence variation has been linked with certain cancers; however, research on glioma is lacking. MethodsWe examined the association of common (minor allele frequency ≥ 5%) germline mtDNA variants and haplogroups with glioma risk in 1,566 glioma cases and 1,017 controls from a US case-control study, and 425 glioma cases and 1,534 matched controls from the UK Biobank cohort (UKB). DNA samples were genotyped using the UK Biobank array that included a set of common and rare mtDNA variants. Risk associations were examined separately for glioblastoma (GBM) and lower grade tumors (non-GBM). ResultsIn the US study, haplogroup W was inversely associated with glioma when compared with haplogroup H (OR = 0.43, 95%CI: 0.23–0.79); this association was not demonstrated in the UKB (OR = 1.07, 95%CI: 0.47–2.43). In the UKB, the variant m.3010G > A was significantly associated with GBM (OR = 1.32; 95%CI: 1.01–1.73; p = 0.04), but not non-GBM (1.23; 95%CI: 0.78–1.95; p = 0.38); no similar association was observed in the US study. In the US study, the variant m.14798 T > C, was significantly associated with non-GBM (OR = 0.72; 95%CI: 0.53–0.99), but not GBM (OR = 0.86; 95%CI: 0.66–1.11), whereas in the UKB, a positive association was observed between this variant and GBM (OR = 1.46; 95%CI: 1.06–2.02) but not non-GBM (OR = 0.92; 95%CI: 0.52–1.63). None of these associations were significant after adjustment for multiple testing. ConclusionThe association of inherited mtDNA variation, including rare and singleton variants, with glioma risk merits further study.

Genetic structure and diversity of the Chilean flat oyster Ostrea chilensis (Bivalvia: Ostreidae) along its natural distribution from natural beds subject to different fishing histories.

Ostrea chilensis (Küster, 1844), the flat oyster, is native to Chile and New Zealand. In Chile, it occurs in a few natural beds, from the northern part of Chiloé Island (41 ºS) to the Guaitecas Archipelago (45 ºS). This bivalve is slow growing, broods its young, and has very limited dispersal potential. The Ostrea chilensis fishery has been over-exploited for a number of decades such that in some locations oysters no longer exist. The aim of this study was to study the genetic diversity of the Chilean flat oyster along its natural distribution to quantify the possible impact of the dredge fishery on wild populations. The genetic structure and diversity of Ostrea chilensis from six natural beds with different histories of fishing activity were estimated. Based on mitochondrial (Cytb) and nuclear (ITS1) DNA sequence variation, our results provide evidence that genetic diversity is different among populations with recent history of wild dredge fishery efforts. We discuss the possible causes of these results. Ultimately, such new information may be used to develop and apply new management measures to promote the sustainable use of this valuable marine resource.

Extensive analysis of mitochondrial DNA quantity and sequence variation in human cumulus cells and assisted reproduction outcomes.

