Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Stressful Body Temperatures as a Maternal Effect on Lizard Reproduction

AbstractUnderstanding the relationship between the environment parents experience during reproduction and the environment embryos experience in the nest is essential for determining the intergenerational responses of populations to novel environmental conditions. Thermal stress has become commonplace for organisms inhabiting areas affected by rising temperatures. Exposure to body temperatures that approach, but do not exceed, upper thermal limits often induces adverse effects in organisms, but the propensity for these temperatures to have intergenerational consequences has not been explored in depth. Here, we quantified the effects of thermal stress on the reproductive physiology and development of brown anoles (Anolis sagrei) when thermal stress is experienced by mothers and by eggs during incubation. Mothers exposed to thermal stress produced smaller eggs and smaller offspring with reduced growth rates, while egg stress reduced developmental time and offspring mass. Hatchling survival and growth were negatively affected by thermal stress experienced by mothers but not by thermal stress experienced as eggs. We found mixed evidence for an additive effect of thermal stress on offspring; rather, thermal stress had specific (and most often negative) effects on different components of offspring phenotypes and fitness proxies when experienced either by mothers or by eggs. Stressful body temperatures therefore can function in a similar manner to other types of maternal effects in reptiles; however, this maternal effect has predominantly negative consequences on offspring.

Responses to saltwater exposure vary across species, populations and life stages in anuran amphibians

To predict the impacts of environmental change on species, we must first understand the factors that limit the present-day ranges of species. Most anuran amphibians cannot survive at elevated salinities, which may drive their distribution in coastal locations. Previous research showed that coastal Hyla cinerea are locally adapted to brackish habitats in North Carolina, USA. Although Hyla squirella and Hyla chrysoscelis both inhabit coastal wetlands nearby, they have not been observed in saline habitats. We take advantage of naturally occurring microgeographic variation in coastal wetland occupancy exhibited by these congeneric tree frog species to explore how salt exposure affects oviposition site choice, hatching success, early tadpole survival, plasma osmolality and tadpole body condition across coastal and inland locations. We observed higher survival among coastal H. cinerea tadpoles than inland H. cinerea, which corroborates previous findings. But contrary to expectations, coastal H. cinerea had lower survival than H. squirella and H. chrysoscelis, indicating that all three species may be able to persist in saline wetlands. We also observed differences in tadpole plasma osmolality across species, locations and salinities, but these differences were not associated with survival rates in salt water. Instead, coastal occupancy may be affected by stage-specific processes like higher probability of total clutch loss as shown by inland H. chrysoscelis or maladaptive egg deposition patterns as shown by inland H. squirella. Although we expected salt water to be the primary filter driving species distributions along a coastal salinity gradient, it is likely that the factors dictating anuran ranges along the coast involve stage-, species- and location-specific processes that are mediated by ecological processes and life history traits.

Incorporating nonlinearity with generalized functional responses to simulate multiple predator effects

Predicting the combined effects of predators on shared prey has long been a focus of community ecology, yet quantitative predictions often fail. Failure to account for nonlinearity is one reason for this. Moreover, prey depletion in multiple predator effects (MPE) studies generates biased predictions in applications of common experimental and quantitative frameworks. Here, we explore additional sources of bias stemming from nonlinearities in prey predation risk. We show that in order to avoid bias, predictions about the combined effects of independent predators must account for nonlinear size-dependent risk for prey as well as changes in prey risk driven by nonlinear predator functional responses and depletion. Historical failure to account for biases introduced by well-known nonlinear processes that affect predation risk suggest that we may need to reevaluate the general conclusions that have been drawn about the ubiquity of emergent MPEs over the past three decades.

