Australia's Oldest Marsupial Fossils and their Biogeographical Implications

Background: We describe new cranial and post-cranial marsupial fossils from the early Eocene Tingamarra Local Fauna in Australia and refer them to Djarthia murgonensis, which was previously known only from fragmentary dental remains. Methodology/Principal Findings: The new material indicates that Djarthia is a member of Australidelphia, a pan-Gondwanan clade comprising all extant Australian marsupials together with the South American microbiotheres. Djarthia is therefore the oldest known crown-group marsupial anywhere in the world that is represented by dental, cranial and postcranial remains, and the oldest known Australian marsupial by 30 million years. It is also the most plesiomorphic known australidelphian, and phylogenetic analyses place it outside all other Australian marsupials. Conclusions/Significance: As the most plesiomorphic and oldest unequivocal australidelphian, Djarthia may approximate the ancestral morphotype of the Australian marsupial radiation and suggests that the South American microbiotheres may be the result of back-dispersal from eastern Gondwana, which is the reverse of prevailing hypotheses

Fear and rumours regarding placental biopsies in a malaria-in-pregnancy trial in Benin.

BACKGROUND: A multi-country, community-based trial on scheduled screening and treatment for malaria in pregnancy was conducted in Benin, The Gambia and Burkina Faso. Despite standardized procedures and outcomes, the study became subject to rumours and accusations of placenta being sold for mystical and financial gain by trial staff, leading to drop-out rates of 30% and the consequent halting of placental biopsy sampling in Benin. This paper explores the role of socio-cultural beliefs related to placenta and identified additional factors contributing these rumours. METHODS: A qualitative comparative emergent-theory design was used to assess social factors related to trial implementation and uptake in the three countries. Data from participant observation, informal conversations, group discussions and interviews were triangulated and analysed with NVivo Qualitative Analysis software. RESULTS: Despite similar sociocultural beliefs about the sacred nature of the placenta in all three study countries, these beliefs did not affect participation rates in Burkina Faso and The Gambia and placenta-related rumours only emerged in Benin. Therefore, the presence of beliefs is not a sufficient condition to have generated placenta-selling fears. The rumours in Benin reflected the confluence of placenta-related beliefs and factors related to the implementation of the trial (including a catalysing adverse event and miscommunication during the informed consent procedure). Furthermore, distinct socio-political factors contributed to the emergence of rumours, including the historical distrust in governmental organizations and the tense relationship between some of the actors involved in the trial. CONCLUSION: Transdisciplinary social science research designs should accompany the implementation of the trial. The integration of multiple stakeholders' knowledge and involvement is required to define and solve upcoming barriers

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Morpho-molecular diversity and phylogeny of Bysmatrum (Dinophyceae) from the South China Sea and France

The dinoflagellate genus Bysmatrum encompasses five epibenthic or tide-pool species and has been characterized by separated anterior intercalary plates. In the present study, we obtained six strains of Bysmatrum from the South China Sea and French Atlantic coast by isolating single cells/cysts from plankton and sediment samples. All strains were examined with light microscopy and scanning electron microscopy. Based on morphological observations, three strains were identified as Bysmatrum subsalsum, characterized by the elongated and rectangular first and a hexagonal second anterior intercalary plate. They differ from each other in the number of sulcal lists and the configuration of the first anterior intercalary plate. One strain was identified as Bysmatrum gregarium and the other two as Bysmatrum granulosum. The cyst-theca relationship of B. subsalsum from the French Atlantic was established by incubation of the cyst, and the geochemical composition of the cyst wall was measured through micro-Fourier transform infrared spectroscopy. Bysmatrum subsalsum from Malaysia shows a bright red stigma in the sulcal area under light microscopy, which was confirmed with transmission electron microscopy: it was identified as a type B eyespot. Small subunit ribosomal DNA (SSU rDNA), partial large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer (ITS) sequences were obtained from all six strains. The maximum likelihood and Bayesian inference analysis based on concatenated SSU, ITS and LSU sequences revealed that Bysmatrum is monophyletic and nested within Peridiniales. Our strains of B. subsalsum form a new ribotype in the molecular phylogeny (designated as ribotype B). The genetic distance based on ITS sequences among Bysmatrum species ranged from 0.34 to 0.47 and those genetic distances at the intraspecific level of B. subsalsum could reach 0.41, supporting the possibility of hidden crypticity within B. subsalsum

Clonality Despite Sex: The Evolution of Host-Associated Sexual Neighborhoods in the Pathogenic Fungus <em>Penicillium marneffei</em>

<div><p>Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen <em>Penicillium marneffei</em> to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of <em>P. marneffei</em>. Genome wide comparisons reveal that all the genes required for meiosis are present in <em>P. marneffei</em>, mating type genes are arranged in a similar manner to that found in other heterothallic fungi, and there is evidence of a putatively meiosis-specific mutational process. Experiments suggest that recombination between isolates of compatible mating types may occur during mammal infection. Population genetic data from 34 isolates from bamboo rats in India, Thailand and Vietnam, and 273 isolates from humans in China, India, Thailand, and Vietnam show that recombination is most likely to occur across spatially and genetically limited distances in natural populations resulting in highly clonal population structure yet sexually reproducing populations. Predicted distributions of three different spatial genetic clusters within <em>P. marneffei</em> overlap with three different bamboo rat host distributions suggesting that recombination within hosts may act to maintain population barriers within <em>P. marneffei</em>.</p> </div