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Propensity for selfing varies within a population of hermaphroditic snails: coexistence of selfers, outcrossers, and mixed-mating individuals

To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. Observed individual selfing rates depend on the environment (e.g., differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail Radix balthica by conducting laboratory mating trials that manipulated mate availability (low vs. moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%), and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness. Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers, and mixed maters. As mate availability did not affect selfing, our "moderate" level might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.

opencc-by-4.0Feb 2022View details →

Data from: Evaluating predator control using two non-invasive population metrics: a camera trap activity index and density estimation from scat genotyping

Includes datasets from the Wimmera and Mallee, Victoria, Australia: - Fox camera trap data used to model activity - Fox scat SECR capture and trap files used to model density

Contaminated sediment in the Detroit River selects for evolved CYP1A and p53 responses in wild brown bullhead (Ameiurus nebulosus) populations

<div> <div> In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (Ameiurus nebulosus) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a protective and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured in both studies with the addition of phase II glutathione-s-transferase (GST) activity in the second. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that was not reached in cleared fish exposed to contaminated sediment. Instead, cleared and F1 bullhead from clean and contaminated sites had overlapping p53 expression patterns in response to contaminated sediment by 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 refractory response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, with clean site fish responding to contaminated sediment more deliberately. By 96 hours, the response patterns of F1 offspring from clean and contaminated sites to clean and contaminated sediment exposures were similar. </div> <div> Because p53, CYP1A and GST activity responses to contaminated sediment dosing overlapped in clean and contaminated farm-raised F1 offspring, these results suggest that contaminated fish have acclimated to the contaminants present in their environments by reaching a tolerance threshold and no evidence of adaptation was detected in these biomarkers. </div> </div>

Tackling local ecological homogeneity: Finding intraspecific trait variability in local populations of Mediterranean plants

Local homogeneity, in ecology, is the often undisclosed assumption that variability within populations is negligible or mostly distributed evenly. In large areas, this can lead to the aggregation of different populations without regard for their unique needs and characteristics, such as drought sensitivity and functional traits distributions. Here we discuss whether this assumption can be justified, and we hypothesize that discerning the source of variation between plasticity and adaptation could be a feasible approach to formulate an informed decision. We test this hypothesis on plants, resorting to a common garden experiment to determine the source of variation of several plant functional traits at a local scale (~60 Km) of three wild species: Quercus ilex, Pistacia lentiscus and Cistus salviifolius. Individuals of each species were sourced from three key sites chosen along a local aridity gradient. Our approach led to the rejection of the local homogeneity assumption for Q. ilex and C. salviifolius at this scale due to the adaptive divergence observed among neighbouring populations. This case study provides evidence that addressing local homogeneity can highlight diverging populations in a relatively simple way. We conclude that gathering empirical evidence on intraspecific variability is a feasible approach that can provide researchers with solid bases to decide whether to adopt the local homogeneity assumption or not.

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

The effects of human population density on trophic interactions are contingent upon latitude

Aim: Studies conducted at a global scale are necessary to make general conclusions on the effect of urbanization on trophic interactions and explore how these effects change along latitudinal gradients. Since biotic interactions are more intense at lower latitudes, we predict they are less likely to be affected by human impacts than at higher latitudes. Therefore, we test the hypothesis that the effect of urbanization (quantified by human population density) on trophic interactions, specifically insect herbivory and bird predation, decreases with an increase in latitude Location: Global (881 study sties) Time period: 2000-2021 Major taxa studied: Birds, arthropods and plants. Methods: We compiled global data on insect herbivory and bird predation from individual studies using similar methodologies, and fitted generalized linear mixed models to test the effect of human population density, latitude and their interaction on these two response variables. Results: The intensity of herbivory and predation decreased with the increase of human population density at lower latitudes, remained unaffected at intermediate latitudes, and increased at higher latitudes. Main conclusions: The effect of urbanization on the intensities of trophic interactions varies across latitudes, with a reversal of the pattern at high vs. low latitudes potentially explained by the urban heat island effect, being this pattern consistent across the two main trophic interaction.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances, and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

Phenotypic and genetic diversity data recorded in island and mainland populations worldwide

We used this dataset to assess the strength of isolation due to geographic and macroclimatic distance across island and mainland systems, comparing published measurements of phenotypic traits and neutral genetic diversity for populations of plants and animals worldwide. The dataset includes 112 studies of 108 species (72 animals and 36 plants) in 868 island populations and 760 mainland populations, with population-level taxonomic and biogeographic information, totalling 7438 records.

