Mitochondrial DNA Sequences Research Articles

Nuclear genetic diversity of head lice sheds light on human dispersal around the world.

The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.

A new family with a case of severe early-onset muscle fatigue and a peculiar maternally inherited painful swelling in chewing muscles associated with homoplasmic m.15992A>T mutation in mitochondrial tRNAPro

A 16-year-old boy was evaluated for a history of exercise-induced fatigability associated with nausea even after minimal effort, lower limbs muscle hypotrophy, and swelling of the masseter muscles after chewing. Laboratory tests were remarkable for hyperlactatemia and metabolic acidosis after short physical activity. The muscle biopsy showed non-specific mitochondrial alterations and an increase in intrafibral lipids. Biochemical analysis showed reduced activity of the respiratory chain complexes. Mitochondrial DNA sequencing revealed the presence of a homoplasmic variant m.15992A>T in the MT-TP gene, coding for the mt-tRNAPro in the patient, in his mother and in his brother. Pathogenic or likely pathogenic variants in MT-TP gene are rare. They are responsible for different clinical presentation, almost ever involving the muscle tissue. We report the first family with exercise-induced muscle weakness and swelling of the chewing muscles due to m.15992A>T variant in absence of J1c10 haplogroup, confirming its pathogenicity.

Initial characterization of mitochondrial DNA control region haplotypes of the Antillean manatee (Trichechus manatus manatus, Sirenia:Trichechidae) in Guatemala

Introduction: Small populations are at risk of losing genetic variability much faster than large populations; this subsequently decreases their ability to adapt when facing environmental changes. A small population of the endangered Antillean manatee (Trichechus manatus manatus) has been identified in Guatemala.
 Objective: This study explored the genetic diversity of the Antillean manatee in Guatemala by analysing mitochondrial DNA control region haplotypes in the two most important habitats for the species, Bahía La Graciosa, a coastal bay and Bocas del Polochic, a coastal wetland, both located in the Izabal State.
 Methods: Genetic samples were collected using non or minimally invasive sampling techniques: scraping of epidermal tissue, collection of floating feces, and collection of tissue from carcasses. DNA extractions, DNA amplification using polymerase chain reaction (PCR), and sequencing of the control D-loop region were used to process and analyse the samples.
 Results: Seven mitochondrial DNA sequences were obtained from 36 samples collected (minimum of four and maximum of seven individuals). Four haplotypes were identified, A01, A03, A04, and J01. No other Central American country has reported this number of haplotypes in a manatee population, and it is the first time that haplotype A01 has been reported for the region. The Guatemalan manatee population comprises at least two genetic lineages, the Florida/Greater Antilles lineage (haplotypes A01, A03, and A04) and the Mesoamerican lineage (J01).
 Conclusion: Further studies, with the use of nuclear markers, are necessary to understand the population dynamics between Bahia La Graciosa and Bocas del Polochic to identify the number of management units present in the country; also, the degree of relatedness with the Belizean population needs to be established to better coordinate conservation efforts.

Phylogeography of two codistributed terrestrial snails in the Maputaland–Pondoland–Albany biodiversity hotspot, South Africa

Abstract We investigated the evolutionary patterns of two forest-dwelling endemic terrestrial snails (Gittenedouardia spadicea and Maizania wahlbergi) in the Maputaland–Pondoland–Albany biodiversity hotspot in South Africa to examine the degree of phylogeographical congruence between the two species. Phylogenetic relationships and divergence time estimations within each species were inferred using the combined mitochondrial DNA (mtDNA) sequence dataset for the cytochrome c oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA). In addition, the rapidly evolving COI datasets were used to infer intraspecific genetic structure and population differentiation within both species. Phylogeographical concordance factor (PCF) analysis was used to statistically estimate the degree of congruence between the two species at localities where both species were sampled. Phylogenetically, G. spadicea exhibited two clades that diverged during the Plio/Pleistocene, while M. wahlbergi formed a single shallow clade that showed Pleistocene divergence. The haplotype networks for the COI locus demonstrated evidence of geographical and genetic isolation within both species. PCF analysis demonstrated partial phylogeographical concordance, suggesting that the two species may have been affected by similar ancient climatic events. Traits other than poor dispersal capabilities and limited gene flow may also influence how a species responds to fluctuating climate change.

