A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics

The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.     

A model for gain of function in superoxide dismutase

Studies have found that mutant, misfolded superoxide dismutase [Cu–Zn] (SOD1) can convert wild type SOD1 (wtSOD1) in a prion-like fashion, and that misfolded wtSOD1 can be propagated by release and uptake of protein aggregates. In developing a prion-like mechanism for this propagation of SOD1 misfolding we have previously shown how enervation of the SOD1 electrostatic loop (ESL), caused by the formation of transient non-obligate SOD1 oligomers, can lead to an experimentally observed gain of interaction (GOI) that results in the formation of SOD1 amyloid-like filaments. It has also been shown that freedom of ESL motion is essential to catalytic function. This work investigates the possibility that restricting ESL mobility might not only compromise superoxide catalytic activity but also serve to promote the peroxidase activity of SOD1, thus implicating the formation of SOD1 oligomers in both protein misfolding and in protein oxidation.     

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara,the World’s Largest Rodent

Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world’s largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.     

Macroevolutionary insights into sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification

Changes in holocentric chromosome number due to fission and fusion have direct and immediate effects on genome structure and recombination rates. These, in turn, may influence ecology and evolutionary trajectories profoundly. Sedges of the genus Carex (Cyperaceae) comprise ca. 2000 species with holocentric chromosomes. The genus exhibits a phenomenal range in the chromosome number (2n = 10 − 132) with almost not polyploidy. In this study, we integrated the most comprehensive cytogenetic and phylogenetic data for sedges with associated climatic and morphological data to investigate the hypothesis that high recombination rates are selected when evolutionary innovation is required, using chromosome number evolution as a proxy for recombination rate. We evaluated Ornstein–Uhlenbeck models to infer shifts in chromosome number equilibrium and selective regime. We also tested the relationship between chromosome number and diversification rates. Our analyses demonstrate significant correlations between morphology and climatic niche and chromosome number in Carex. Nevertheless, the amount of chromosomal variation that we are able to explain is very small. We recognized a large number of shifts in mean chromosome number, but a significantly lower number in climatic niche and morphology. We also detected a peak in diversification rates near intermediate recombination rates. In combination, these analyses point toward the importance of chromosome evolution to the evolutionary history of Carex. Our work suggests that the effect of chromosome evolution on recombination rates, not just on reproductive isolation, may be central to the evolutionary history of sedges.     

Geographical vs. ecological diversification in Carex section Phacocystis (Cyperaceae): Patterns hidden behind a twisted taxonomy

Carex section Phacocystis (Cyperaceae) is one of the most diverse and taxonomically complex groups of sedges (between 116 and 147 species), with a worldwide distribution in a wide array of biomes. It has a very complicated taxonomic history, with numerous disagreements among different treatments. We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group. We used a large species sampling of the section (82% of extant species) to build a phylogeny based on four DNA regions, constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations. Our phylogenetic results recovered section Phacocystis s.s. (core Phacocystis) as sister to section Praelongae. Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene. Wide distributions were recurrently inferred across deep nodes. Large Northern Hemisphere lineages with geographical congruence were retrieved, pointing toward the importance of allopatric divergence at deep phylogenetic levels, whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level. The Southern Hemisphere (Neotropics, SW Pacific) was colonized several times from the Northern Hemisphere. The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny. Nevertheless, ecological differentiation seems to gain importance toward recent times.     

A field test of the dilution effect hypothesis in four avian multi-host pathogens

The Dilution Effect Hypothesis (DEH) argues that greater biodiversity lowers the risk of disease and reduces the rates of pathogen transmission since more diverse communities harbour fewer competent hosts for any given pathogen, thereby reducing host exposure to the pathogen. DEH is expected to operate most intensely in vector-borne pathogens and when species-rich communities are not associated with increased host density. Overall, dilution will occur if greater species diversity leads to a lower contact rate between infected vectors and susceptible hosts, and between infected hosts and susceptible vectors. Field-based tests simultaneously analysing the prevalence of several multi-host pathogens in relation to host and vector diversity are required to validate DEH. We tested the relationship between the prevalence in house sparrows (Passer domesticus) of four vector-borne pathogens–three avian haemosporidians (including the avian malaria parasite Plasmodium and the malaria-like parasites Haemoproteus and Leucocytozoon) and West Nile virus (WNV)–and vertebrate diversity. Birds were sampled at 45 localities in SW Spain for which extensive data on vector (mosquitoes) and vertebrate communities exist. Vertebrate censuses were conducted to quantify avian and mammal density, species richness and evenness. Contrary to the predictions of DEH, WNV seroprevalence and haemosporidian prevalence were not negatively associated with either vertebrate species richness or evenness. Indeed, the opposite pattern was found, with positive relationships between avian species richness and WNV seroprevalence, and Leucocytozoon prevalence being detected. When vector (mosquito) richness and evenness were incorporated into the models, all the previous associations between WNV prevalence and the vertebrate community variables remained unchanged. No significant association was found for Plasmodium prevalence and vertebrate community variables in any of the models tested. Despite the studied system having several characteristics that should favour the dilution effect (i.e., vector-borne pathogens, an area where vector and host densities are unrelated, and where host richness is not associated with an increase in host density), none of the relationships between host species diversity and species richness, and pathogen prevalence supported DEH and, in fact, amplification was found for three of the four pathogens tested. Consequently, the range of pathogens and communities studied needs to be broadened if we are to understand the ecological factors that favour dilution and how often these conditions occur in nature.     

Structural changes of vegetation and its association with microclimate in a successional gradient of low thorn forest in northeastern Mexico

Understanding how microclimate and vegetation are associated during secondary succession is of primary importance for plant conservation in the face of the increasing land cover modification. However, these patterns are still unstudied for many plant communities. This study aimed to evaluate the structure (species richness, Shannon's diversity index, Simpson´s dominance index, abundance of each species, average height of species, species cover (%), species composition, and indicator values) of a low thorn forest fragment and to analyze its relation with microclimate along a successional gradient. Four stages of succession were delimited by the analysis of Landsat images, in the state of Tamaulipas, northeast Mexico. Statistical models incorporated species richness, diversity indices, abundance, height, and cover, as variables for searching differences between stages, or to evaluate microclimate associations. A total of 70 species, 54 genera, and 27 families were determined. Height of tree layer was the most important variable for discrimination of the successional stages. Conserved areas differed floristically from other stages, associated mainly with the lowest values of wind speed originated by tree layer characteristics. A significant association between species and microclimate was found, being wind speed and relative humidity the most important variables. Some species, due to their high importance values and their patterns of association with microclimate, may be considered as key taxa for low thorn forest, which is a threatened semitropical community in northeast Mexico. Conserved and late successional areas account for climatic regulation of this plant community, and the importance of these forest patches may be considered when establishing biodiversity protection areas.