Data from: Novel methods to define invasive procedures at the end-of-life were developed to improve quality of end of life care research: A population-based cohort study in colorectal cancer

Background Understanding the use of invasive procedures (IPs) at the end-of-life (EoL) is important to avoid under- and overtreatment, but epidemiologic analysis is hampered by limited methods to define treatment intent and EoL phase. This study applied novel methods to report IPs at the EoL using a colorectal cancer (CRC) case study. Methods An English population-based cohort of adult patients diagnosed between 2013 and 2015 was used with follow-up to 2018. Procedure intent (curative, non-curative, diagnostic) by cancer site and stage at diagnosis was classified by two surgeons independently. Joinpoint regression modelled weekly rates of IPs for 36 sub-cohorts of patients with incremental survival of 0-36 months. EoL phase was defined by a significant IP rate change before death. Zero-inflated Poisson regression explored associations between IP rates and clinical/sociodemographic variables. Results Of 87,731 patients included, 41,972 (48%) died. 9,492 procedures were classified by intent (interrater agreement 99.8%). Patients received 502,895 IPs (1.39 and 3.36 per person year for survivors and decedents). Joinpoint regression identified significant increases in IPs four weeks before death in those living 3-6 months, and eight weeks before death in those living 7–36 months from diagnosis. 7,908 (18.8%) patients underwent IPs at the EoL, with stoma formation the most common major procedure. Younger age, early-stage disease, men, lower comorbidity, those receiving chemotherapy and living longer from diagnosis were associated with IPs. Conclusions Methods to identify and classify IPs at the EoL were developed and tested within a CRC population. This approach can be now extended and validated to identify potential under- and overtreatment.

Data from: Two focal populations and three regional populations of Sobralia chrysostoma

The dispersal and colonization of plant populations allow species to occupy novel habitats, migrate, and undergo range shifts in response to changing environmental factors and, as such, are fundamental ecological processes for ensuring the long-term persistence of species. Natural landscape disturbance often generates habitats available for colonization. Patterns of colonization and population expansion can be inferred from the levels and partitioning of genetic variation of plant populations with known disturbance histories, such as recent volcanic eruptions. We sampled and mapped 496 individuals from two populations of the colonizing terrestrial orchid, Sobralia chrysostoma, on the 1992 lava flow of Volcán Arenal in central Costa Rica. We used neutral co-dominant markers to genotype individuals and estimate population genetic statistics. Both populations had high mean levels of genetic diversity (P = 100%; AP = 3.31; He = 0.259) suggesting that the lava flow was colonized by numerous individuals that likely originated from multiple source populations. However, significant spatial genetic structure (SGS) was only present in one population at the smallest distance class (≤ 2 m) and was low (r = 0.032). That these large and genetically diverse populations had such low SGS and an absence of SGS respectively is contrary to expectations and differs significantly from the pattern in Epidendrum radicans (Orchidaceae), with which S. chrysostoma is growing sympatrically. Our results suggest that these two populations either consist primarily of immigrant individuals or that seeds produced in situ dispersed over longer distances, thereby producing larger seed shadows and greater overlap of seed shadows.

Dataset for: Population decline in a Pleistocene refugium: stepwise, drought-related dieback of a South Australian eucalypt

Refugia can facilitate the persistence of species through long-term environmental change, but it is not clear if Pleistocene refugia will remain functional under anthropogenic climate change. Dieback of species within refugia therefore raises concerns about their long-term persistence. Using repeat field surveys, we investigate dieback patterns of an isolated population of Eucalyptus macrorhyncha during two droughts and discuss prospects for its continued persistence in a Pleistocene refugium. We first confirm that the Clare Valley in South Australia has constituted a long-term refugium for the species, with the population being genetically highly distinct from other conspecific populations. However, the population lost >40% of individuals and biomass through the two droughts, with mortality being just below 20% after the Millennium Drought (2000–2009) and almost 25% after the Big Dry (2017-2019). The best predictors of mortality differed after each drought. While the north-facing aspect of a sampling location was a significant positive predictor after both droughts, biomass density and slope were significant negative predictors only after the Millennium Drought, and distance to the north-west corner of the park, which intercepts hot, dry winds, was significant after the Big Dry only. This suggests that more marginal sites with low biomass and located on exposed, flat plateaus were more vulnerable initially, but that heat-stress was an important driver of dieback during the Big Dry. Therefore, the causative drivers of dieback may change during population decline. Regeneration occurred predominantly on southern and eastern aspects, which would receive the least solar radiation. Occurrence in a refugium did not protect this population from dieback. However, gullies with lower solar radiation are continuing to support relatively healthy, regenerating stands of red stringybark, providing hope for persistence in small pockets. Monitoring and managing these pockets during future droughts will be essential to ensure the persistence of this isolated and genetically unique population.