A melting pot of Roman dogs north of the Alps with high phenotypic and genetic diversity and similar diets

Several dog skeletons were excavated at the Roman town of Augusta Raurica and at the military camp of Vindonissa, located in the northern Alpine region of Switzerland (Germania Superior). The relationships between them and the people, the nature of their lives, and the circumstances of their deaths are unclear. In order to gain insight into this dog population, we collected 31 dogs deposited almost simultaneously in two wells (second half of the third century CE), three dogs from burial contexts (70–200 CE and third to fifth century CE) at Augusta Raurica, and two dogs from burial contexts at Vindonissa (ca. first century CE). We detected a mixed population of young and adult dogs including small, medium and large sized individuals. Three small dogs had conspicuous phenotypes: abnormally short legs, and one with a brachycephalic skull. Stable isotope analysis of a subset of the dogs showed that their diets were omnivorous with a substantial input of animal proteins and little variation, except one with a particularly low δ15N value, indicating a diet low in animal proteins. Partial mitochondrial DNA sequences from 25 dogs revealed eight haplotypes within canine haplogroup A (11 dogs; 44%; 5 haplotypes), C (8 dogs; 32%; 1 haplotype), D (4 dogs, 16%; 1 haplotype) and B (2 dogs, 8%; 1 haplotype). Based on shotgun sequencing, four Roman mitogenomes were assembled, representing sub-haplogroups A1b3, A1b2 and C2. No canine pathogens were identified, weakening the assumption of infectious disease as a cause for dog disposal. The genetic and morphological diversity observed in dogs of Augusta Raurica and Vindonissa is similar to modern dog diversity.

Characterization and phylogenetic analysis of the complete mitochondrial genome of a unique economic plant <i>Lycium barbarum</i> L.

<i>Lycium barbarum</i> L. (<i>L. barbarum</i>), an important medicinal and food crop from the Solanaceae family, is known for excellent tolerance to saline–alkaline and drought stresses. Therefore, it has significant research and application value. The nuclear and chloroplast genomes of <i>L. barbarum</i> have been previously reported; however, its mitochondrial genome is still unexplored. In this study, mitochondrial DNA sequencing and assembly in <i>L. barbarum</i> were studied via second- and third-generation sequencing technologies using the anthers collected from the main cultivars “Ningqi No.1” (fertile line) and its male-sterile natural mutant “Ningqi No.5” from Ningxia, China. The results revealed that “Ningqi No.1” and “Ningqi No.5” have the same mitochondrial circular genome structure with a total length of 413,881 bp. In total, 61 genes were annotated, including 35 protein-coding genes, four rRNA genes, 22 tRNA genes, and 2,242 open reading frames with unknown functions. The repeat sequences in mtDNA were analyzed, in which short repeats (30–59 bp) exhibited the highest number. Overall, 23 protein-coding genes in “Ningqi No.1” and “Ningqi No.5” exhibited RNA-editing phenomenon, with different RNA-editing site number and distribution position. Phylogenetic analysis demonstrated that <i>L. barbarum</i> has the closest relationship with <i>Hyoscyamus niger</i>. These results provided a basis for a comprehensive understanding of the mitochondrial genome of <i>L. barbarum</i> and the relevant data for omics studies on <i>L. barbarum</i>.

The known unknowns of mitochondrial carcinogenesis: de novo NUMTs and intercellular mitochondrial transfer.

The translocation of mitochondrial DNA (mtDNA) sequences into the nuclear genome, resulted in the occurrence of nuclear sequences of mitochondrial origin (NUMTs) which can be detected in nearly all sequenced eukaryotes. However, de novo mtDNA insertions can contribute to the development of pathological conditions including cancer. Recent data indicate that de novo mtDNA translocation into chromosomes can occur due to genotoxic influence of DNA double-strand break-inducing environmental mutagens. This confirms the hypothesis of the involvement of genome instability in the occurrence of mtDNA fragments in chromosomes. Mounting evidence indicates that mitochondria can be transferred from normal cells to cancer cells and recover cellular respiration. These exchanged mitochondria can facilitate cancer progression and metastasis. This review article provides a comprehensive overview of the potential carcinogenicity of mtDNA insertions, and the relevance of mtDNA escape in cancer progression, metastasis, and treatment resistance in humans. Potential molecular targets involved in mtDNA escape and exchange of mitochondria that can be of possible clinical benefits are presented and discussed. Understanding these processes could lead to improved diagnostic approaches, novel therapeutic strategies, and a deeper understanding of the intricate relationship between mitochondria, nuclear DNA, and cancer biology.

