Bat species assemblage predicts coronavirus prevalence.

Anthropogenic disturbances and the subsequent loss of biodiversity are altering species abundances and communities. Since species vary in their pathogen competence, spatio-temporal changes in host assemblages may lead to changes in disease dynamics. We explore how longitudinal changes in bat species assemblages affect the disease dynamics of coronaviruses (CoVs) in more than 2300 cave-dwelling bats captured over two years from five caves in Ghana. This reveals uneven CoV infection patterns between closely related species, with the alpha-CoV 229E-like and SARS-related beta-CoV 2b emerging as multi-host pathogens. Prevalence and infection likelihood for both phylogenetically distinct CoVs is influenced by the abundance of competent species and naïve subadults. Broadly, bat species vary in CoV competence, and highly competent species are more common in less diverse communities, leading to increased CoV prevalence in less diverse bat assemblages. In line with the One Health framework, our work supports the notion that biodiversity conservation may be the most proactive measure to prevent the spread of pathogens with zoonotic potential.

Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region.

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.

Sperm Storage in a Family-Living Lizard, the Tree Skink (Egernia striolata).

The ability to produce viable offspring without recently mating, either through sperm storage or parthenogenesis, can provide fitness advantages under a suite of challenging ecological scenarios. Using genetic analysis, we demonstrate that 3 wild-caught female Tree Skinks (Egernia striolata) reproduced in captivity with no access to males for over a year, and that this is best explained by sperm storage. To the best of our knowledge, this is the first time female sperm storage has been documented in any monogamous family-living reptile, including social Australian egerniine skinks (from the subfamily Egerniinae). Furthermore, by using paternal reconstruction of genotypes we show that captive-born offspring produced by the same females in the preceding year, presumably without sperm storage, were sired by different males. We qualitatively compared aspects of these females' mates and offspring between years. The parents of each litter were unrelated, but paternal and offspring genotypes from litters resulting from stored sperm were more heterozygous than those inferred to be from recent matings. Family-living egerniine skinks generally have low rates of multiple paternity, yet our study suggests that female sperm storage, potentially from outside social partners, offers the real possibility of benefits. Possible benefits include increasing genetic compatibility of mates and avoiding inbreeding depression via cryptic female choice. Sperm storage in Tree Skinks, a family-living lizard with a monogamous mating system, suggests that females may bet-hedge through extra-pair copulation with more heterozygous males, reinforcing the idea that females could have more control on reproductive outcomes than previously thought.

Microgeographical adaptation corresponds to elevational distributions of congeneric montane grasshoppers.

Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine-scale shifts in species' niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth: one broader, K. usitatus (1400-2200 m), and one narrower, K. tristis (1600-2000 m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using FST outlier tests and environmental association analyses (EAAs) applied to single nucleotide polymorphism (SNP) data (K. usitatus: 9017 SNPs, n = 130; K. tristis: 7363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were nonlinearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographical adaptation.

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest.

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.

Conservation prioritization can resolve the flagship species conundrum.

Conservation strategies based on charismatic flagship species, such as tigers, lions, and elephants, successfully attract funding from individuals and corporate donors. However, critics of this species-focused approach argue it wastes resources and often does not benefit broader biodiversity. If true, then the best way of raising conservation funds excludes the best way of spending it. Here we show that this conundrum can be resolved, and that the flagship species approach does not impede cost-effective conservation. Through a tailored prioritization approach, we identify places containing flagship species while also maximizing global biodiversity representation (based on 19,616 terrestrial and freshwater species). We then compare these results to scenarios that only maximized biodiversity representation, and demonstrate that our flagship-based approach achieves 79-89% of our objective. This provides strong evidence that prudently selected flagships can both raise funds for conservation and help target where these resources are best spent to conserve biodiversity.

The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus.

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.

Social Barriers in Ecological Landscapes: The Social Resistance Hypothesis.

Across animal societies, individuals invest time and energy in social interactions. The social landscape that emerges from these interactions can then generate barriers that limit the ability of individuals to disperse to, and reproduce in, groups or populations. Therefore, social barriers can contribute to the difference between the physical capacity for movement through the habitat and subsequent gene flow. We call this contributing effect 'social resistance'. We propose that social resistance can act as an agent of selection on key life-history strategies and promote the evolution of social strategies that facilitate effective dispersal. By linking landscape genetics and social behaviour, the social resistance hypothesis generates predictions integrating dispersal, connectivity, and life-history evolution.

Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum).

Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900-km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise FST  = 0.0003-0.08), landscape genetic resistance modelling identified a positive nonlinear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas and forest. Together, FST outlier tests and environmental association analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultraviolet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.

Morphological Variation Tracks Environmental Gradients in an Agricultural Pest, Phaulacridium vittatum (Orthoptera: Acrididae).

Invertebrate pests often show high morphological variation and wide environmental tolerances. Knowledge of how phenotypic variation is associated with environmental heterogeneity can elucidate the processes underpinning these patterns. Here we examine morphological variation and relative abundance along environmental gradients in a widespread agricultural pest, native to Australia, the wingless grasshopper Phaulacridium vittatum (Sjöstedt). We test for correlations between body size, wing presence, and stripe polymorphism with environmental variables. Using multiple regression and mixed-effects modeling, body size and stripe polymorphism were positively associated with solar radiation, and wing presence was positively associated with foliage projective cover (FPC). There were no associations between body size or morphological traits with relative abundance. However, relative abundance was positively associated with latitude, soil moisture, and wind speed, but was negatively associated with FPC. Therefore, sites with low relative abundance and high forest cover were more likely to contain winged individuals. Overall, our results suggest that environmental and climatic conditions strongly influence the relative abundance and the distribution of morphotypes in P. vittatum, which is likely to affect dispersal and fitness in different landscapes. This knowledge is useful for informing how environmental change might influence the future spread and impact of this agricultural pest.