Find research datasets worth reusing

Data for: The climatic variability hypothesis and trade–offs in thermal performance in coastal and inland populations of Mimulus guttatus

Ecologists and evolutionary biologists have long predicted that organisms in more climatically variable environments should be adapted to handle a wider range of conditions. This intuitive idea, known as the Climatic Variability Hypothesis, has gained mixed support from empirical studies. We tested the Climatic Variability Hypothesis in a novel system by comparing the thermal breadth of coastal and inland populations of Mimulus guttatus. To quantify thermal breadth, we performed a thermal performance experiment and built performance curves. Using these performance curves, we also evaluated evidence for a breadth–performance trade–off and the Hotter–is–Better hypothesis. We did not find support for the Climatic Variability Hypothesis; coastal and inland populations did not differ in thermal breadth. However, we found evidence for a breadth performance trade–off and the Hotter–is–Better hypothesis. Surprisingly, the two most inland populations differed the most in the thermal performance traits we evaluated. Our results highlight the importance of explicitly measuring thermal performance to test explanations of species distribution patterns and the need to examine alternative mechanisms by which organisms occupy different climatic regimes.

opencc-by-4.0Jan 2023View details →

Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis

Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis

The timings of host diapause and epidemic progression mediate host genetic diversity and future epidemic size in Daphnia-parasite populations

Epidemics commonly exert parasite-mediated selection and cause declines in host population genetic diversity. This could lead to evolution of resistance in the long-term and smaller subsequent epidemics. Alternatively, the loss of genetic diversity could increase host vulnerability to future disease spread and larger future epidemics. Matters are made more complex by the fact that a great many host organisms produce diapausing life stages in response to environmental change (often as a result of sexual reproduction) e.g., plant seeds and invertebrate resting eggs. These diapausing stages can disrupt the relationship between past epidemics, host genetic diversity and future epidemics because they allow host dispersal through time. Specifically, temporally dispersing hosts avoid infection and thus selection from contemporary parasites, and also archive genetic variation for the future. We studied 80 epidemics in 20 semi-natural populations of the temporally dispersing crustacean Daphnia magna and its sterilising bacterial parasite Pasteuria ramosa, and half of these populations experienced a simulated environmental disturbance treatment. We found that early initiation of diapause relative to the timing of the epidemic led to greater host genetic diversity and reduced epidemic size in the subsequent year, but this was unaffected by environmental disturbance.

Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration

To explore the diversity of microbial growth responses, we have compiled 247 measurements of half-saturation concentrations K and maximum growth rates gmax from previously-published studies (see Methods). The data includes a wide range of resources, including sources of carbon, nitrogen, phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate having the largest number of measurements due to their emphasis in marine and laboratory systems. Organisms include prokaryotes and eukaryotes as well as autotrophs and heterotrophs. This data has been analyzed in a companion research article. For data plots and a discussion of results, please refer to: <div class="csl-bib-body"> <div class="csl-entry">Fink, Justus Wilhelm, Noelle A. Held, and Michael Manhart. "Microbial Population Dynamics Decouple Growth Response from Environmental Nutrient Concentration." Proceedings of the National Academy of Sciences 120, no. 2 (January 10, 2023). <a href="https://doi.org/10.1073/pnas.2207295120">https://doi.org/10.1073/pnas.2207295120</a>.</div> </div>

Long-term responses to large-scale disturbances: Spatiotemporal variation in gastropod populations and communities

