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opencc-by-4.0Oct 2020View details →

The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations

This data accompanies the pending publication "The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations" by Lynn et al. The work is also published under Austin Lynn's PhD Dissertation, which is under embargo until 2022.

opencc-by-4.0Sep 2022View details →

Complex plant quality - microbiota - population interactions modulate the response of a specialist herbivore to the defense of its host plant.

1. Many specialist herbivores have evolved strategies to cope with plant defenses, with gut microbiota potentially participating to such adaptations. 2. In this study we assessed whether the history of plant use (population origin) and microbiota may interact with plant defense adaptation. 3. We tested whether microbiota enhance the performance of Melitaea cinxia larvae on their host plant, Plantago lanceolata and increase their ability to cope the defensive compounds, iridoid glycosides (IGs). 3. The gut microbiota was significantly affected by both larval population origin and host plant IG level. Contrary to our prediction, impoverishing the microbiota with antibiotic treatment did not reduce larval performance. 5. As expected for this specialized insect herbivore, sequestration of one of IGs was higher in larvae fed with plants producing higher concentration of IGs. These larvae also showed metabolic signature of intoxication (i.e. decrease in Lysine levels). However, intoxication on highly defended plants was only observed when larvae with history of poorly defended plants were simultaneously treated with antibiotics. 6. Our results suggest that both adaptation and microbiota contribute to the metabolic response of herbivores to plant defense though complex interactions.

Differential changes in lifecycle-event phenology provide a window into regional population declines

Climate change affects the phenology of annual lifecycle events of organisms, such as reproduction and migration. Shifts in the timing of these events could have important population implications directly, or provide information about the mechanisms driving population trajectories, especially if they differ between lifecycle event. We examine if such shifts occur in a declining migratory passerine bird (Willow Warbler, Phylloscopus trochilus), which exhibits latitudinally diverging population trajectories. We find evidence of phenological shifts in breeding initiation, breeding progression and moult that differ across geographic and spring temperature gradients. Moult initiation following warmer springs advances faster in the south than in the north, resulting in proportionally shorter breeding seasons, reflecting higher nest failure rates in the south and in warmer years. Tracking shifts in multiple lifecycle events allowed us to identify points of failure in the breeding cycle in regions where the species has negative population trends, thereby demonstrating the utility of phenology analyses for illuminating mechanistic pathways underlying observed population trajectories.

Data for Contrasting life-history responses to climate variability in eastern and western North Pacific sardine populations

Massive populations of sardines inhabit both the western and eastern boundaries of the world's subtropical ocean basins, supporting both commercial fisheries and populations of marine predators. Sardine populations in western and eastern boundary current systems have responded oppositely to decadal scale anomalies in ocean temperature, but the mechanism for differing variability has remained unclear. Here, based on otolith microstructure and high-resolution stable isotope analyses, we show that habitat temperature, early life growth rates, energy expenditure, metabolically optimal temperature and, most importantly, the relationship between growth rate and temperature were remarkably different between the two subpopulations in the western and eastern North Pacific. Varying metabolic response to environmental changes partly explain the contrasting growth responses. Consistent differences in the life-history traits are observed between subpopulations in the western and eastern boundary current systems around South Africa. These growth and survival characteristics can facilitate the contrasting responses of sardine populations to climate change.

Comparing climatic suitability and niche distances to explain populations responses to extreme climatic events

