A new rainfrog of the genus Pristimantis (Anura, Brachycephaloidea) from central and eastern Panama

Substantial molecular and morphological character differences lead us to the description of a new species of the genus Pristimantis from the cloud forest of Cerro Chucantí, Maje Mountains, Darien Province, as well as from several other mountain ranges in eastern and central Panama. Pristimantis gretathunbergaesp. nov. is a sister species to the allopatric P. erythropleura-penelopus group from northern Colombia with a mtDNA sequence divergence of > 4.4% at 16S and > 14.6% at COI. Its closest congener in sympatry is P. cruentus that differs by a large sequence divergence of > 9.6% in 16S mtDNA and 19.0% at COI, and from which it differs also by ventral and groin coloration, unusually prominent black eyes, a contrasting light upper lip, commonly a single conical to spine-like tubercle on the upper eyelid, and a larger head. While the habitat continuity at most sites in eastern Panama is moderate, habitats in central Panama are severely fragmented. Cerro Chucantí and the surrounding Maje Mountains are highly threatened by rapid deforestation and replaced by plantations and cattle pastures. Thus, investigations on the ecology of the new species and its population status, especially at the type locality, are highly recommended. As a flagship species, this new frog can help to preserve the Chucantí cloud forest including several recently described species known only from this isolated area in eastern Panama.

Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas

Background: Somatic mutations, copy-number variations, and genome instability of mitochondrial DNA (mtDNA) have been reported in different types of cancers and are suggested to play important roles in cancer development and metastasis. However, there is scarce information about pheochromocytomas and paragangliomas (PCCs/PGLs) formation. Material: To determine the potential roles of mtDNA alterations in sporadic PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of seventy-seven human tumors, using next-generation sequencing, and compared the results with normal adrenal medulla tissues. We also performed an analysis of copy-number alterations, large mtDNA deletion, and gene and protein expression. Results: Our results revealed that 53.2% of the tumors harbor a mutation in at least one of the targeted susceptibility genes, and 16.9% harbor complementary mitochondrial mutations. More than 50% of the mitochondrial mutations were novel and predicted pathogenic, affecting mitochondrial oxidative phosphorylation. Large deletions were found in 26% of tumors, and depletion of mtDNA occurred in more than 87% of PCCs/PGLs. The reduction of the mitochondrial number was accompanied by a reduced expression of the regulators that promote mitochondrial biogenesis (PCG1α, NRF1, and TFAM). Further, P62 and LC3a gene expression suggested increased mitophagy, which is linked to mitochondrial dysfunction. Conclusion: The pathogenic role of these finding remains to be shown, but we suggest a complementarity and a potential contributing role in PCCs/PGLs tumorigenesis.

A New Species of Diaphus Associated with Seamounts of the Emperor Chain, North-Western Pacific Ocean (Teleostei: Myctophiformes: Myctophidae)

A new species, Diaphus balanovi, is described based on 35 specimens collected over the Emperor Seamount Chain in the north-western Pacific Ocean. It belongs to the D. fulgens species complex and is most similar to D. kuroshio both morphologically and genetically. Nevertheless, the new species can be distinguished from D. kuroshio by its higher gill-rakers count, large luminous scale at PLO, large Dn, somewhat higher position of SAO3, otolith shape, and larger absolute size. The CO1 mtDNA sequence of D. balanovi differs by 16 substitutions from that of D. kuroshio. Diaphus balanovi may represent a benthopelagic derivate of D. kuroshio endemic to the Emperor Seamounts.

Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens

Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.

Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169–23.880% for COI, 1.336–23.434% for 12S, and 7.897–71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.

EPID-12. MITOCHONDRIAL DNA SEQUENCE VARIATION AND MENINGIOMA

Meningiomas are the most common primary central nervous system tumors. Risk factors include female sex, African American race, a higher body mass index, and exposure to ionizing radiation. Genome-wide association studies have identified two risk loci for meningioma in the nuclear genome (rs12770228 and rs2686876). Whereas mitochondrial DNA (mtDNA) sequence variants and haplogroups have been linked with certain cancers, research on meningioma is lacking. We examined the association of 42 common (minor allele frequency ≥ 5%) germline mtDNA variants, haplogroups, and genes with meningioma risk in 1,080 controls and 478 cases from a case-control study conducted at medical centers in the southeastern US. Participant 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 meningioma overall, WHO grade 1 (n=409) and WHO grade 2/3 (n=69) meningiomas. Overall, meningioma risk was significantly higher among women (OR=2.86; 95% CI:2.21-3.71) compared to men, higher among African Americans (OR=2.37, 95% CI:1.41-3.99) compared to Caucasians, and higher among those who were overweight (OR=1.48; 95% CI:1.11-1.98) or obese (OR= 1.73; 95% CI:1.26-2.38) compared to those of normal weight. The variant m.16362T >C (rs62581341) in the mitochondrial control region was positively associated with grade 2/3 meningiomas (OR=2.33; 95% CI: 1.14-4.79), but not with grade 1 tumors (OR=0.99; 95% CI:0.64-1.53). Haplogroup L, a marker for African ancestry, was identified among 3.6% of controls and 8.6% of cases and was associated with meningioma risk overall (OR=2.56; 95% CI:1.52-4.30). When stratifying by self-reported race, the association between haplogroup L and meningioma was only apparent among the small number of self-reported Caucasians with this haplogroup (OR=6.68; 95% CI=1.66-26.91) when compared to non-L haplogroups, combined. No other common mtDNA variant (minor allele >5%), haplogroup, or gene was associated with meningioma risk. These findings merit further study.

