Find research datasets worth reusing

opencc-zeroOct 2020View details →

Data from: Ecological and evolutionary responses of an arctic plant to variation in microclimate and soil

The arctic and alpine regions are predicted to experience some of the highest rates of climate change, and the arctic vegetation is expected to be especially sensitive to such changes. Understanding the ecological and evolutionary responses of arctic plant species to changes in climate is therefore a key objective. Geothermal areas, where natural temperature gradients occur over small spatial scales, and without many of the confounding environmental factors present in latitudinal and other gradient studies, provide a natural experimental setting in which to examine the response of arctic-alpine plants to increasing temperatures. To test the ecological and evolutionary response of the circumpolar alpine bistort (Persicaria vivipara) to temperature, we collected plant material and soil from areas with low, intermediate, and high soil temperatures and grew them at three different temperatures in a threefactorial growth chamber experiment. At higher experimental soil temperatures, sprouting was earlier, and plants had more leaves. Sprouting was earlier in soil originating from intermediate temperature and plants had more leaves when grown in soil originating from low temperatures. We did not find evidence of local adaptation or genetic variation in reaction norms among plants originating from areas with low, intermediate, and high soil temperature. Our findings suggest that the alpine bistort has a strong plastic response to warming, but that differences in soil temperature have not resulted in genetic differentiation. The lack of an observed evolutionary response may, for example, be due to the absence of temperature-mediated selection on P. vivipara, the low rate of sexual recombination, or high levels of gene flow balancing differences in selection. When placed within the context of other studies, we conclude that arctic-alpine plant species often show strong plastic responses to spring warming, while evidence of evolutionary responses varies among species.

opencc-zeroDec 2021View details →

Mountain's ecological and evolutionary variables

Aim. High levels of species richness in mountains are associated with their hypothetical roles as cradles and/or museums of diversity but the generality of these roles remains unknown. To fill this gap, we tested these two hypotheses at a global scale and assessed the direct and indirect effects of abiotic regional features on the variation of montane amphibian richness worldwide. Location. Global Time period: Last 300 million years Major taxa studied. Amphibians Methods. Using an amphibian phylogeny containing 7238 species, along with species distribution and climatic data, we estimated species richness, speciation rates, evolutionary time, terrain roughness, area, and climatic stability for 514 of the world's mountain ranges. Then, we evaluated the direct and indirect effects of these variables on richness patterns across these mountains using structural equation models. Results. We found that most diverse mountain ranges for amphibians are concentrated in the Neotropics, but the fastest speciation rates are not restricted to this region. Instead, we found that evolutionary time, area and climatic stability better explained the global patterns of amphibian diversity in mountains. Species richness is higher in mountain regions with large and climatically stable areas, where early derived lineages originated/established and accumulated through time. Main conclusions. Mountains host and invaluable biodiversity shaped through deep time. Differences in speciation rates do not play a major role in explaining amphibian species richness across mountains. Instead, mountains experiencing milder historical climatic oscillations and having greater available areas for species persistence likely faced lower extinction rates leading to an increased accumulation of amphibian species through time. This condition highlights the importance of mountains as museums of deep evolutionary legacies and speciose biotas

Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli

Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.

opencc-zeroDec 2014View details →

Data from: Tackling extremes: challenges for ecological and evolutionary research on extreme climatic events

1. Extreme climatic events (ECEs) are predicted to become more frequent as the climate changes. A rapidly increasing number of studies - though few on animals - suggest that the biological consequences of ECEs can be severe. 2. However, ecological research on the impacts of extreme climatic events (ECEs) has been limited by a lack of cohesiveness and structure. ECEs are often poorly defined and have often been confusingly equated with climatic variability, making comparison between studies difficult. Additionally, a focus on short-term studies has provided us with little information on the long-term implications of ECEs, and the descriptive and anecdotal nature of many studies has meant it is still unclear what the key research questions are. 3. Synthesizing the current state of work is essential to identify ways to make progress. We conduct a synthesis of the literature and discuss conceptual and practical challenges faced by research on ECEs. 4. We consider three steps to advance research. First, we discuss the importance of choosing an ECE definition and identify the pros and cons of 'climatological' and 'biological' definitions of ECEs. Second, we advocate research beyond short-term descriptive studies to address questions concerning the long-term implications of ECEs, focussing on selective pressures and phenotypically plastic responses and how they might differ from responses to a changing climatic mean. Finally, we encourage a greater focus on multi-event studies that help us understand the implications of changing patterns of ECEs, through the combined use of modelling, experimental and observational field studies. 5. This paper aims to open a discussion on the definitions, questions and methods currently used to study ECEs, which will lead to a more cohesive approach to future ECE research.

