14 research outputs found
Small Mammals
The Bornean tropical rainforests harbour some of the most
remarkable diversity of flora and fauna in the world (Jennings et al.,
2015; Sodhi et al., 2004). Tropical biodiversity is highly threatened
by land conversion for agricultural purposes. This calls for greater
conservational prioritization (Wilcove & Koh, 2010; Fitzherbert et
al., 2008) as many have become fragmented and disconnected.
There are a total of 247 species of mammals recorded in Borneo,
and small mammals make up approximately 81%, which can be
sub-categorized into bats, shrews, treeshrews, rats, mice, squirrels
and flying squirrels (Phillipps & Phillipps, 2016). Borneo is regarded
as one of the biodiversity hotspots, sustaining a high concentration
of endemism, including approximately 19% of mammals (5% of the
99 bats species and 26 Rodentia), 20% of snakes and 6% of birds
(Mohd-Azlan & Lawes, 2011).
Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent
Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown. Samples from contaminated localities exhibited significantly higher numbers of haplotypes and polymorphic loci, elevated genetic diversity, and a significantly higher average number of substitutions per site across mitochondrial gene regions. Observed genetic variation was dominated by synonymous mutations, which may indicate a history of purify selection against nonsynonymous or insertion/deletion mutations. These significant differences were not attributable to sample size artifacts. The observed increase in mitochondrial genomic diversity in voles from radioactive sites is consistent with the possibility that chronic, continuous irradiation resulting from the Chernobyl disaster has produced an accelerated mutation rate in this species over the last 25 years. Our results, being the first to demonstrate this phenomenon in a wild mammalian species, are important for understanding genetic consequences of exposure to low-dose radiation sources. © 2017 John Wiley & Sons Ltd
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
INTRODUCTION
Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic.
RATIONALE
We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs).
RESULTS
Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants.
CONCLUSION
Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century
Photoâinactivation of bacteria in hospital effluent via thiolated ironâdoped nanoceria
Larger gains from improved management over sparingâsharing for tropical forests
Tropical forests are globally significant for both biodiversity conservation and the production of economically valuable wood products. Two contrasting approaches have been suggested to simultaneously produce timber and conserve biodiversity; one partitions forests to deliver these objectives separately (sparing), the other integrates both objectives in the same location (sharing). To date, the âsparing or sharingâ debate has focused on agricultural landscapes, with scant attention paid to forest management. Here we explored the sparing-to-sharing continuum through spatial optimisations with set economic returns for the forests of East Kalimantan, Indonesia â a global biodiversity hotspot. We found that neither sparing nor sharing extremes are optimal, although the greatest conservation value was attained towards the sparing end of the continuum. Critically, improved management strategies, such as reduced-impact logging, accounted for larger conservation gains than altering the balance between sparing and sharing, particularly for endangered species. Ultimately, debating sparing versus sharing has limited value while large gains remain from improving forest management