Multiple TP53 p.R337H haplotypes and implications for tumor susceptibility

The germline TP53 p.R337H mutation is reported as the most common germline TP53 variant. It exists at a remarkably high frequency in the population of southeast Brazil as founder mutation in two distinct haplotypes with the most frequent co-segregating with the p.E134∗ variant of the XAF1 tumor suppressor and an increased cancer risk. Founder mutations demonstrate linkage disequilibrium with neighboring genetic polymorphic markers that can be used to identify the founder variant in different geographic regions and diverse populations. We report here a shared haplotype among Brazilian, Portuguese, and Spanish families and the existence of three additional distinct TP53 p.R337H alleles. Mitochondrial DNA sequencing and Y-STR profiling of Brazilian carriers of the founder TP53 p.R337H allele reveal an excess of Native American haplogroups in maternal lineages and exclusively European haplogroups in paternal lineages, consistent with communities established through male European settlers with extensive intermarriage with Indigenous women. The identification of founder and independent TP53 p.R337H alleles underlines the importance for considering the haplotype as a functional unit and the additive effects of constitutive polymorphisms and associated variants in modifier genes that can influence the cancer phenotype.

Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods.

The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, H O = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median-joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam-Fujian, Myanmar-West Yunnan, and Laos-Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation-by-distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male-biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam-Fujian clade and the Myanmar-West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on-site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.

Population genetic structure of a Chihuahuan Desert endemic mammal, the desert pocket gopher, Geomys arenarius.

The biogeographic history of the Chihuahuan Desert is complex, driven by numerous physiographic events and climatic changes. This dynamic history would have influenced the flora and fauna of the region including the desert pocket gopher, Geomys arenarius, a subterranean rodent endemic to the northern Chihuahuan Desert. G. arenarius is restricted to sandy soils and are considered to have a disjunct distribution. Two subspecies are recognized: G. a. arenarius and G. a. brevirostris. We used multilocus nuclear (amplified fragment length polymorphisms) and mitochondrial DNA (ND2) sequence data to uncover patterns of genetic diversity within and among populations of G. arenarius. We evaluated correspondence of genetic patterns to traditionally accepted subspecies boundaries, mapped the distribution of potentially suitable soils to identify barriers or corridors to dispersal and to guide future survey efforts, provided evidence that could be used to recognize distinct population segments, and quantified genetic diversity within populations. Both datasets were largely concordant and demonstrated hierarchical patterns of genetic divergence. The greatest divergence was consistent with the two recognized subspecies. Mapping of potentially habitable soils revealed likely barriers to dispersal contributing to the allopatric pattern of geographic distribution and areas, which may be occupied by G. arenarius but not yet documented. Because G. arenarius is restricted to soils with high sand content, and these habitable soils are disjunct within the region occupied by this species, historical factors that impacted soil deposition and deflation likely contributed to the observed patterns of genetic divergence. Genetic diversity was higher within populations of the southern subspecies (G. a. arenarius) compared to G. a. brevirostris. This may be due to a greater availability of continuous suitable soils within the range of G. a. arenarius or higher density due to greater food availability (currently or historically)-both of which could allow for a higher effective population size.

The bear necessities: A sensitive qPCR assay for bear DNA detection from bile and derived products to complement wildlife forensic enforcement

Demand for bear bile, a prized component of traditional Asian medicines, threaten Asiatic and sun bear population sustainability. While laws exist to prevent poaching and trafficking of bear parts and derivatives, smuggling persists with demand extending to surrogate species, including American black bears (Ursus americanus). Mitochondrial DNA (mtDNA) sequencing can identify products putatively containing biological bear material but can be undermined by PCR inhibitors in bile and a lack of sensitivity at trace levels. Quantitative PCR (qPCR) assays can be used to distinguish between closely related target species, while concomitantly evaluating inhibition and false negative results in low quality/quantity DNA applications. Herein, we develop a multiplexed qPCR assay to detect and differentiate among bear species, including highly diluted bile samples mixed within liquors as common dilutants. The assay detects as little as 10 locus copies/reaction of bear DNA with 95% confidence, distinguishing among sun, Asiatic and American black bears. Demonstrating the sensitivity and applicability of this assay in context of current bile mixture recipes, dilutions of 1:5,000 bile with ethanol, red wine, and spirits, all yielded clear quantifiable detections, where our data suggests as little as 1 drop of bile per 750 mL bottle of alcohol would still exceed the limits of detection (e.g., 1:15000 dilution or <0.05 mL bile per 750 mL bottle). Overall, this study provides a rapid, sensitive, and specific test to identify and distinguish among bear species commonly used for bile production to aid wildlife enforcement applications.