A novel analytical framework to quantify co-gradient and countergradient variation

Spatial covariance between genotypic and environmental influences on phenotypes (Cov_GE ) can result in the nonrandom distribution of genotypes across environmental gradients and is a potentially important factor driving local adaptation. However, a framework to quantify the magnitude and significance of Cov_GE has been lacking. We develop a novel quantitative/analytical approach to estimate and test the significance of Cov_GE from reciprocal transplant or common garden experiments, which we validate using simulated data. We demonstrate how power to detect Cov_GE changes over a range of experimental designs. We confirm an inverse relationship between gene-by-environment interactions (GxE) and Cov_GE , as predicted by first principles, but show how phenotypes can be influenced by both. The metric provides a way to measure how phenotypic plasticity covaries with genetic differentiation and highlights the importance of understanding the dual influences of Cov_GE and GxE on phenotypes in studies of local adaptation and species' responses to environmental change.

Divergence in heritable life history traits suggests potential for local adaptation and trade-offs associated with a coal ash disposal site

Globally, human activities have resulted in rapid environmental changes that present unique challenges for wildlife. However, investigations of local adaptation in response to simultaneous exposure to multiple anthropogenic selection pressures are rare and often generate conflicting results. We used an in situ reciprocal transplant design within a quantitative genetic framework to examine how adaptive evolution and phenotypic plasticity contribute to the persistence of an amphibian population inhabiting an environment characterized by high levels of multiple toxic trace elements. We found evidence of phenotypic divergence that is largely consistent with local adaptation to an environment contaminated with multiple chemical stressors, tied to potential trade-offs in the absence of contaminants. Specifically, the population derived from the contaminated environment had a reduced risk of mortality and greater larval growth and in the contaminated environment, relative to offspring from the naïve population. Further, while survival in the uncontaminated environment was not compromised in offspring from the contaminant-exposed population, they did show delayed development and reduced growth rates over larval development, relative to the naïve population. We found no evidence of reduced additive genetic variation in the contaminant-exposed population, suggesting long-term selection in a novel environment has not reduced the evolutionary potential of that population. We also saw little evidence that past selection in the ASH environment had reduced trait plasticity in the resident population. Maternal effects were prominent in early development, but we did not detect any trends suggesting these effects were associated with the maternal transfer of toxic trace elements. Our results demonstrate the potential for adaptation to multiple contaminants in a wild amphibian population, which may have facilitated long-term persistence in a heavily impacted environment.

Molecular mechanisms of local adaptation for salt-tolerance in a treefrog

Salinization is a global phenomenon affecting ecosystems and forcing freshwater organisms to deal with increasing levels of ionic stress. However, our understanding of mechanisms that permit salt tolerance in amphibians is limited. This study investigates mechanisms of salt tolerance in locally adapted, coastal populations of a treefrog, Hyla cinerea. Using a common garden experiment, we (i) determine the extent that environment (i.e., embryonic and larval saltwater exposure) or genotype (i.e., coastal vs. inland) affects developmental benchmarks and transcriptome expression, and (ii) identify genes that may underpin differences in saltwater tolerance. Differences in gene expression, survival, and plasma osmolality were most strongly associated with genotype. Population genetic analyses on expressed genes also delineated coastal and inland groups based on genetic similarity. Coastal populations differentially expressed osmoregulatory genes including ion transporters (atp1b1, atp6V1g2, slc26a), cellular adhesion components (cdh26, cldn1, gjb3, ocln), and cytoskeletal components (odc1-a, tgm3). Several of these genes are the same genes expressed by euryhaline fish after exposure to freshwater, which is a novel finding for North American amphibians and suggests that these genes may be associated with local salinity adaptation. Coastal populations also highly expressed glycerol-3-phosphate dehydrogenase 1 (gpd1), which indicates they use glycerol as a compatible osmolyte to reduce water loss - another mechanism of saltwater tolerance previously unknown in frogs. These data signify that Hyla cinerea inhabiting coastal, brackish wetlands have evolved a salt-tolerant ecotype, and highlights novel candidate pathways that can lead to salt tolerance in freshwater organisms facing habitat salinization.