Are relative mitochondrial DNA (mtDNA) content and mitochondrial genome (mtGenome) variants in human cumulus cells (CCs) associated with oocyte reproductive potential and assisted reproductive technology (ART) outcomes? Neither the CC mtDNA quantity nor the presence of specific mtDNA genetic variants was associated with ART outcomes, although associations with patient body mass index (BMI) were detected, and the total number of oocytes retrieved differed between major mitochondrial haplogroups. CCs fulfil a vital role in the support of oocyte developmental competence. As with other cell types, appropriate cellular function is likely to rely upon adequate energy production, which in turn depends on the quantity and genetic competence of the mitochondria. mtDNA mutations can be inherited or they can accumulate in somatic cells over time, potentially contributing to aging. Such mutations may be homoplasmic (affecting all mtDNA in a cell) or they may display varying levels of heteroplasmy (affecting a proportion of the mtDNA). Currently, little is known concerning variation in CC mitochondrial genetics and how this might influence the reproductive potential of the associated oocyte. This was a prospective observational study involving human CCs collected with 541 oocytes from 177 IVF patients. mtDNA quantity was measured in all the samples with a validated quantitative PCR method and the entire mtGenome was sequenced in a subset of 138 samples using a high-depth massively parallel sequencing approach. Associations between relative mtDNA quantity and mtGenome variants in CCs and patient age, BMI (kg/m2), infertility diagnosis and ART outcomes were investigated. Massively parallel sequencing permitted not only the accurate detection of mutations but also the precise quantification of levels of mutations in cases of heteroplasmy. Sequence variants in the mtDNA were evaluated using Mitomaster and HmtVar to predict their potential impact. The relative mtDNA CC content was significantly associated with BMI. No significant associations were observed between CC mtDNA quantity and patient age, female infertility diagnosis or any ART outcome variable. mtGenome sequencing revealed 4181 genetic variants with respect to a reference genome. The COXI locus contained the least number of coding sequence variants, whereas ATPase8 had the most. The number of variants predicted to affect the ATP production differed significantly between mitochondrial macrohaplogroups. The total number of retrieved oocytes was different between the H-V and J-T as well as the U-K and J-T macrohaplogroups. There was a non-significant increase in mtDNA levels in CCs with heteroplasmic mitochondrial mutations. N/A. Although a large number of samples were analysed in this study, it was not possible to analyse all the CCs from every patient. Also, the results obtained with respect to specific clinical outcomes and macrohaplogroups should be interpreted with caution due to the smaller sample sizes when subdividing the dataset. These findings suggest that the analysis of mtDNA in CCs is unlikely to provide an advantage in terms of improved embryo selection during assisted reproduction cycles. Nonetheless, our data raise interesting biological questions, particularly regarding the interplay of metabolism and BMI and the association of mtDNA haplogroup with oocyte yield in ovarian stimulation cycles. This study was funded by National Institutes of Health grant 5R01HD092550-02. D.J.N. and C.R. co-hold patent US20150346100A1 and D.J.N. holds US20170039415A1, both for metabolic imaging methods. D.W. receives support from the NIHR Oxford Biomedical Research Centre. The remaining authors have no conflicts of interest to declare.

Mitochondrial DNA sequence variation and risk of meningioma.

Risk factors for meningioma include female gender, African American race, high body mass index (BMI), and exposure to ionizing radiation. Although genome-wide association studies (GWAS) have identified two nuclear genome risk loci for meningioma (rs12770228 and rs2686876), the relation between mitochondrial DNA (mtDNA) sequence variants and meningioma is unknown. We examined the association of 42 common germline mtDNA variants (minor allele frequency ≥ 5%), haplogroups, and genes with meningioma in 1080 controls and 478 meningioma cases from a case-control study conducted at medical centers in the southeastern United States. Associations were examined separately for meningioma overall and by WHO grade (n = 409 grade I and n = 69 grade II/III). Overall, meningioma was significantly associated with being female (OR 2.85; 95% CI 2.21-3.69), self-reported African American race (OR 2.38, 95% CI 1.41-3.99), and being overweight (OR 1.48; 95% CI 1.11-1.97) or obese (OR 1.70; 95% CI 1.25-2.31). The variant m.16362T > C (rs62581341) in the mitochondrial control region was positively associated with grade II/III meningiomas (OR 2.33; 95% CI 1.14-4.77), but not grade I tumors (OR 0.99; 95% CI 0.64-1.53). Haplogroup L, a marker for African ancestry, was associated with meningioma overall (OR 2.92; 95% CI 1.01-8.44). However, after stratifying by self-reported race, this association was only apparent among the few self-reported Caucasians with this haplogroup (OR 6.35; 95% CI 1.56-25.9). No other mtDNA variant, haplogroup, or gene was associated with meningioma. Common mtDNA variants and major mtDNA haplogroups do not appear to have associations with the odds of developing meningioma.

High levels of mitochondrial DNA sequence divergence among isolated populations of Fontigens (Truncatelloidea: Emmericiidae) in eastern USA

ABSTRACT Populations of the minute emmericiid gastropod Fontigens inhabit isolated springs, caves and groundwaters widely scattered across eastern and midwestern USA. Nine species are currently recognized, with a tenth species, Fontigens cryptica, of uncertain status. Here, we survey intrapopulation, interpopulation and interspecific sequence variation of cytochrome c oxidase subunit I among six of the nine species (13 populations, 87 individuals), documenting up to 14.4% sequence divergence among conspecific populations. Interspecific divergence ranges from 8.7% to 21.9%. We also include in our analysis a single putative individual of F. cryptica, recently sampled from Kentucky, evaluating whether the population it represents may be genetically distinct. Fit within a larger phylogenetic context, the 14.4% sequence divergence demonstrated between this individual and its nearest neighbour, F. bottimeri sampled from Washington, DC, supports the specific status of F. cryptica.

