Trpc2 pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss

This work was supported by the National Science Foundation Graduate Research Fellowship and NSF-DEB 144214

Robust evidence for bats as reservoir hosts is lacking in most African virus studies : a review and call to optimize sampling and conserve bats

DATA ACCESSIBILITY : Data used in this study are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.c866t1gcx [222]. Supplementary material is available online [223].Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus–bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus–host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people’s beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human–bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.Open access funding provided by the Max Planck Society. Bucknell University and, in part, by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH); the German Academic Exchange Service; the German Research Foundation the Institut Universitaire de France; the South African Research Chair Initiative of the Department of Science and Innovation and administered by the National Research Foundation (NRF) of South Africa; in part, by NSF and National Geographic and Rolex grants.https://royalsocietypublishing.org/journal/rsblam2024Medical VirologyNon

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

The nature and dynamics of bacterial genomes

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell

New species of Lonchophylla

14 p. : ill., map ; 26 cm.Includes bibliographical references (p. 10-11).Lonchophylla is a diverse genus of glossophagines characterized by large, forwardly projecting inner upper incisors and the absence of zygomatic arches. Seven species are currently recognized, including the large-bodied (greatest length of skull >24.5 mm) robusta, handleyi, hesperia, and bokermanni and the small-bodied (greatest length of skull <24.5 mm) thomasi, dekeyseri, and mordax. Lonchophylla species range throughout the Neotropics and include endemics in Amazonia, the Cerrado, and the arid regions of coastal Peru and Ecuador. In this paper I describe a new large-bodied species, Lonchophylla chocoana, from the subtropical rainforests of the Chocó in southwestern Colombia and northwestern Ecuador. I also document the diagnostic external, craniodental, and mitochondrial characters of the new species and summarize morphological characteristics for the new species and its sympatric congeners

Data from: Strength of selection on Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution

Vestigial characters are common across the tree of life, but the underlying evolutionary processes shaping phenotypic loss are poorly understood. The mammalian vomeronasal system, which detects social chemical cues important to fitness, is an impressive example of a sensory system lost multiple times. Three times more losses are inferred among bats than in other mammalian orders. We characterized the relationship between amino acid substitutions in a gene tightly linked to vomeronasal function (Trpc2) and the accessory olfactory bulb, a brain region that processes the detection of these vomeronasal chemical cues. By applying a phylogenetic logistic regression, we found a strong negative relationship between the branch lengths representing rates of codon changes in the Trpc2 gene tree and the presence or absence of an accessory olfactory bulb. Longer branch lengths predict loss of the accessory olfactory bulb, suggesting selection has relaxed on the system as a whole. Based on this relationship, we predicted the absence of an accessory olfactory bulb in 19 bat species with unknown morphology. Several species with predicted losses have specialized skull morphology, suggesting a potential tradeoff between adaptation in skull shape and maintenance of the vomeronasal system. This study offers a new approach to relate genetic mechanisms and phenotypes at a macroevolutionary scale