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Limited divergent adaptation despite a substantial environmental cline in wild pea

Isolation by environment (IBE) is a wide spread phenomenon in nature. It is commonly expected that the degree of differences among environments is proportional to the level of divergence between populations in these environments. Consequentially, it is assumed that species' genetic diversity displays pattern of IBE in the presence of a strong environmental cline if geneflow does not mitigate isolation. We tested this common assumption by analyzing the genetic diversity and demographic history of Pisum fulvum. P. fulvum inhabits very contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations what makes it an ideal test case. Ecogeographic and subpopulation structure was analyzed and compared. Correlation of genetic with environmental distances was calculated to test the effect of IBD and IBE and detect the main drivers of these effects. Historic effective population size was estimated using stairwayplots. Limited overlap of ecogeographic and genetic clustering was observed, and correlation of genetic with environmental distances was statistically significant yet small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to the past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive geneflow.

Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

Agricultural intensification heightens food safety risks posed by wild birds

1. Agricultural intensification and simplification are key drivers of recent declines in wild bird populations, heightening the need to better balance conservation with food production. This is hindered, however, by perceptions that birds threaten food safety. While birds are known reservoirs of foodborne pathogens, there remains uncertainty about the links between landscape context, farming practices, and actual crop contamination by birds. 2. Here, we examine relationships between landscape context, farming practices, and pathogen contamination by birds using a barrier-to-spillover approach. First, we censused bird communities using point count surveys. Second, we collected 2024 faecal samples from captured birds alongside 1215 faecal samples from brassica fields and food processing areas across 50 farms spanning the USA West Coast. We then estimated the prevalence of three foodborne pathogens across landscape and livestock intensification gradients. Finally, we quantified the number of plants with faeces. 3. Campylobacter spp. were detected in 10.2% of faeces from captured birds and 13.1% of faeces from production areas. Nonnative birds were 4.1 times more likely to have Campylobacter spp. than native birds. Salmonella spp. were detected in 0.2% of faeces from production areas and were never detected in captured birds. We detected evidence of Shiga toxigenic E. coli in 1 sample across the >3200 tested. 4. Campylobacter spp. prevalence in faeces from production areas increased with increasing mammalian livestock densities in the landscape but decreased with increasing amounts of natural habitat. 5. We encountered bird faeces on 3.3% of plants examined. Despite the impact on pathogen prevalence, landscape context did not increase the number of plants with bird faeces, although on-farm mammalian livestock density slightly did. 6. Synthesis and applications. Food safety and wildlife conservation are often thought to be in conflict. However, our findings suggest that natural habitat around farms may reduce crop contamination rates by birds. This is perhaps because natural habitat can promote native birds that are less likely to harbour foodborne pathogens or because it decreases contact with livestock waste. Our results suggest that preservation of natural habitats around farms could benefit both conservation and food safety, contrary to current standards for "best practices."

opencc-zeroJan 2020View details →

Data for: Evaluating the impact of physical frailty during ageing in wild chimpanzees (Pan troglodytes schweinfurthii)

While declining physical performance is an expected consequence of aging, human clinical research has placed increasing emphasis on physical frailty as a predictor of death and disability in the elderly. We examined non-invasive measures approximating frailty in a richly-sampled longitudinal dataset on wild chimpanzees. Using urinary creatinine to assess lean body mass, we demonstrated moderate but significant declines in physical condition with age in both sexes. While older chimpanzees spent less of their day in the trees and feeding, they did not alter activity budgets with respect to travel or resting. There was little evidence that declining lean body mass had negative consequences independent of age. Old chimpanzees with poor lean body mass rested more often but did not otherwise differ in activity. Males, but not females, in poor condition were more likely to exhibit respiratory illness. Poor muscle mass was associated acutely with death in males, but it did not predict future mortality in either sex. While there may be some reasons to suspect biological differences in the susceptibility to frailty in chimpanzees versus humans, our data are consistent with recent reports from humans that lean, physically active individuals can successfully combat frailty.