opencc-zeroDec 2014View details →

Data from: Avian malaria: a new lease of life for an old experimental model to study the evolutionary ecology of Plasmodium

Avian malaria has historically played an important role as a model in the study of human malaria, being a stimulus for the development of medical parasitology. Avian malaria has recently come back to the research scene as a unique animal model to understand the ecology and evolution of the disease, both in the field and in the laboratory. Avian malaria is highly prevalent in birds and mosquitoes around the world and is amenable to laboratory experimentation at each stage of the parasite's life cycle. Here, we take stock of 5 years of experimental laboratory research carried out using Plasmodium relictum SGS1, the most prevalent avian malaria lineage in Europe, and its natural vector, the mosquito Culex pipiens. For this purpose, we compile and analyse data obtained in our laboratory in 14 different experiments. We provide statistical relationships between different infection-related parameters, including parasitaemia, gametocytaemia, host morbidity (anaemia) and transmission rates to mosquitoes. This analysis provides a wide-ranging picture of the within-host and between-host parameters that may bear on malaria transmission and epidemiology.

Data from: Evolutionary ecology of Early Paleocene planktonic foraminifera: size, depth habitat and symbiosis

The carbon stable isotope (δ13C) composition of the calcitic tests of planktonic foraminifera has an important role as a geochemical tracer of ocean carbon system changes associated with the Cretaceous/Paleogene (K/Pg) mass extinction event and its aftermath. Questions remain, however, about the extent of δ13C isotopic disequilibrium effects and the impact of depth habitat evolution on test calcite δ13C among rapidly evolving Paleocene species, and the influence this has on reconstructed surface-to-deep ocean dissolved inorganic carbon (DIC) gradients. A synthesis of new and existing multispecies data, on the relationship between δ13C and δ18O and test size, sheds light on these issues. Results suggest that early Paleocene species quickly radiated into a range of depths habitats in a thermally stratified water column. Negative δ18O gradients with increasing test size in some species of Praemurica suggest either ontogenetic or ecotypic dependence on calcification temperature that may reflect depth/light controlled variability in symbiont photosynthetic activity. The pattern of positive δ13C test-size correlations allows us to (1) identify metabolic disequilibrium δ13C effects in small foraminifera tests, as occur in the immediate aftermath of the K/Pg event, (2) constrain the timing of evolution of foraminiferal photosymbiosis to 63.5 Ma, ∼0.9 Myr earlier than previously suggested, and (3) identify the apparent loss of symbiosis in a late-ranging morphotype of Praemurica. These findings have implications for interpreting δ13C DIC gradients at a resolution appropriate for incoming highly resolved K/Pg core records.

opencc-zeroDec 2016View details →

Data from: Evolutionary ecology of beta-lactam gene clusters in animals

Beta-lactam biosynthesis was thought to occur only in fungi and bacteria, but we recently reported the presence of isopenicillin N synthase in a soil-dwelling animal, Folsomia candida. However, it has remained unclear whether this gene is part of a larger beta-lactam biosynthesis pathway and how widespread the occurrence of penicillin biosynthesis is among animals. Here, we analyzed the distribution of beta-lactam biosynthesis genes throughout the animal kingdom and identified a beta-lactam gene cluster in the genome of F. candida (Collembola), consisting of isopenicillin N synthase (IPNS), δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS), and two cephamycin C genes (cmcI and cmcJ) on a genomic scaffold of 0.76 Mb. All genes are transcriptionally active and are inducible by stress (heat shock). A beta-lactam compound was detected in vivo using an ELISA beta-lactam assay. The gene cluster also contains an ABC transporter which is co-regulated with IPNS and ACVS after heat shock. Furthermore, we show that different combinations of beta-lactam biosynthesis genes are present in over 60% of springtail families but they are absent from genome- and transcript libraries of other animals including close relatives of springtails (Protura, Diplura, and insects). The presence of beta-lactam genes is strongly correlated with an eudaphic (soil-living) lifestyle. Beta-lactam genes IPNS and ACVS each form a phylogenetic clade in between bacteria and fungi, while cmcI and cmcJ genes cluster within bacteria. This suggests a single horizontal gene transfer event most probably from a bacterial host, followed by differential loss in more recently evolving species.

opencc-zeroDec 2015View details →

Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.

opencc-zeroDec 2017View details →

Data from: Ecology and macroevolution – evolutionary niche monopolisation as a mechanisms of niche conservatism