Small vs. large eggs: comparative population connectivity and demographic history along a depth gradient in deep-sea crangonid Argis shrimps

Abstract The crangonid shrimps Argis hozawai, A. lar and A. toyamaensis, co-distributed in the Sea of Japan, exhibit intriguing differences in geographical and bathymetric distributions and in reproductive biology. Argis hozawai (150–250 m depth) and A. lar (200–300 m) are broadly distributed in the north-western Pacific Ocean and spawn relatively large numbers of small eggs, whereas A. toyamaensis (250–2000 m) is distributed in the Sea of Japan and spawns a small number of large eggs. We examined the relationship between egg size and dispersal patterns in the deep sea by comparing genetic population structures using mitochondrial DNA sequence variation. We found little or no genetic divergence within the Sea of Japan for A. hozawai and A. lar, whereas there was a slight but significantly higher genetic differentiation in A. toyamaensis. This suggests that A. toyamaensis has lower dispersal ability than A. hozawai and A. lar, and therefore might maximize larval survival through larger size at hatching, with either direct or abbreviated larval development, to adapt to the deep-sea environment in the Sea of Japan. We also detected the effects of drastic environmental changes during the Pleistocene glacial periods on their demographic processes in the Sea of Japan.

Sperm parameters and mitochondrial DNA sequence variants among patients at a fertility clinic in Ghana.

PurposeThe present study sought to investigate the common abnormalities and mtDNA mutations in the sperm of Ghanaian men attending the fertility Clinic at the Korle-Bu Teaching Hospital (KBTH). The study therefore provides a baseline data mtDNA mutations in a cross-section of Ghanaian men on referral to the fertility clinic at the KBTH.Materials and methodsThe semen of 55 men attending the fertility clinic were collected from the Urology and the Obstetrics and Gynaecology Departments of the KBTH. Demographic and clinical data were also collected using questionnaires. Semen analyses were performed and were followed by amplification and purification of mtDNA from total DNA extracted from the semen. Sequencing of the mtDNA amplicons was performed using the next generation sequencer (Illumina-MiSeq).ResultsAsthenozoospermia, oligospermia and oligoasthenoteratozoospermia were observed in 1.79%, 5.36% and 28.57%, respectively, of the study participants. There was no association between drinking and/or smoking and history of gonorrhea infection on sperm status/morphology. A total of 785 point mutations were detected in the non-coding control regions, rRNA genes, tRNA genes and the coding regions of the mtDNA samples from the participants. Amongst these mutations, 16 transition mutations were predominantly detected in the mtDNA samples. Missense mutations that were present in only specific sperm abnormalities were identified and they may contribute to infertility in the study population.ConclusionThe present study has identified various abnormal sperm phenotypes that are prevalent in the study population and provided a baseline data on mtDNA mutations in the spermatozoa of the patients. A wide range of sperm abnormalities were detected in the study population with no association with life style or history of gonorrhea infection. The mtDNA point mutations detected in the selected genes that were analysed were mostly transition mutations. These transition mutations might be critical for the development of abnormal sperm phenotypes underlying male infertility in the Ghanaian population.

Evaluation of the efficacy of mitochondrial ATP 6 and 8, Cyt b and 16S rDNA genes for differentiation of Iranian honeybees (Apis mellifera meda) from commercial subspecies of Apis mellifera L. and comparison with geometric morphometric method

