High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator

Author summary Understanding how levels of genetic diversity levels are maintained in natural populations and their relationship to species abundance is central to many conservation problems. We address this question in ecologically important crown-of-thorns sea stars to advance our understanding about the determinants of genetic diversity in species undergoing extreme population size fluctuations or outbreaks. In this work, we report the first germline mutation rate estimate for a marine invertebrate using whole-genome sequencing of parent-offspring trios. Our results reveal that unexpectedly high mutational contributions and reduced effective population size (stronger genetic drift than predicted by abundance) shape genetic diversity in this species, despite outbreaking populations sizes exceeding 20–90 million individuals. Our results are consistent with theory on mutation rate evolution, whereby elevated mutation rates evolve in response to reduced effective population size or generation time length. Our findings highlight the potential importance of high mutation rates in maintaining extreme deleterious mutational loads observed in marine invertebrate taxa and moderate genetic diversity levels despite population declines. Such fundamental knowledge advances our understanding about the determinants of genetic diversity in large marine populations and is valuable for testing future hypotheses on mutation rate evolution across diverse animal phyla.

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

Author Summary Phylogenetic networks display the evolutionary history of groups of individuals (species or populations) including reticulation events such as hybridization, horizontal gene transfer or migration. Here, we present a likelihood method to learn networks from molecular sequences at multiple genes. Our model accounts for several biological processes: mutations, incomplete lineage sorting of alleles in ancestral populations, and reticulations in the network. The likelihood is decomposed into 4-taxon subsets to make the analyses scale to many species and many genes. Our work makes it possible to learn large phylogenetic networks from large data sets, with a statistical approach and a biologically relevant model.

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva

Author summary Survival in extreme environments for prolonged periods is a challenge that only a few organisms, are capable of. It is not well understood, which molecular and biochemical pathways are utilized by such cryptobiotic organisms, and how long they might suspend life. Here, we show that a soil nematode Panagrolaimus kolymaensis, suspended life for 46,000 years in the Siberian permafrost. Through comparative analysis, we find that P. kolymaensis and model organism C. elegans utilize similar adaptive mechanisms to survive harsh environmental conditions for prolonged periods. Our findings here are important for the understanding of evolutionary processes because generation times could be stretched from days to millennia, and long-term survival of individuals of species can lead to the refoundation of otherwise extinct lineages.

Spinal cord extracts of amyotrophic lateral sclerosis spread TDP-43 pathology in cerebral organoids

Author summary Amyotrophic lateral sclerosis (ALS) is a disease characterized by the degeneration of selected groups of neuronal cells. Mislocalization of the TAR DNA-binding protein 43 kDa (TDP-43) from the nucleus of neuronal cells toward the cytoplasm is a pathological hallmark of most cases of ALS. Owing to its structure TDP-43 has a high aggregation propensity when outside the nucleus. Here we used a a form of self-organizing three-dimensional cell culture model (aka cerebral organoid) to test if TDP-43 could contribute the progression of the disease that occurs across the central nervous system of patients. TDP-43 is hypothesized to contribute to the progression of the disease by inducing the propagation of its aggregated form across cells. Protein extracts prepared from postmortem spinal cord of ALS patients showing aggregated TDP-43 were separately injected into cerebral organoids derived from an ALS case and from a control individual. This approach demonstrated the spreading of aggregated TDP-43 across the cells of the injected organoids derived from an ALS case; by comparison, the same spreading was very limited within organoids from the control individual. Critically, protein extracts prepared from non-diseased individuals did not result in the propagation of aggregated TDP-43. Our finding could be used to evaluate treatments aiming to prevent the propagation of aggregated TDP-43 established to be pathogenic.

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PLOS announces publishing agreement with the largest research institution in Mexico - The Official PLOS Blog

UNAM joins a growing list of institutions to sign agreements with PLOS