Population-biased sQTL catalog

Population-biased sQTL catalog generated by <a href="https://github.com/guigolab/sqtlseeker2-nf/tree/interaction">sqtlseeker2.int-nf</a> in the <a href="https://www.gtexportal.org/home/">GTEx</a> dataset, as described in the publication A fast non-parametric test of association for multiple traits by Garrido-Martín et al. in Genome Biology (<a href="https://doi.org/10.1186/s13059‑023‑03076‑8">https://doi.org/10.1186/s13059‑023‑03076‑8</a>).

Genomic diversity and population structure of teosintes (Zea spp.) and its conservation implications

The wild species of the genus Zea commonly named teosintes, comprise nine different taxa, distributed from northern Mexico to Costa Rica. Although this genus of plants has been extensively studied from a morphological, ecogeographical and genetic point of view, most contributions have been limited to the study of a few populations and taxa. To understand the great variability that exists between and within teosinte species, it is necessary to include the vast majority of known populations. In this context, the objective of this work was to evaluate the diversity and genomic structure of 276 teosinte populations. Molecular analyzes were performed with 3,604 plants and with data from 33,929 SNPs. The levels of genetic diversity by taxonomic group show a marked difference between species, races and sections, where the highest values of genomic diversity were found in ssp. parviglumis and ssp. mexicana. The lower values were obtained for the Luxuriantes section as well as ssp. huehuetenagensis of the section Zea. The results of the structure show that there is a great genetic differentiation in all the taxonomic groups considered. For ssp. parviglumis and mexicana, which are the taxa with the largest number of populations, a marked genomic differentiation was found that is consistent with their geographic distribution patterns. These results showed a loss of diversity in several teosinte populations, making a strong case for further collection, and ex situ and in situ conservation. Also, this study highlights the importance of integrating genomic diversity and structure for the applications of conservation and management.

Age Structure and Body Size of The Tibetan Toad (Bufo tibetanus) Populations from Two Different Altitudes in China

Knowledge about the altitudinal patterns in age and body size helps to highlight the evolution of life history parameters in animals. In this study, we investigated the demographic traits of the Tibetan toad (Bufo tibetanus) between populations from low and high altitude habitats (2650 vs 3930m) using skeletochronology. We found 1) the mean age and body size of females were significantly greater than those of males in either population; 2) both sexes of toads from the higher altitude tended to be significantly older in age and larger in body size; 3) a significant positive relationship between age and body size within each sex of the toad at both altitudes; 4) growth rates varied between the two populations, with the higher rate observed in the low-altitude population, and lower in the high-altitude population. Our results suggest that factors other than age can influence altitudinal patterns in body size, such as altitude-associated temperature. Future research should pay attention to these factors and evaluate their influences on the growth patterns of animals.Knowledge about the altitudinal patterns in age and body size helps to highlight the evolution of life history parameters in animals. In this study, we investigated the demographic traits of the Tibetan toad (Bufo tibetanus) between populations from low and high altitude habitats (2650 vs 3930m) using skeletochronology. We found 1) the mean age and body size of females were significantly greater than those of males in either population; 2) both sexes of toads from the higher altitude tended to be significantly older in age and larger in body size; 3) a significant positive relationship between age and body size within each sex of the toad at both altitudes; 4) growth rates varied between the two populations, with the higher rate observed in the low-altitude population, and lower in the high-altitude population. Our results suggest that factors other than age can influence altitudinal patterns in body size, such as altitude-associated temperature. Future research should pay attention to these factors and evaluate their influences on the growth patterns of animals.