• 16S rDNA differentiated the commercial subspecies from Iranian honeybees. • Cluster analyses discriminated the commercial subspecies from Iranian honeybees. • The phylogenetic tree of the 16S rDNA affirmed the geometric morphometric method. Mitochondrial DNA sequence variations and the geometric morphometric method can be used to differentiate honeybee subspecies and evolutionary lineages. Molecular markers are powerful tools for discriminating honeybee subspecies. In this study, 19 beekeeping sites were selected to collect Iranian honeybee samples. The honeybee forewing images stored at Oberursel (the Bee Data Bank) were used to compare with those of Iranian honeybees using the geometric morphometric method. Furthermore, the abilities of DNA markers to differentiate Iranian honeybees ( A. m. meda ) from the most common commercial subspecies ( A. m. carnica and A. m. ligustica ) were assessed. In the present research, 16S rDNA (Mitochondrial 16S rDNA Region) showed greater ability in differentiating Iranian honeybees from other subspecies compared with ATP 6 and 8 and Cyt b. The phylogenetic tree derived from 16S rDNA differentiated A. m. carnica and A. m. ligustica from Iranian honeybees. Principle component analysis (PCA) discriminated C lineage and Z subgroup from A and M lineages using 16S rDNA. In addition, the phylogenetic tree of the 16S rDNA affirmed the findings of the cluster analysis derived from the geometric morphometric method in differentiating A. m. carnica and A. m. ligustica from Iranian honeybees. The cluster analysis grouped reference subspecies of A. m. meda with Iranian honeybees. Moreover, the Discriminant Function Analyses (DFA) differentiated Iranian honeybees from A. m. ligustica and A. m. carnica .

Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America.

Isthmian Central America (ICA) is one of the most biodiverse regions in the world, hosting an exceptionally high number of species per unit area. ICA was formed <25 million years ago and, consequently, its biotic assemblage is relatively young and derived from both colonization and in situ diversification. Despite intensive taxonomic work on the local fauna, the potential forces driving genetic divergences and ultimately speciation in ICA remain poorly studied. Here, we used a landscape genetics approach to test whether isolation by distance, topography, habitat suitability, or environment drive the genetic diversity of the regional frog assemblage. To this end, we combined data on landscape features and mitochondrial DNA sequence variation for nine codistributed amphibian species with disparate life histories. In five species, we found that at least one of the factors tested explained patterns of genetic divergence. However, rather than finding a general pattern, our results revealed idiosyncratic responses to historical and ecological processes, indicating that intrinsic life-history characteristics may determine the effect of different drivers of isolation on genetic divergence in ICA. Our work also suggests that the convergence of several factors promoting isolation among populations over a heterogeneous landscape might maximize genetic differentiation, despite short geographical distances. In conclusion, abiotic factors and geographical features have differentially affected the genetic diversity across the regional frog assemblage. Much more complex models (i.e., considering multiple drivers), beyond simple vicariance of Caribbean and Pacific lineages, are needed to better understand the evolutionary history of ICA's diverse biotas.

A new bat species of the genus Myotis with comments on the phylogenetic placement of M. keaysi and M. pilosatibialis

Molecular studies of Neotropical Myotis (Chiroptera, Vespertilionidae) in the last decade have uncovered substantial cryptic diversity. One example is M. keaysi pilosatibialis , which is characterized by a complex taxonomy derived from low morphological variation. Herein, we studied cryptic diversity of a high elevation clade from premontane and montane forest of Chiriqui Province (Panama), Cordillera Oriental (Ecuador), and Valle del Silencio (Costa Rica). Additionally, we disentangle relationships of M. k. keaysi and M. k. pilosatibialis by determining their phylogenetic placement within the Neotropical Myotis radiation. In the process, we identified a new lineage of species level hierarchy that is described herein. We used an integrative taxonomy approach, using a combination of linear morphometrics, qualitative morphology, molecular phylogenetics, and climatic analysis. The newly identified lineage is a sister species to M. pilosatibialis str., but differs from M. sp. (Quintana Roo, Mexico), M. keaysi str. , and M . oxyotus gardneri in size and other quantitative morphological characters in addition to both nuclear and mitochondrial DNA sequence divergence. Based on our phylogenetic analysis of partial cytochrome b sequence, the polyphyly of M . keaysi str. and M. pilosatibialis str. is resolved, with M . keaysi str. paraphyletic to M . ruber and M . simus . Myotis pilosatibialis is part of a monophyletic clade that is sister to the newly identified species. This report refines our understanding of taxonomy and systematics of the Myotis pilosatibialis complex of bats, identifies and describes a new species of Myotis, and more broadly it contributes to efforts to characterize species in this genus in Neotropical environments. Based on its distribution, we classified this newly described species as paramontane due to its restriction to premontane and montane forest of Chiriqui Province (Panama), Valle del Silencio (Costa Rica), and Cordillera Oriental (Ecuador). These habitats are susceptible to the effects of climate change, in addition to ongoing habitat destruction.