Social network position experiences more variable selection than weaponry in wild subpopulations of forked fungus beetles

1. The phenotypic expression and fitness consequences of behaviors that are exhibited during social interactions are especially sensitive to their local social context. This context-dependence is expected to generate more variation in the sign and magnitude of selection on social behavior than that experienced by static characters like morphology. Relatively few studies, however, have examined selection on behavioral traits in multiple populations. 2. We estimated sexual selection in the wild to determine if the strength and form of selection on social phenotypes is more variable than that on morphology. 3. We compared selection gradients on social network position, body size, and weaponry of male forked fungus beetles (Bolitotherus cornutus) as they influenced mating success across nine natural subpopulations. 4. Male horn length consistently experienced positive sexual selection. However, the sign and magnitude of selection on individual measures of network centrality (strength and betweenness) differed significantly among subpopulations. Moreover, selection on social behaviors occurred at local scale ("soft selection"), whereas selection on horn length occurred at the metapopulation scale ("hard selection"). 5. These results indicate that an individual with a given social phenotype could experience different fitness consequences depending on the network it occupies. While individuals seem to be unable to escape the fitness effects of their morphology, they may have the potential to mediate the pressures of selection on behavioral phenotypes by moving among subpopulations or altering social connections within a network.

Effects of soil salinity on the expression of direct and indirect defences in wild cotton (Gossypium hirsutum)

Previous studies have reported effects of abiotic factors on herbivore-induced plant defences based on effects on single plant traits. However, plants commonly express multiple defences simultaneously and these traits are often correlated. Thus, a fuller understanding of abiotic-context dependency in plant defence requires measuring multiple traits and addressing their patterns of correlated expression. We evaluated the effects of soil salinity on the induction of direct (phenolic compounds, gossypol gland density) and indirect (volatile organic compounds, extrafloral nectar) defensive traits in wild cotton (Gossypium hirsutum). We asked whether soil salinity affects the induction of these traits, and whether it shapes trait correlations potentially underlying salinity effects on trait induction. We conducted a factorial experiment with 16 cotton genotypes where we manipulated soil salinity and defence induction by applying artificial leaf damage (25% mechanical damage and caterpillar oral secretions) and measured defence levels at different time points post-damage. Leaf damage induced most traits except gossypol gland density, whereas salinity did not have a mean effect (across constitutive and induced levels) on any of the measured traits. Nonetheless, salinity prevented the induction of phenolic compounds (condensed and hydrolysable tannins), and also affected trait correlations. Specifically, phenolic compounds were negatively associated with nectar production only under salinized conditions, an apparent trade-off that presumably affects the induced levels of phenolic compounds. In addition, positive correlations between phenolic compounds and gland density and root biomass observed under control conditions were lost under salinized conditions. By investigating the effects of soil salinity on the expression of multiple direct and indirect defensive traits and their underlying correlations, these findings build toward a better understanding of how abiotic context-dependency shapes plant allocation to and expression of multiple defensive traits.

Data from: Wild samango monkeys, Cercopithecus mitis, balance risk and opportunity to interact with novel objects in village gardens

Research suggests that wild animals in urban areas exhibit heightened behavioral flexibility when they encounter novel human-made objects, but most such studies compared responses in urban populations with those from disjunct populations in less disturbed environments. We therefore know little about intrapopulation variation in cognitive or behavioral flexibility under different conditions of anthropogenic exposure. Here, we investigate object exploration and behavioral flexibility in a single group of samango monkeys (Cercopithecus mitis) in an environment where individuals forage in both gardens and natural forest. Over two months, we presented monkeys with novel, human-made objects in both natural and disturbed areas, varying the position of objects in trees to represent exposed or safer foraging zones. We video-recorded and analyzed interactions with these novel objects, assessing interaction times (an indicator of persistence), exploratory diversity (or motor diversity), and the occurrence of foraging innovations. Results from 67 interactions (29 in natural habitats and 38 in disturbed) indicate that samango monkeys exhibited a spatially complex response to novel objects: in contrast to other species, exploration diversity decreased significantly in anthropogenic environments, even as persistence remained largely static across contexts. Monkeys also exhibited foraging innovations by pulling on strings to bring objects closer. This may reduce exposure to danger, as string-pulling was most prevalent in the highest risk condition (ground level in human gardens). Significant intrapopulation variation in behavioral flexibility suggests that samango monkeys adjust the expression of problem-solving behaviors in relation to the degree of human disturbance in their immediate environment.