Explaining macroevolution from microevolution is a key issue in contemporary evolutionary theory. A recurrent macroevolutionary pattern is that some niche‐related traits consistently evolve slower than others, so called niche conservatism. Despite a growing amount of data, the underlying evolutionary processes are not fully understood. I here analyse adaptive radiations in an individual‐based eco‐evolutionary model. I find a coevolutionary mechanism – evolutionary niche monopolisation – as a possibly important generator of niche conservatism. A single lineage of a radiating clade can monopolise, and later diversify within, a substantial part of the available niche space – much larger than what can be explained by limiting similarity. This leads to niche conservatism, since no species evolves into or out of the monopolised region. The region can in this sense also be described as an adaptive zone. The model indicates that evolutionary niche monopolisation is operative in a large part of parameter space, underlining its possible importance. The mechanism is driven by competitive interactions and differences in niche widths in alternative niche dimensions. I discuss plausible examples of evolutionary niche monopolisation in well‐studied natural systems.

opencc-zeroOct 2019View details →

Supplementary data for: Mosquito phytophagy – sources exploited, ecological function, and evolutionary transition to haematophagy

This dataset consists of two files: Floral visitation records of mosquitoes Plant sugar, primarily in the form of floral nectar, is the ubiquitous basic food of adult mosquitoes. However, records of mosquito floral visitation are not usually the focus of research publications and, as such, are often reported as secondary parts of larger studies and are scattered throughout more than a century of scientific literature. Here we provide a summary of more than 500 recorded literature and field instances of floral and extra-floral nectary visitation by mosquitoes, including the plant and mosquito species involved as well as known pollination records. file name: Summary_of_Field_Mosquito_Floral_Visitation_Instances.xlsx Summary of floral semiochemical blends that are attractive to mosquitoes Floral nectar is the primary food source of adult mosquitoes and mosquitoes, along with many other pollinators, use floral semiochemicals to locate this resource. Here we provide a summary of floral semiochemical blends attractive to mosquitoes that have been reported in the literature. The mosquito species involved have also been listed. file name: Summary_of_Floral_Semiochemical_Blends_Attractive_to_Mosquitoes.xlsx

opencc-zeroDec 2014View details →

Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.

Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research

Despite much discussion of the importance of quantifying and reporting genotyping error in molecular studies, it is still not standard practice in the literature. This is particularly a concern for amplified fragment length polymorphism (AFLP) studies, where differences in laboratory, peak-calling and locus-selection protocols can generate data sets varying widely in genotyping error rate, the number of loci used and potentially estimates of genetic diversity or differentiation. In our experience, papers rarely provide adequate information on AFLP reproducibility, making meaningful comparisons among studies difficult. To quantify the extent of this problem, we reviewed the current molecular ecology literature (470 recent AFLP articles) to determine the proportion of studies that report an error rate and follow established guidelines for assessing error. Fifty-four per cent of recent articles do not report any assessment of data set reproducibility. Of those studies that do claim to have assessed reproducibility, the majority (~90%) either do not report a specific error rate or do not provide sufficient details to allow the reader to judge whether error was assessed correctly. Even of the papers that do report an error rate and provide details, many (≥23%) do not follow recommended standards for quantifying error. These issues also exist for other marker types such as microsatellites, and next-generation sequencing techniques, particularly those which use restriction enzymes for fragment generation. Therefore, we urge all researchers conducting genotyping studies to estimate and more transparently report genotyping error using existing guidelines and encourage journals to enforce stricter standards for the publication of genotyping studies.

opencc-zeroDec 2015View details →

Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance

A comprehensive monitoring strategy is vital for tracking the spread of mosquito-borne Japanese encephalitis virus (JEV), the leading cause of viral encephalitis in Asia. Virus detection consists of passive surveillance of primarily humans and swine, and/or active surveillance in mosquitoes, which may be a valuable proxy in providing insights into ecological processes underlying the spread and persistence of JEV. However, it has not been well characterized whether passive surveillance alone can capture the circulating genetic diversity to make reasonable inferences. Here, we develop phylogenetic models to infer JEV host changes, spatial diffusion patterns, and evolutionary dynamics from data collected through active and passive surveillance. We evaluate the feasibility of using JEV sequence data collected from mosquitoes to estimate the migration histories of genotypes GI and GIII. We show that divergence times estimated from this dataset were comparable to estimates from all available data. Increasing the amount of data collected from active surveillance improved time of most recent common ancestor estimates and reduced uncertainty. Phylogenetic estimates using all available data and only mosquito data from active surveillance produced similar results, showing that GI epidemics were widespread and diffused significantly faster between regions than GIII. In contrast, GIII outbreaks were highly structured and unlinked suggesting localized, unsampled infectious sources. Our results show that active surveillance of mosquitoes can sufficiently capture circulating genetic diversity of JEV to confidently estimate spatial and evolutionary patterns. While surveillance of other hosts could contribute to more detailed disease tracking and evaluation, comprehensive JEV surveillance programs should include systematic surveillance in mosquitoes to infer the most complete patterns for epidemiology, and risk assessment.

Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)

Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown pomacentrid diversification has not slowed through time as expected under a scenario of a single adaptive radiation resulting from an early burst of diversification. Evolutionary modeling of trophic traits similarly rejected the hypothesis of early among-lineage partitioning of ecologically important phenotypic diversity. Instead, damselfishes are shown to have experienced iterative convergent radiations wherein subclades radiate across similar trophic strategies (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies. Regionalization of coral reefs, competition, and functional constraints may have fueled iterative ecological radiation and convergent evolution of damselfishes. Through the Pomacentridae, we illustrate that radiations may be strongly structured by the nature of the constraints on diversification.

opencc-zeroDec 2017View details →

Data from: Eco-evolutionary dynamics in metacommunities: ecological inheritance, helping within species, and harming between species

Understanding selection on intra- and inter-specific interactions that take place in dispersal-limited communities is a challenge for ecology and evolutionary biology. The problem is that local demographic stochasticity generates eco-evolutionary dynamics that are generally too complicated to make tractable analytical investigations. Here, we circumvent this problem by approximating the selection gradient on a quantitative trait that influences local community dynamics, assuming that such dynamics are deterministic with a stable fixed point. We nonetheless incorporate unavoidable kin selection effects arising from demographic stochasticity. Our approximation reveals that selection depends on how an individual expressing a trait-change influences: (1) its own fitness and the fitness of its current relatives; and (2) the fitness of its downstream relatives through modifications of local ecological conditions (i.e., through ecological inheritance). Mathematically, the effects of ecological inheritance on selection are captured by dispersal-limited versions of press-perturbations of community ecology. We use our approximation to investigate the evolution of helping within- and harming between-species when these behaviours influence demography. We find that altruistic helping evolves more readily when intra-specific competition is for material resources rather than for space because in this case, the costs of kin competition tend to paid by downstream relatives. Similarly, altruistic harming between species evolves when it alleviates downstream relatives from inter-specific competition. Beyond these examples, our approximation can help better understand the influence of ecological inheritance on a variety of eco-evolutionary dynamics in metacommunities, from consumer-resource and predator-prey coevolution to selection on mating systems with demographic feedbacks.

opencc-zeroNov 2021View details →

Supplementary material from "Evolutionary dynamics of sustainability ideas in China: inferences from ecological and economic concepts usage in People's Daily"

Previous cultural evolutionary analyses have exploited the use of neutral models, or random copying models, analogous to neutral genetic drift, as null models to distinguish the unbiased copying and biased transmission of neutral cultural traits, but the dynamics and underlying mechanism of non-neutral cultural traits have not yet been explored. Adopting an ecological perspective, we define ecological and economic concepts as non-neutral cultural traits constitute a complex ecosystem of meaning representing sustainability ideas. We analyse the frequency distribution, turnover and innovation rates of nearly 4000 concepts appearing in People's Daily from 1946 to 2015. The results reveal that, ecological concepts show stronger tendency towards random copying than economic concepts. The popular ecological and economic concepts may experience conformist bias and anti-conformist bias respectively. Semantic and pragmatic differences of popular concepts affect the variability which indicate stronger cultural drift in the ontological domain. The frequency change in popular concepts also suggests positive selection due to political strategy and governmental policy.

opencc-by-4.0Nov 2017View details →

Figure 2 from: Wildish DJ (2017) Evolutionary ecology of driftwood talitrids: a review. Zoosystematics and Evolution 93(2): 353-361. https://doi.org/10.3897/zse.93.12582

Figure 2 - Hypothetical pathway of land colonization by talitrids. Oval boxes are generalists, oblong boxes are specialists. Dashed arrows are hypothetical and those with solid arrows indicate some genetic evidence.

opencc-by-4.0Nov 2017View details →

Figure 1 from: Wildish DJ (2017) Evolutionary ecology of driftwood talitrids: a review. Zoosystematics and Evolution 93(2): 353-361. https://doi.org/10.3897/zse.93.12582

Figure 1 - Driftwood decay succession in the marine/estuarine environment. Primary colonizers include cellulolytic fungi and bacteria, gribbles and chelurid amphipods. Secondary colonizers include talitrids, isopods, chilopods, insect larvae, ants, termites.

opencc-by-4.0Feb 2018View details →

Figure 1 from: Sánchez-Fernández D, Rizzo V, Bourdeau C, Cieslak A, Comas J, Faille A, Fresneda J, Lleopart E, Millán A, Montes A, Pallares S, Ribera I (2018) The deep subterranean environment as a model system in ecological, biogeographical and evolutionary research. Subterranean Biology 25: 1-7. https://doi.org/10.3897/subtbiol.25.23530

Figure 1 Relationship between the temperature inside the cave and the surface (Mean Annual Temperature (°C) of each pixel (0.08° cells).