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

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

New species of Lonchophylla ‪(‬Chiroptera, Phyllostomidae‪)‬ from the eastern Andes of northwestern South America. American Museum novitates, no. 3635.

16 p. : ill., maps ; 26 cm. Includes bibliographical references (p. 14-15).Since 2004 five new species have been described in the nectar-feeding phyllostomid bat genus Lonchophylla. All the new species are endemic to one Neotropical ecoregion, suggesting that more species remain to be discovered among collected specimens currently referred to several widespread taxa. Herein we describe a new species, Lonchophylla orienticollina, endemic to the middle elevations of the eastern Andes of Venezuela, Colombia, and Ecuador. The new species superficially resembles its sympatric congener L. robusta, but its cranial morphology and combination of measurements are distinctive. Throughout its range, L. orienticollina is sympatric with L. robusta, and it also overlaps with L. handleyi in the Cordillera Oriental of Ecuador. The evolutionary processes leading to the divergence among Lonchophylla species, as well as the ecological mechanisms that enable multiple, subtly different species to coexist will remain obscure without new field and phylogenetic studies