Functional groups of wild bees respond differently to faba bean (Vicia faba L.) cultivation at landscape scale

1. Concerns about insect declines are growing and the provisioning of ecosystem services like pollination may be threatened. To safeguard biodiversity, greening measures were introduced within the reform of the EU's Common Agricultural Policy. One measure commonly applied by farmers is the cultivation of nitrogen fixing crops. Although underlying studies are largely missing, this measure is criticized as providing no significant biodiversity benefit. 2. Using a landscape-scale approach, we selected 30 paired study landscapes (1km x 1km) in Germany, i.e. 15 study landscapes with faba bean (FB) fields (Vicia faba L.) and 15 without any grain legumes. Flower-visiting wild bees were recorded with transect walks at the field margins of different crops using a stratified sampling approach. We analyzed the effect of FB cultivation and landscape composition on the abundance and species richness of wild bees as well as on the functional composition of the bee communities. 3. Bumblebee densities (Bombus spp. Latreille) were more than twice as high in FB compared to control landscapes after the flowering of the beans. Non-Bombus wild bee densities, however, were not affected by FB cultivation, but were enhanced by increasing amounts of semi-natural habitats (SNH). 4. After the beans` blooming had ceased, FB landscapes had a higher proportion of wild bees collecting pollen from Fabaceae than control landscapes. The community weighted means for bee size, measured as intertegular distance, were not affected by FB cultivation, but we found smaller species and species with shorter tongues with an increasing percentage of SNH. 5. Synthesis and applications. The cultivation of faba bean (V. faba L.) strongly increased bumblebee densities throughout the season. This indicates that also on-field greening measures can support biodiversity. Nevertheless, since only functional groups adapted to faba bean benefit, measures to promote semi-natural habitats in agricultural landscapes need to be implemented. We conclude that the combination of on- and off-field measures is essential to maintain farmland biodiversity and the Common Agricultural Policy should furthermore promote both.

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms) with climate and geography, among 140 wild accessions. RDA, SEM, and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.

Data from: Multi-scale predictors of parasite risk in wild male savanna baboons (Papio cynocephalus)

Several factors are thought to shape male parasite risk in polygynous and polygynandrous mammals, including male-male competition, investment in potentially immunosuppressive hormones, and dispersal. Parasitism is also driven by processes occurring at larger scales, including host social groups and populations. To date, studies that test parasite-related costs of male behavior at all three scales—individual hosts, social groups, and the host population—remain rare. To fill this gap, we investigated multi-scale predictors of helminth parasitism in 97 male savanna baboons (Papio cynocephalus) living in the Amboseli ecosystem in Kenya over a five-year span. Controlling for multi-scale processes, we found that many of the classic indicators of male mating effort—high dominance rank, testosterone, and glucocorticoids—did not predict helminth infection risk. However, we identified two parasite-related costs associated with male behavior: (i) socially connected males exhibited higher Trichuris trichiura egg counts and greater parasite species richness than socially isolated males; and (ii) males with stable group residency exhibited higher parasite species richness than males who frequently dispersed to new social groups. At the population level, males harbored more parasites following periods of drought than rainfall. Lastly, parasites exhibited positive covariance suggesting that infection risk increases if a host already harbors one or more parasite taxa. These results indicate that multi-scale processes are important in driving male parasite risk, and that some aspects of male behavior are costly. Together, our results provide an unusually holistic perspective on the drivers of parasite risk in the context of male behaviors and life histories.