Genetic connectivity constrained by natural barriers in a key agricultural pest: insights from mitochondrial DNA analysis

In the context of anthropogenic global change, the study of landscape effects on species movement has garnered increasing attention. Landscape genetics offer indirect yet attractive means to capture species dispersal events across generations and their interaction with landscapes. However, landscape genetic patterns tend to exhibit significant variations across taxa and rely on the molecular makers adopted. Here, we investigated how landscapes influence population connectivity of an important tea pest, Empoasca onukii, using mitochondrial DNA sequences of 1,518 individuals from 57 locations in mainland China and offshore islands. We analyzed the inter-population genetic divergence and integrated multiple models to explicitly quantify their association with geographic distance, environmental heterogeneity, and landscape barriers. Analyses revealed a reduction in gene flow on islands, along the Yangtze River, and across mountainous regions of Western China. Models explicitly detected the predominant contributions of topographic complexity to population divergence and evidenced that mountains may serve as effective dispersal barriers for E. onukii. These results suggest that the limited gene exchange resulting from low population connectivity among mountains might generate the observed patterns of mitochondrial genetic variations, which contrasts the climate-related pattern previously observed on microsatellites. The findings enhance our comprehension of the evolutionary and epidemic dynamics of E. onukii, and highlight the demand of considering species-specific traits when studying population landscape genetic patterns. Moreover, the study emphasizes the necessity of employing multiple molecular markers to comprehensively elucidate landscape effects on population connectivity across diverse species for valuable insights into biodiversity conservation, pest control, and other management decisions.

Molecular Identification and Evolutionary Divergence of the Sri Lankan Sambar Deer, Rusa unicolor (Kerr 1792).

The Sambar is one of the largest deer species distributed mainly in Asia, and it has been listed as a vulnerable species. Taxonomy based on morphological characterization has been the gold standard method used to identify the Sambar deer species. Yet, morphological identification is challenging and requires expertise. To conduct species identification and taxonomic decisions, we performed the molecular identification of R. unicolor found in Sri Lanka using DNA barcodes, COI, and Cyt b to compare the Sri Lankan R. unicolor with the Indian R. unicolor and other R. unicolor subspecies. We obtained mitochondrial DNA sequences from COI and Cyt b from blood samples collected from the wet zone in Sri Lanka. A phylogenetic tree was constructed based on the Bayesian analyses using MrBayes 3.2.7. Molecular dating was implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST v1.8.2) on the concatenated sequence using a log-normal relaxed clock and Yule species tree prior, with four categories. The results showed that the Sri Lankan R. unicolor is genetically different from the Indian R. unicolor and other R. unicolor subspecies. The divergence occurred approximately 1.1 MYA (million years ago) in the Pleistocene era. The results are essential for designing new conservation platforms for these Sambar deer species.

DNA barcoding of the genus Apaidia Hampson, 1900 for species delimitation from Western Mediterranean fauna (Lepidoptera, Erebidae).

The genus Apaidia Hampson, 1900 is a relict Western Mediterranean genus in the South-western part of Europe and the North-western areas of the Mediterranean Africa comprising so far three species, Apaidia rufeola (Rambur, 1832), Apaidia mesogona (Godart, [1824]) and Apaidia barbarica Legrand, 1939. According to the examined material, COI mitochondrial DNA sequences and adult morphology integration supports the existence of three main lineages of Apaidia with sequence divergence rates of approximately 4.5%, which are within the range reported for other well-defined insect species. In addition, we recovered three different BINS, suggesting the presence of different species with unique and specific identifier for A. mesogona (AEC6797), A. rufeola (AEI9539), and the Iberian-Balearic A. barbarica (AEI9540). This study contributes to a better understanding of the taxonomy of the genus Apaidia and challenges future revision of this genus in Northern Africa, as well as the presence of the Apaidia species in Western Mediterranean islands and populations located in Italy.