Induction of daytime downward migration in a field-derived Daphnia population by the fish kairomone CPS – a mesocosm approach

The fish-borne bile salt 5α-cyprinol sulfate (CPS) has been identified as a kairomone inducing the predator avoidance behavior "diel vertical migration" (DVM) in Daphnia magna in response to fish. Conclusions about the ecological significance of CPS have been derived from laboratory experiments only. Using a mesocosm approach, we investigate whether the role of CPS as a kairomone can be confirmed in the field. We demonstrate that CPS induces downward migration during daytime in a field-derived Daphnia community consisting of D. longispina and D. cucullata and in D. longispina in particular. In the study lake, D. longispina shows a similar pattern of DVM. Quantification of CPS by HPLC-MS confirms that CPS in situ concentrations in the lake are sufficiently high for induction of daytime downward migration of D. longispina in this oligo-mesotrophic lake. Conclusively, we provide evidence for the significance of CPS as a kairomone in freshwater systems.

Dataset for study Long-term changes in urban bird populations: correspondence of the trends between urban and rural areas

Dataset used for a study "Long-term changes in urban bird populations: correspondence of the trends between urban and rural areas" Data structure: Type = type of environment (R - rural, U - urban) POID = unique identifier of each census point across all transects Transect = unique identifier of a transect (each contains 20 census points) Point = unique identifier of a point within one transect Year = year of the count Species    = scientific name of bird species Count = number of birds counted Each species has its own datafile.

Supporting data for "Population Genomics of Postglacial Western Eurasia"

This repository contains supplemental data from Allentoft, Sikora et al. "Population Genomics of Postglacial Western Eurasia". The following files are included supplementary_figures/ Hi-res versions of supplementary figures  ibd/ Aggregate total IBD sharing rates between pairs of individuals in the full dataset. Includes auxiliary metadata files to use for IBD-based mixture models (code available at <a href="https://github.com/martinsikora/mixmodel_ibd">https://github.com/martinsikora/mixmodel_ibd</a>) For additional details on data generation, curation and sample metadata please consult the main paper.

Climate change does not equally affect temporal patterns of natural selection on reproductive timing across populations in two songbird species

Climate change has led to changes in the strength of directional selection on seasonal timing. Understanding the causes and consequences of these changes is crucial to predicting the impact of climate change. But are observed patterns in one population generalisable to others, and can spatial variation in selection be explained by environmental variation among populations? We used long-term data (1955–2022) on blue and great tits co-occurring in four locations across the Netherlands to assess inter-population variation in temporal patterns of selection on laying date. To analyse selection, we combine reproduction and adult survival into a joined fitness measure. We found distinct spatial variation in temporal patterns of selection which overall acted towards earlier laying, and which was due to selection through reproduction rather than through survival. The underlying relationships between temperature, bird and caterpillar phenology were however the same across populations, and the spatial variation in selection patterns is thus caused by spatial variation in the temperatures and other habitat characteristics to which birds and caterpillars respond. This underlines that climate change is not necessarily equally affecting populations, but that we can understand this spatial variation, which enables us to predict climate change effects on selection for other populations.

Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific

The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S. viridula, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S. zebrina, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S. zebrina, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species.

Data from: Divergence in the internal genital morphology of females is correlated with divergence in male intromittent structures among populations of a millipede

Our understanding of genital evolution comes largely from studies of male genitalia. Females have received far less attention because of the difficulties inherent in quantifying the shapes of their internal genital structures. Here we combine advances in micro-computed tomography with a new landmark free method of quantifying three-dimensional trait shape, to document patterns of divergence in female genital shape, and the correlated divergence of male genitalia among populations of the millipede Antichiropus variabilis. We used single nucleotide polymorphisms to estimate levels of neutral genetic divergence among seven populations of millipede. Genetic divergence was high and correlated with geographic distance. Comparing phenotypic divergence in genital shape to neutral genetic divergence, we found that genital shape for both females and males has diverged more than would be expected from random drift, consistent with a pattern of directional selection. While there was significant covariation between female and male genital shape across populations, the magnitude of divergence in genital shape between the sexes was not correlated. Our results demonstrate the utility of using three-dimensional scanning technologies to examine female genital traits and add to a small but growing number of studies showing that like male genitalia, female genitalia can be under strong directional selection.