Data from: Predicting evolutionary responses to interspecific interference in the wild

Many interspecifically territorial species interfere with each other reproductively, and in some cases, aggression toward heterospecifics may be an adaptive response to interspecific mate competition. This hypothesis was recently formalized in an agonistic character displacement (ACD) model which predicts that species should evolve to defend territories against heterospecific rivals above a threshold level of reproductive interference. To test this prediction, we parameterized the model with field estimates of reproductive interference for 32 sympatric damselfly populations and ran evolutionary simulations. Asymmetries in reproductive interference made the outcome inherently unpredictable in some cases, but 80% of the model's stable outcomes matched levels of heterospecific aggression in the field, significantly exceeding chance expectations. In addition to bolstering the evidence for ACD, this paper introduces a new, predictive approach to testing character displacement theory that, if applied to other systems, could help resolve longstanding questions about the importance of character displacement processes in nature.

Code and data for: Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population

This is a Data package that contains three separate datasets and the analysis code for a manuscript 'Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population '. The first Dataset (pairs_data_2007_10) and the second dataset (pairs_data_2011_14) contain the data used to analyse the influence of meeting time of a pair of Great tits (i.e. month in the first dataset, week in the second dataset, when a pair was first detected in a flock together) on different components of breeding success of a pair. The third dataset (meeting_and_divorce) was used to analyse whether meeting time of a pair (in winter prior to the breeding season t) influence the probability of a pair to stay together or separate (divorce) to the following breeding season (t+1).

opencc-zeroOct 2020View details →

Data from: Social selectivity in aging wild chimpanzees

Humans prioritize close, positive relationships during aging, and socioemotional selectivity theory proposes that this shift causally depend on capacities for thinking about personal future time horizons. To examine this theory, we tested for key elements of human social aging in longitudinal data on wild chimpanzees. Aging male chimpanzees have more mutual friendships characterized by high, equitable investment, whereas younger males have more one-sided relationships. Older males are more likely to be alone, but they also socialize more with important social partners. Further, males show a relative shift from more agonistic interactions to more positive, affiliative interactions over their life span. Our findings indicate that social selectivity can emerge in the absence of complex future-oriented cognition, and they provide an evolutionary context for patterns of social aging in humans.

Data from: Development time mediates the effect of larval diet on ageing and mating success of male antler flies in the wild

High-quality developmental environments often improve individual performance into adulthood, but allocating toward early life traits, such as growth, development rate and reproduction, may lead to trade-offs with late-life performance. It is, therefore, uncertain how a rich developmental environment will affect the ageing process (senescence), particularly in wild insects. To investigate the effects of early life environmental quality on insect life-history traits, including senescence, we reared larval antler flies (Protopiophila litigata) on four diets of varying nutrient concentration, then recorded survival and mating success of adult males released in the wild. Declining diet quality was associated with slower development, but had no effect on other life-history traits once development time was accounted for. Fast-developing males were larger and lived longer, but experienced more rapid senescence in survival and lower average mating rate compared to slow developers. Ultimately, larval diet, development time and body size did not predict lifetime mating success. Thus, a rich environment led to a mixture of apparent benefits and costs, mediated by development time. Our results indicate that 'silver spoon' effects can be complex and that development time mediates the response of adult life-history traits to early life environmental quality.

Tracking sickness effects on social encounters via continuous proximity-sensing in wild vampire bats

Sickness behaviors can slow the spread of pathogens across a social network. We conducted a field experiment to investigate how sickness behavior affects individual connectedness over time using a dynamic social network created from high-resolution proximity data. After capturing adult female vampire bats (Desmodus rotundus) from a roost, we created 'sick' bats by injecting a random half of bats with the immune-challenging substance, lipopolysaccharide, while the control group received saline injections. Over the next three days, we used proximity sensors to continuously track dyadic associations between 16 'sick' bats and 15 control bats under natural conditions. Compared to control bats, 'sick' bats associated with fewer bats, spent less time near others, and were less socially connected to more well-connected individuals (sick bats had on average a lower degree, strength, and eigenvector centrality). High-resolution proximity data allow researchers to flexibly define network connections (association rates) based on how a particular pathogen is transmitted (e.g., contact duration of >1 vs >60 minutes, contact proximity of <1 vs <10 meters). Therefore, we inspected how different ways of measuring association rates changed the observed effect of LPS. How researchers define association rates influences the magnitude and detectability of sickness effects on network centrality.