Genome-wide and cuticular hydrocarbon evidence shed light on potential drivers of speciation in a Neotropical ant species complex

Reproductive isolation between geographically separated populations is generally considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence and mitonuclear conflict. Here we performed an integrative study based on two genome-wide techniques, 3RAD and ultraconserved elements, coupled with cuticular hydrocarbon and mtDNA sequence data, to assess the species limits within the E. ruidum species-complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex, two widely distributed along the Neotropics and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, cuticular hydrocarbon differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.

Whole Mitochondrial Genome Analysis of the Daur Ethnic Minority from Hulunbuir of the Inner Mongolia Autonomous Region, China

Background: Mitochondrial DNA (mtDNA) variations are often associated with bioenergetics, disease, and speciation and can be used to track the history of women. Although advances in massively parallel sequencing (MPS) technology have greatly promoted our understanding of the population’s history (especially genome-wide data and whole Y chromosome sequencing), the whole mtDNA sequence of many important groups has not been fully studied. In this study, we employed whole mtDNA genomes of 209 healthy and unrelated individuals from the Daur group, a Mongolic-speaking representative population of the indigenous groups in the Heilongjiang River basin (also known as the Amur River basin). Results: The dataset presented 127 distinct mtDNA haplotypes, resulting in a haplotype diversity of 0.9933. The majority of haplotypes were assigned to eastern Eurasian-specific lineages, such as D4 (19.62%), B4 (9.09%), D5 (7.66%) and M7 (4.78%). We collected whole mitochondrial genomes from the 1000 Genomes Project, the Human Genome Diversity Project and published papers for population comparisons and phylogenetic analysis, and the results showed that the Daurians do have certain connections with the ancient populations in the Heilongjiang River basin but the matrilineal genetic composition of the Daur group was also greatly influenced by other non-Mongolic groups from neighboring areas. Conclusions: Collectively, the whole mtDNA data generated in the present study will augment the existing mtDNA database and deepen our understanding of the history of the Daurians as well as other populations from northern East Asia.

Phylogeographic Structure of Freshwater Tor sp. in River Basins of Sabah, Malaysia

We characterized the genetic diversity, phylogeography, and demography of Tor sp. (Cyprinidae) from Sabah, Malaysian Borneo, by examining nucleotide variation in the D-loop region of the mtDNA. Sequence analysis of 18 populations (N = 173) yielded 35 unique mtDNA haplotypes with mean haplotype and nucleotide diversity of 0.833 and 0.023, respectively. Phylogenetic reconstructions using Bayesian, neighbor-joining, and maximum parsimony methods, as well as haplotype network, revealed four well-defined clades, namely, the eastern, central, northwestern, and southwestern clades, which corresponded to evolutionarily significant units (ESUs). These ESUs were estimated to have become separated since the late Miocene to Pliocene era (between 5 and 1 million years ago), with the central highlands of Sabah Crocker Trusmadi Range (CTR) constituting the main barrier to genetic exchange between clades. Analysis of molecular variance (AMOVA) and pairwise genetic differentiation showed significant population structuring (Φct = 0.575–1.000, p < 0.05). We further identified eight major groups of river systems harboring reproductively isolated Tor subpopulations. Neutrality statistics and Bayesian skyline plots (BSP) suggested constant population size over time for most Tor populations. Tor sp. in Sabah is comprised of four ESUs (eastern, central, northwestern, and southwestern ESUs), and that each ESU can be compartmentalized into 1–4 MUs. Due to isolation by distance, the highest number of MU occurs in the low-elevation drainages of Eastern Sabah, which is the largest in terms of land area. The evidence provided by this study supports the hypothesis that the four ESU represent genetically distinct subpopulations of Tor and highlight the urgent need for the in situ conservation of these subpopulations.