Successful transcatheter mitral valve repair for functional mitral regurgitation in a patient with mitochondrial cardiomyopathy: a case report

Abstract Background Mitochondrial diseases are a group of genetic disorders caused by nuclear or mitochondrial DNA gene mutations and characterized by multiorgan disorders, including cardiomyopathy. Mitochondrial cardiomyopathy is occasionally complicated by hypertrophic cardiomyopathy with/without left ventricular systolic dysfunction, dilated cardiomyopathy, and left ventricular non-compaction. In such cases, the dilated left ventricle impairs coaptation of the mitral leaflets and leads to functional mitral regurgitation. To date, valvular interventions in patients with mitochondrial cardiopathy have not been investigated. Case summary A 64-year-old woman with mitochondrial cardiopathy was referred to our hospital owing to dyspnoea. She experienced her first admission with heart failure at age 60 years. At 62 years old, she was diagnosed with maternally inherited diabetes and deafness with mitochondrial cardiomyopathy based on mitochondrial DNA sequencing. Despite administration of guideline-directed medical therapy and high-dose taurine supplementation, she was repeatedly hospitalized for heart failure. At admission, transthoracic echocardiography revealed severe functional mitral regurgitation due to left ventricular dilatation. Surgical risk was considered high (Society of Thoracic Surgeons score of 12.6%); therefore, transcatheter edge-to-edge repair with the MitraClip system was performed. Two devices deployed at the middle segment of the anterior and posterior leaflet successfully reduced mitral regurgitation. The patient was free from cardiovascular events during the 2-year follow-up period. Discussion Transcatheter edge-to-edge repair is a less invasive and effective treatment for severe drug-refractory mitral regurgitation in patients with mitochondrial disease. Given the limited therapeutic options for mitochondrial cardiopathy, further studies are required to uncover the mechanism underlying mitochondrial diseases and establish disease-specific treatments.

Taxonomic classification on phylogenic information appears a debatable approach: Lessons from the order Cypriniformes

Genes are often selected for molecular taxonomy citing their agreement to taxonomically derived species trees. These results are then used to define and edit existing taxonomic hierarchies of species. We counter the validity of this practice experimentally using mitochondrial genes routinely employed for the purpose. We constructed trees from complete mitochondrial DNA sequence (except D-loop) and its thirteen protein-coding genes namely ND1, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6, ATP8, COI, COII, COIII, and CYTB of 255 species of Cypriniformes fish using the maximum likelihood and Bayesian methods. While ND4, ND5, COI, COII, COIII, and CYTB formed trees at par with the species tree, no gene produced complete concurrence. Similarly, while few genes formed similar branching patterns at family (COI and COIII) or broad group (ND1, ND2, and ND3; ND5 and COII) levels, no two gene trees fully agreed with each other. Tajima's D estimates of all studied genes indicated non-random evolution, violating the basic assumption of molecular phylogenetics. Bootstrap or Posterior probability values were also poor for several taxa indicating low robustness. Our findings reiterate that tree concurrence noted in studies involving smaller sample sizes is not a reflection of the evolutionary signature of the species.

Notes on the ecology and distribution of a water flea complex (Anomopoda, Daphniidae) revealed by new DNA barcodes in the Iberian Peninsula

AbstractAvailable DNA barcodes of freshwater zooplankton are scarce in regions like the Iberian Peninsula, which harbours many rare and endemic species and is considered a hotspot of crustacean biodiversity. Recently, a new species of Ceriodaphnia (Cladocera: Daphniidae) was described using morphological analysis of specimens in the Mediterranean region and molecular data on a single locality in southern Spain. In our study, we detected the presence of the newly discovered taxa and here, we provide new DNA sequences on the barcoding region mitochondrial cytochrome c oxidase I together with ecological information of the recently described Ceriodaphnia smirnovi. Additionally, we built a molecular phylogenetic tree and genetically compared these specimens with previously available mitochondrial DNA sequences and with new sequences of the genus recovered in Iberia. Our data suggest that this morphospecies might contain some cryptic taxa and might be more common than previously thought, occupying temporary to semi‐permanent ecosystems, with vegetation and highly variable pH and turbidity conditions. Moreover, the existence of a non‐identified clade within our phylogenetic tree requires additional morphological research. Our study highlights the need for further research on microcrustacean biota to better constrain its spatial boundaries, phylogenetic relationship and determine species hiding cryptic diversity.