opencc-zeroOct 2020View details →

Fitness costs of parasites explain multiple life history tradeoffs in a wild mammal

Reproduction in wild animals can divert limited resources away from immune defence, resulting in increased parasite burdens. A longstanding prediction of life history theory states that these parasites can harm the individual, reducing the organism's subsequent fitness and producing reproduction-fitness tradeoffs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent fitness in a wild population of individually identified red deer ( Cervus elaphus ). Using path analysis, we investigated whether costs of lactation for downstream survival and fecundity were mediated by changes in strongyle nematode count and mucosal antibody levels. Lactating females exhibited increased parasite counts, which were in turn associated with substantially decreased fitness in the following year in terms of overwinter survival, fecundity, subsequent calf weight, and parturition date. This study offers observational evidence for parasite regulation of multiple life history tradeoffs, supporting the role of parasites as an important mediating factor in wild mammal populations.

zenodo36/100

Model output data for Marine Wild-Capture Fisheries after Nuclear War

This is the model data material for Scherrer at al., PNAS. [Scherrer K. J. N., et al. Marine wild-capture fisheries after nuclear war, PNAS in press]. Input files include time series of gridded global oceanic Sea Surface Temperature and Net Primary Productivity (output from the CESM model) and socioeconomic input for the global fisheries model (BOATS). Output files include globally integrated time series (used in Figs. 1-3 and 6) and global gridded model output (used in Figs. 4-5) for each of the five ensemble member runs.

opencc-by-4.0Dec 2019View details →

opencc-zeroNov 2020View details →

Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers

Pea (Pisum sativum L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (Pisum sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of Pisum, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of Pisum utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of Pisum fulvum, Pisum abyssinicum and some wild P. sativum accessions, whereas groups II and III consisted of the two genetic groups under P. sativum representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of Pisum, P. fulvum and P. abyssinicum possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of P. sativum described by some authors were not supported in this study, with the exception of several genotypes of P. sativum subsp. elatius that were clustered with P. fulvum and P. abyssinicum. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.

opencc-zeroNov 2021View details →

Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows

Co-infection with microparasites (e.g., bacteria) and macroparasites (e.g., helminths) is often the natural state for wild animals. Despite evidence that gut helminths can bias immune responses away from inflammatory processes, few field studies have examined the role that helminths, or their potential interactions with internal microbial communities, play in modulating immunity in free-living, wild birds. Here, we used anthelmintic drugs to treat wild Song Sparrows (Melospiza melodia) for helminth infections and measured markers of systemic inflammation (heterothermia and locomotor activity) in response to an immune challenge with lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria. Using birds from a population that previously showed high helminth prevalence, we monitored skin temperature and activity remotely using automated radio telemetry. We also collected cloacal swabs to determine whether drug treatment was associated with changes in the cloacal microbiota, and whether cloacal microbial community structure was associated with the severity of birds' immune responses. Because helminths can reduce the severity of inflammatory immune responses in other species, we predicted that in comparison with untreated control birds, anthelmintic-treated birds would be more lethargic and display higher fevers when challenged with LPS. Consistent with these predictions, anthelmintic-treated birds expressed higher fevers in response to immune challenge. However, all LPS-challenged birds decreased locomotor activity to a similar degree, regardless of anthelmintic treatment. Although several individual indicator bacterial taxa were strongly associated with anthelmintic treatment, this treatment did not alter overall bacterial alpha- and beta- diversity. Similarly, we did not find evidence that bacterial community diversity influenced the severity of immune responses to LPS. These results suggest that under field conditions, natural helminth infection can reduce the severity of songbirds' thermoregulatory responses (fever) during an immune challenge, without major impacts on internal microbial communities or behavioral responses to infection.