Choice consequences: salinity preferences and hatchling survival in the mangrove rivulus (Kryptolebias marmoratus)

In heterogeneous environments, mobile species should occupy habitats in which their fitness is maximized. Mangrove rivulus fish inhabit mangrove ecosystems where salinities range from 0 to 65 ppt, but are most often collected from areas with salinities of ∼25 ppt. We examined the salinity preference of mangrove rivulus in a lateral salinity gradient, in the absence of predators and competitors. Fish could swim freely for 8 h throughout the gradient with chambers containing salinities ranging from 5 to 45 ppt (or 25 ppt throughout in the control). We defined preference as the salinity in which the fish spent most of their time, and also measured preference strength, latency to begin exploring the arena, and number of transitions between chambers. To determine whether these traits were repeatable, each fish experienced three trials. Mangrove rivulus spent a greater proportion of time in salinities lower (5-15 ppt) than they occupy in the wild. Significant among-individual variation in the (multivariate) behavioral phenotype emerged when animals experienced the gradient, indicating strong potential for selection to drive behavioral evolution in areas with diverse salinity microhabitats. We also showed that mangrove rivulus had a significantly greater probability of laying eggs in low salinities compared with control or high salinities. Eggs laid in lower salinities also had higher hatching success compared with those laid in higher salinities. Thus, although mangrove rivulus can tolerate a wide range of salinities, they prefer low salinities. These results raise questions about factors that prevent mangrove rivulus from occupying lower salinities in the wild, whether higher salinities impose energetic costs, and whether fitness changes as a function of salinity.

Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift

Sea level rise is mixing formerly isolated freshwater communities with saltwater communities. The structure of these new aquatic communities is jointly controlled by pre- and post-colonization processes. Similarly, since salinity is a strong abiotic determinant of post-colonization survival in coastal systems, changes in salinity will likely impact community composition. In this study, we examine how a strong abiotic gradient affects the diversity and structure of bacterial and zooplankton communities and associated ecosystem functions (decomposition and carbon mineralization). We ran a six week dispersal experiment using mesocosm ponds with four distinct salinity profiles (0, 5, 9, and 13 psu). We find that salinity is the primary driver of both bacterial and zooplankton community composition. We find evidence that as bacterial richness increases so does the amount of decomposition. A phenomenological model suggests carbon mineralization may decrease at mid-salinities; this warrants future work into possible mechanisms for this apparent loss of function. Understanding how salinization changes community structure and ecosystem function may be paramount for managing and conserving coastal plain ecosystems where salinity is increasing due to sea level rise, saltwater intrusion, storm surges, and drought.

Influence of density and salinity on larval development of salt-adapted and salt-naïve frog populations

Environmental change and habitat fragmentation will affect population densities for many species. For those species that have locally adapted to persist in changed or stressful habitats, it is uncertain how density dependence will affect adaptive responses. Anurans (frogs and toads) are typically freshwater organisms, but some coastal populations of green treefrogs (Hyla cinerea) have adapted to brackish, coastal wetlands. Tadpoles from coastal populations metamorphose sooner and demonstrate faster growth rates than inland populations when reared solitarily. Although saltwater exposure has adaptively reduced the duration of the larval period for coastal populations, increases in densities during larval development typically increase time to metamorphosis and reduce rates of growth and survival. We test how combined stressors of density and salinity affect larval development between salt-adapted ("coastal") and nonsalt-adapted ("inland") populations by measuring various developmental and metamorphic phenotypes. We found that increased tadpole density strongly affected coastal and inland tadpole populations similarly. In high-density treatments, both coastal and inland populations had reduced growth rates, greater exponential decay of growth, a smaller size at metamorphosis, took longer to reach metamorphosis, and had lower survivorship at metamorphosis. Salinity only exaggerated the effects of density on the time to reach metamorphosis and exponential decay of growth. Location of origin affected length at metamorphosis, with coastal tadpoles metamorphosing slightly longer than inland tadpoles across densities and salinities. These findings confirm that density has a strong and central influence on larval development even across divergent populations and habitat types and may mitigate the expression (and therefore detection) of locally adapted phenotypes.