The Anthropocene is characterized by complex, primarily human-generated, disturbance regimes that include combinations of long-term press (e.g. climate change, pollution) and episodic pulse (e.g. cyclonic storms, floods, wildfires, land use change) disturbances. Within any regime, disturbances occur at multiple spatial and temporal scales, creating complex and varied interactions that influence spatiotemporal dynamics in the abundance, distribution, and biodiversity of organisms. Moreover, responses to disturbance are context-dependent, with the legacies of previous disturbances affecting responses to ensuing perturbations. We use three decades of annual data to evaluate the effects of repeated pulse disturbances and global warming on gastropod populations and communities in Puerto Rico at multiple spatial scales. More specifically, we quantify (1) the relative importance of large-scale and small-scale aspects of disturbance on variation in abundance, biodiversity, and species composition; and (2) the spatial scales at which populations and communities integrate information in the spatially heterogenous environments created by disturbances. Gastropods do not exhibit consistent decreases in abundance or biodiversity in association with global warming: abundance for many species has increased over time and species richness does not evince a temporal trend. Nonetheless, gastropods are sensitive to hurricane severity, spatial environmental variation, and successional trajectories of the flora. In addition, they exhibit context-dependent (i.e. legacy effects) responses that are scale-dependent. The Puerto Rican biota has evolved in a disturbance-mediated system. This historical exposure to repeated, severe hurricane-induced disturbances has imbued the biota with high resistance and resilience to the current disturbance regime, resulting in an ability to persist or thrive under current environmental conditions. Nonetheless, these ecosystems may yet be threatened by worsening direct and indirect effects of climate change. In particular, more frequent and severe hurricanes may prevent the establishment of closed-canopy forests, negatively impacting populations and communities that rely on these habitats.

opencc-zeroDec 2022View details →

On the fast track: Hybrids adapt more rapidly than parental populations in a novel environment

Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time, climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher's Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.

A big data–model integration approach for predicting epizootics and population recovery in a keystone species

Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex non-linear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a non-parametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001–2020 from eight USDA Forest Service National Grasslands across the range of BTPD in central North America. We then modeled extinctions due to plague and colony recovery of BTPD in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summer/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally > 0.80). Thus, these spatially-explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data–model integration approach provides a general framework for spatially-explicit forecasting of disease-induced population fluctuations, for use in natural resource management decision-making.

Genomic diversity and differentiation between island and mainland populations of White‐tailed Eagles (Haliaeetus albicilla)

Using whole genome shotgun sequences from 92 white-tailed eagles (Haliaeetus albicilla) sampled from Greenland, Iceland, Norway, Denmark, Estonia, and Turkey between 1885–1950 and after 1990, we investigate the genomic variation within countries over time, and between countries. Clear signatures of ancient biogeographic substructure across Europe and the North‐East Atlantic are observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110‐115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

The accurate delimitation of species boundaries in non-bilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondria]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi colour morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.

Divergent selection on behavioural and chemical traits between reproductively isolated populations of Drosophila melanogaster

Speciation is driven by traits that can act to prevent mating between nascent lineages, including male courtship and female preference for male traits. Mating barriers involving these traits evolve quickly because there is strong selection on males and females to maximize reproductive success, and the tight co-evolution of mating interactions can lead to rapid diversification of sexual behavior. Populations of D. melanogaster show strong asymmetrical reproductive isolation that is correlated with geographic origin. Using strains that capture natural variation in mating traits, we ask two key questions: which specific male traits are females selecting, and are these traits under divergent sexual selection? These questions have proven extremely challenging to answer, because even in closely related lineages males often differ in multiple traits related to mating behavior. We address these questions by estimating selection gradients for male courtship and cuticular hydrocarbons for two different female genotypes. We identify specific behaviors and particular cuticular hydrocarbons that are under divergent sexual selection and could potentially contribute to premating reproductive isolation. Additionally, we report that a subset of these traits are plastic; males adjust these traits based on the identity of the female genotype they interact with. These results suggest that even when male courtship is not fixed between lineages, ongoing selection can act on traits that are important for reproductive isolation.