Habitat suitability calculated from Species Distribution Models (SDMs) has been used to assess population performance, but empirical studies have provided weak or inconclusive support to this approach. Novel approaches measuring population distances to niche centroid and margin in environmental space have been recently proposed to explain population performance, particularly when populations experience exceptional environmental conditions that may place them outside of the species niche. Here, we use data of co-occurring species' decay, gathered after an extreme drought event occurring in the SE of the Iberian Peninsula which highly affected rich semiarid shrubland communities, to compare the relationship between population decay (mortality and remaining green canopy) and (1) distances between populations' location and species niche margin and centroid in the environmental space, and (2) climatic suitability estimated from frequently used SDMs (here MaxEnt) considering both the extreme climatic episode and the average reference climatic period before this. We found that both SDMs-derived suitability and distances to species niche properly predict populations performance when considering the reference climatic period; but climatic suitability failed to predict performance considering the extreme climate period. In addition, while distance to niche margins accurately predict both mortality and remaining green canopy responses, centroid distances failed to explain mortality, suggesting that indexes containing information about the position to niche margin (inside or outside) are better to predict binary responses. We conclude that the location of populations in the environmental space is consistent with performance responses to extreme drought. Niche distances appear to be a more efficient approach than the use of climate suitability indices derived from more frequently used SDMs to explain population performance when dealing with environmental conditions that are located outside the species environmental niche. The use of this alternative metrics may be particularly useful when designing conservation measures to mitigate impacts of shifting environmental conditions.

Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations

The pet trade and Traditional Chinese Medicine (TCM) consumption are major drivers of global biodiversity loss. Tokay geckos (Gekko gecko) are among the most traded reptile species worldwide. In Hong Kong, pet and TCM markets sell tokay geckos while wild populations also persist. To clarify connections between trade sources and destinations, we compared genetics and stable isotopes of wild tokays in local and nonlocal populations to dried individuals from TCM markets across Hong Kong. We found that TCM tokays are likely not of local origin. Most wild tokays were related to individuals in South China, indicating a probable natural origin. However, two populations contained individuals more similar to distant populations, indicating pet trade origins. Our results highlight the complexity of wildlife trade impacts within trade hubs. Such trade dynamics complicate local legal regulation when endangered species are protected, but the same species might also be non-native and possibly damaging to the environment.

Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns

Long term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments, and chance events all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2,000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor were evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing-returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.

Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population

Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6,291 genome-wide single nucleotide polymorphisms (SNPs), 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D. batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (Ne), and catch per unit effort (CPUE) estimates from the trammel-net survey. Although each method was characterised by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site-fidelity in D. batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.

Discordant population structure among rhizobium divided genomes and their legume hosts

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole-genome resequencing of a hierarchically-structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize the population structures of this bacterial symbiont and its host plant Medicago truncatula. Sinorhizobium meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.

Savanna monkey (Chlorocebus spp.) population genetics/genomics pipeline

In the last 300 thousand years, the genus Chlorocebus expanded from equatorial Africa into the southernmost latitudes of the continent, where colder climate was a likely driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 (UCP1) gene region—implicated in non-shivering thermogenesis (NST)— in 73 wild savanna monkeys from three taxa representing this southern expansion (Chlorocebus pygerythrus hilgerti, Chlorocebus cynosuros and Chlorocebus pygerythrus pygerythrus) ranging from Kenya to South Africa. We found 17 SNPs with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant linkage disequilibrium with each other. Phylogenetic generalized least-squares modelling with ecological covariates suggests that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance are demonstrated by a relatively isolated population in the southern coastal belt of South Africa. We suggest that sunbathing behaviours common to savanna monkeys, in combination with the strength of solar irradiance, may mediate adaptations to thermal stress via NST among savanna monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

opencc-by-4.0Dec 2021View details →

A gridded dataset on population densities, real estate prices, transport and land use inside 192 worldwide urban areas

This dataset provides, on a systematic basis, gridded population densities, rents, real estate prices, and transport times (both in public transport and private car) in 192 cities across the world.