Genetic analysis of federally endangered Cape Sable seaside sparrow subpopulations in the Greater Everglades, USA

The federally endangered Cape Sable seaside sparrow (Ammospiza maritima mirabilis) is endemic to the Greater Everglades ecosystem in southern Florida, inhabiting fragmented marl prairies in six individual subpopulations. The subspecies is threatened by loss of breeding habitat from fire and water management. Genetic information is severely limited for the subspecies but could help inform decisions regarding subpopulation protections and potential translocations for genetic rescue. To provide genetic data and inform management efforts, feather samples were collected across five subpopulations (designated A–E) and protocols were tested to optimize DNA extraction yields. We assessed four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) in 108 sparrows. Mitochondrial DNA sequences revealed low haplotype diversity, with NADH dehydrogenase-2 haplotypes matching to most other extant subspecies and to the Atlantic coast subspecies. Nuclear diversity was low compared to other subspecies, but similar across subpopulations. Samples grouped as one population when analyzed by Principal Component Analysis, Bayesian modelling and genetic distance metrics. Limited genetic emigration was detected from one putative migrant. Relatedness was significantly different for sparrows in the most geographically distant subpopulation (A), likely reflecting high self-recruitment and natal site fidelity (P = 0.003). The low to moderate effective population size (NE = 202.4; NE:NC = 0.06) and generation time estimates indicated that unique genetic variation could be lost quickly during stochastic events. The sample sizes were limited, which reduced the power to comprehensively address recent population size reductions and any subsequent loss of genetic diversity.

Mitochondrial DNA mutations can influence the post-implantation development of human mosaic embryos.

Introduction: Several healthy euploid births have been reported following the transfer of mosaic embryos, including both euploid and aneuploid blastomeres. This has been attributed to a reduced number of aneuploid cells, as previously reported in mice, but remains poorly explored in humans. We hypothesized that mitochondrial function, one of the most critical factors for embryonic development, can influence human post-implantation embryonic development, including a decrease of aneuploid cells in mosaic embryos. Methods: To clarify the role of mitochondrial function, we biopsied multiple parts of each human embryo and observed the remaining embryos under in vitro culture as a model of post-implantation development (n = 27 embryos). Karyotyping, whole mitochondrial DNA (mtDNA) sequencing, and mtDNA copy number assays were performed on all pre- and post-culture samples. Results: The ratio of euploid embryos was significantly enhanced during in vitro culture, whereas the ratio of mosaic embryos was significantly reduced. Furthermore, post-culture euploid and culturable embryos had significantly few mtDNA mutations, although mtDNA copy numbers did not differ. Discussion: Our results indicate that aneuploid cells decrease in human embryos post-implantation, and mtDNA mutations might induce low mitochondrial function and influence the development of post-implantation embryos with not only aneuploidy but also euploidy. Analyzing the whole mtDNA mutation number may be a novel method for selecting a better mosaic embryo for transfer.

Phylogeography of the Cow Knob Salamander (Plethodon punctatus Highton): populations on isolated Appalachian mountaintops are disjunct but not divergent

Although many studies have examined how taxa responded to Pleistocene climate fluctuations in the Appalachian Mountains, impacts on high-elevation endemics of Central Appalachia are not yet understood. We use mitochondrial (ND4 &amp;amp; Cytb) and nuclear (GAPD) DNA sequences to investigate the phylogeography of the Cow Knob Salamander (Plethodon punctatus), a woodland species from Central Appalachian highlands thought to have origins in the Pleistocene. Data from 72 tail tips representing 25 sites revealed that the species comprises two geographically cohesive mitochondrial clades with a narrow, putative contact zone on Shenandoah Mountain. Molecular clock estimates indicate the clades diverged in the Middle Pleistocene. The population size of the Southern clade appears to have remained stable for at least 50,000 years. Despite spanning several isolated mountain systems, the Northern clade has exceptionally low genetic diversity, probably due to recent demographic expansion. Palaeodemographic hypothesis testing supported a scenario in which a founder effect characterized the Northern clade as it diverged from the Southern clade. Species distribution models predicted no suitable habitat for the species during the Last Glacial Maximum. Ultimately, Pleistocene glacial climates may have driven the species from the northern half of its current range, with recolonization events by members of the Northern clade as climates warmed. Density dependent processes may now maintain a narrow contact zone between the two clades.