Data for: Perishing rich, expanding poor: Demography and population genetic patterns in two congeneric butterflies

In human-altered landscapes, specialist butterflies typically form spatially restricted populations, genetically differentiated due to dispersal restrictions. Generalists, in contrast, display minimum differentiation but high genetic diversity. While local-level actions suffice to conserve specialists and landscape-level actions are necessary for generalists, minimum information exists regarding conservation of species with intermediate features. We targeted two congeneric butterflies, the recently re-expanding Argynnis adippe and the strongly declining A. niobe, co-occurring in the pastoral landscape of the Carpathian Mountains, Czech Republic. We integrated species distribution models, mark-recapture, and microsatellite analysis to compare their habitat requirements, adult demography, dispersal, and genetic patterns, and expanded the genetic analysis across the Carpathian Arc and beyond to delimit spatial conservation units. In two mountain valleys, both species formed interconnected populations numbering thousands of individuals. Mobility patterns suggested the populations' interconnection across the Czech Carpathians. Genetic diversity was extremely poor in the non-threatened A. adippe and moderate in the declining A. niobe. No population differentiation was detected within the Czech Carpathians (ca 1500 km2). Low genetic diversity and no differentiation was preserved in A. adippe across East Central Europe, whereas in A. niobe, populations from Serbia were differentiated from the Carpathian Arc + Alps. The high adult mobility linked to low differentiation probably reflect the distribution of larval resources, historically widespread but sparse and currently declining for A. niobe (grazing-disturbed grounds), while currently increasing for A. adippe (abandonment scrub, disturbed woodlands). Units as large as entire mountain systems define population boundaries, and hence conservation management units, for both species.

Population cytogenetics of the spiny-tailed goanna

Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting geneflow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at geneflow within and between populations with rearrangements. We found that geneflow was present between individuals with chromosome rearrangements within populations, but there was no geneflow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.

Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals

Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of the latter two revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-western Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples for calibration of the molecular clock. We found that across the three species, divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat to the interglacial environments. In European narrow-headed voles, we identified multiple time-structured mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Different waves of postglacial recolonisation and genomic structure of bank vole population in NE Poland

Previous studies indicated that in some species phylogeographic patterns obtained in analyses of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check if there was any discordance between mitochondrial and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in analyses of other genetic markers and functional genes. However, genome-wide SNP analyses revealed a more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as previously recognised in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for an insufficient amount of time to develop significant genetic differentiation.

openDec 2022View details →

Data from: Population recovery and occurrence of the endemic Rhine sculpin (Cottus rhenanus)

Two datasets belonging to the paper "Population recovery and occurrence of the endemic Rhine sculpin (Cottus rhenanus)" published in Knowledge and Management of Aquatic Ecosystems, are provided here. Since little was known about the occurrence, densities and habitat use of C. rhenanus, this study was conducted. The study area was located in the River Geul and tributaries, in the south of the Netherlands. The first dataset "WFD 2005-2010-2015 fish data.csv" contains data of fish in transects sampled as part of ecological status assessments of water systems according to the EU Water Framework Directive. Average 300-metre transects in upstream direction in one run using handheld backpack electrofishing equipment. The second dataset "Habitat characterization Cottus rhenanus 2014.csv" contains data of the Rhine sculpin (and other encountered fish species) in relation to its habitat. The data were collected in the same way as described above. In addition, we estimated the relative abundance of each sediment type (bed substratum) per transect, which yielded the ordinal categories: 0%, <5%, 5-10%, 11-25%, 26-50%, 51-75%, and 76-100%. Distinguished sediment types were silt (mud/sludge), sand, fine granule (0.1-20 mm), pebble (21-65 mm), cobble (66-200 mm), and boulder (>200 mm). Furthermore, we estimated the percentage area of large structures (e.g., woody debris) and riffles. Finally, we measured stream width (m) and depth (cm). This was done by recording width with a tape measure and depth with a measuring rod at five (beginning, middle, end and two representatives in between) locations in a transect. The mean values were recorded as stream width and depth. The included coordinates refer to the start and end of a transect. The coordinate system used here concerns Amersfoort RD (EPSG: 28992).  Abstract The Rhine sculpin (Cottus rhenanus) is a benthic rheophilic fish species that is endemic to tributaries of the rivers Rhine and Meuse in North-western Europe. Little is known about its occurrence and individuals density in relation to habitat characteristics. A core population of C. rhenanus occurs in the River Geul in the Netherlands. Since the late 19th century, this river was heavily polluted by communal and industrial wastewater, causing a strong population decline. As the core population of C. rhenanus is recovering, the status, distribution, and habitat use should be studied to facilitate recovery in other locations. Cottus rhenanus density of individuals significantly increased over the period 2005-2015 and it became one of the most abundant fish species in assemblages. Negative relationships were observed between C. rhenanus densities and a high abundance of boulders (> 200 mm), large structures such as woody debris, and water depth. The population increase and recolonization of C. rhenanus coincided with water quality improvement, which suggests that this fish species can be used to assess small streams ecosystem integrity. The recent range expansion of the Ponto-Caspian round goby (Neogobius melanostomus) poses a high risk of negative effects on C. rhenanus populations via food and shelter competition. Further water quality improvement, habitat conservation, and prevention of the spread of invasive gobies could favour C. rhenanus populations within their natural range.