Temporal change in the contribution of immigration to population growth in a wild seabird experiencing rapid population decline

The source-sink paradigm predicts that populations in poorer-quality habitats ("sinks") persist due to continued immigration from more-productive areas ("sources"). However, this categorisation of populations assumes that habitat quality is fixed through time. Globally, we are in an era of wide-spread habitat degradation, and consequently, there is a pressing need to examine dispersal dynamics in relation to local population change. We used an integrated population model to quantify immigration dynamics in a long-lived colonial seabird, the black-legged kittiwake Rissa tridactyla, that is classified as globally "Vulnerable". We then used a transient life table response experiment to evaluate the contribution of temporal variation in vital rates, immigration rates, and population structure to realised population growth. Finally, we used a simulation analysis to examine the importance of immigration to population dynamics. We show that the contribution of immigration changed as the population declined. This study demonstrates that immigration is unlikely to maintain vulnerable sink populations indefinitely, emphasising the need for temporal analyses of dispersal to identify shifts that may have dramatic consequences for population viability.

Epidendrum radicans - genetic data of 4 regional populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092 – 0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2

Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis—including parameter optimization—as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.

Genomic variation in the Black-throated Green Warbler (Setophaga virens) suggests divergence in a disjunct Atlantic Coastal Plain population (S. v. waynei)

We used whole-genome resequencing to estimate genetic distinctiveness in the Black-throated Green Warbler (Setophaga virens)—including S. v. waynei—a putative subspecies that occupies a narrow disjunct breeding range along the Atlantic Coastal Plain. Despite detecting low-global differentiation (FST = 0.027) across the entire species, the principal components analysis of genome-wide differences shows the main axis of variation separates S. v. waynei from all other S. v. virens samples. We also estimated a low-migration rate for S. v. waynei, but found them to be most similar to another disjunct population from the Piedmont of North Carolina, and detected evidence of a historical north-to-south geographic dispersal among the entire species. New World wood warblers (family: Parulidae) can exhibit strong phenotypic differences among species, particularly, in song and plumage; however, within-species variation in these warblers—often designated as subspecies—is much more subtle. The existence of several isolated Black-throated Green Warbler populations across its eastern North American breeding range offers an excellent opportunity to further understand the origin, maintenance, and conservation status of subspecific populations. Our results, combined with previously documented ecological and morphological distinctiveness, support that S. v. waynei be considered a distinct and recognized subspecies worthy of targeted conservation efforts.

Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

opencc-zeroOct 2022View details →

Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

An important challenge in ecology is to understand variation in species' maximum intrinsic rate of population increase, 𝑟𝑚𝑎𝑥, not least because 𝑟𝑚𝑎𝑥 underpins our understanding of the limits of fishing, recovery potential, and ultimately extinction risk. Across many vertebrate species, terrestrial and aquatic, body mass and environmental temperature are important correlates of 𝑟𝑚𝑎𝑥. In sharks and rays, specifically, 𝑟𝑚𝑎𝑥 is known be lower in larger species, but also in deep-sea ones. We use an information-theoretic approach that accounts for phylogenetic relatedness to evaluate the relative importance of body mass, temperature and depth on 𝑟𝑚𝑎𝑥. We show that both temperature and depth have separate effects on shark and ray 𝑟𝑚𝑎𝑥 estimates, such that species living in deeper waters have lower 𝑟𝑚𝑎𝑥. Furthermore, temperature also correlates with changes in the mass scaling coefficient, suggesting that as body size increases, decreases in 𝑟𝑚𝑎𝑥 are much steeper for species in warmer waters. These findings suggest that there are (as-yet understood) depth-related processes that limit the maximum rate at which populations can grow in deep sea sharks and rays. While the deep ocean is associated with colder temperatures, other factors that are independent of temperature, such as food availability and physiological constraints, may influence the low 𝑟𝑚𝑎𝑥 observed in deep sea sharks and rays. Our study lays the foundation for predicting the intrinsic limit of fishing, recovery potential, and extinction risk species based on easily accessible environmental information such as temperature and depth, particularly for data-poor species. This repository contains the data and a minimum working example of the model-fitting process used for the article "Body mass, temperature, and depth shape productivity in sharks and rays", which is currently in press at Ecology and Evolution.