Williams, R. C. | Search bioRxiv

bioRxiv2019

Next-generation in situ conservation and capacity building in Madagascar using a mobile genetics lab

Madagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. Within country, new generations of Malagasy scientists and conservationists are taking on leadership roles, although many lack access to modern genetic sequencing and are underrepresented in academic publications, when compared to international counterparts.\n\nWith the recent advent of portable and affordable genetic technologies, it is now possible to tackle logistical considerations. Mobile genetics labs, with the capacity for in situ DNA extraction, amplification and sequencing, can produce scientifically reproducible data under field conditions, minimizing the time between sample collection and data analysis. Additionally, mobile labs offer powerful training opportunities for in-country scientists that enable local students and researchers to actively participate and contribute fully to the research enterprise, and that further empower these communities to contribute to the conservation dialog.\n\nHere, we show \"proof of concept\" by deploying a miniaturized thermal cycler alongside the Oxford Nanopore MinION DNA sequencer in Madagascar, including in the newly established Anjajavy Protected Area in northwestern Madagascar. We successfully extracted DNA from tissue samples collected using minimally-invasive techniques, amplified and sequenced a phylogenetically informative mitochondrial gene (cytochrome-b; cytb), and thereby confirmed the presence of Danfoss mouse lemur (M. danfossi) within the Anjajavy Reserve.\n\nTo demonstrate the reproducibility of our methods, we successfully performed our established molecular and analytical pipeline at two additional locations in Madagascar, where we also conducted two-day workshops at local higher-education Institutions to demonstrate the process from tissue samples to DNA sequencing. Ultimately, we show that a mobile genetics lab can provide reliable and expeditious results, become a powerful educational tool, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ.

genetics↗

bioRxiv2019

Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and chromosomal hotspots across mammals

Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and Cheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly-speciose and morphologically-cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus Mus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as V1R \"hotspots.\"

genomics↗