Population genomics and phylogeography of four Australasian waterfowl

Biogeographic barriers can restrict gene flow, but variation in ecological drivers of dispersal influences the effectiveness of these barriers among different species. Detailed information about the genetic connectivity and movement of waterfowl across biogeographic barriers in northern Australia and Papua New Guinea is limited. We compared genetic connectivity for four species of Australasian waterfowl that vary in their capacity and predisposition for dispersal: Radjah Shelduck (Tadorna radjah), Wandering Whistling-Duck (Dendrocygna arcuata), Green Pygmy-Goose (Nettapus pulchellus), and Pacific Black Duck (Anas superciliosa). We obtained >2,700 loci from double-digest restriction-associated DNA sequencing for 15 to 40 individuals per species and found idiosyncratic patterns of population structure among the four species. The mostly sedentary Radjah Shelduck exhibited clear genetic differences between New Guinea and Australia as well as among locations within Australia. In contrast, the presumed sedentary Green Pygmy-Goose did not show obvious structure. Likewise, populations of the more dispersive Wandering Whistling Duck and Pacific Black Duck were unstructured and genetically indistinguishable between southern New Guinea and northern Australia. Our data suggest some Australo-Papuan biogeographical barriers are insufficient to impede gene flow in waterfowl species capable of dispersing great distances. In sedentary species like the Radjah Shelduck, these barriers, perhaps coupled with its ecology and natural history, restrict gene flow. Our findings bring new insight into the population ecology of Australo-Papuan waterfowl.

Code for the population genetic models of the evolution of preference strength

Sexual selection has a rich history of mathematical models that consider why preferences favor one trait phenotype over another (for population genetic models) or what specific trait value is preferred (for quantitative genetic models). Less common is exploration of the evolution of choosiness or preference strength: that is, by how much a trait is preferred. We examine both population and quantitative genetic models of the evolution of preferences, specifically developing "baseline models" of the evolution of preference strength during the Fisher process. Using a population genetic approach based on the classic model of Kirkpatrick (1982), we find selection for stronger and stronger preferences when trait variation is maintained by mutation. However, this force is quite weak and likely to be swamped by drift in moderately-sized populations. In a quantitative genetic model based on Lande (1981), unimodal preferences will generally not evolve to be increasingly strong without bounds when male traits are under stabilizing viability selection, but evolve to extreme values when viability selection is directional. Our results highlight that different shapes of fitness and preference functions lead to qualitatively different trajectories for preference strength evolution ranging from no evolution to extreme evolution of preference strength.

Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction affected Ne. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.

opencc-by-4.0Feb 2023View details →

Differences in volcanic risk perception among Goma's population before the Nyiragongo eruption of May 2021, Virunga volcanic province (DR Congo)

A short presentation of a study published focussing on the Differences in volcanic risk perception among Goma’s population before the Nyiragongo eruption of May 2021, Virunga volcanic province (DR Congo).