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opencc-zeroJul 2020View details →

Data from: Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations

Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilising populations has led to the hypothesis that species with this mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilising species. To test this hypothesis we simulated populations under stabilizing selection subjected to an environmental change. We demonstrate that, when the mutation rate is high (but realistic), selfing populations are better able to store genetic variance than outcrossing populations through genetic associations, notably due to the reduced effective recombination rate associated with predominant selfing. Following an environmental shift, this diversity can be partially remobilized, which increases the additive variance and adaptive potential of predominantly (but not completely) selfing populations. In such conditions, despite initially lower observed genetic variance, selfing populations adapt as readily as outcrossing ones within a few generations. For low mutation rates, purifying selection impedes the storage of diversity through genetic associations, in which case, as previously predicted, the lower genetic variance of selfing populations results in lower adaptability compared to their outcrossing counterparts. The population size and the mutation rate are the main parameters to consider, as they are the best predictors of the amount of stored diversity in selfing populations. Our results and their impact on our knowledge of adaptation under high selfing rates are discussed.

opencc-by-4.0Dec 2019View details →

Transpiration from subarctic deciduous woodlands: environmental controls and contribution to ecosystem evapotranspiration

Data from the paper:  Sabater, AM, Ward, HC, Hill, TC, et al. Transpiration from subarctic deciduous woodlands: Environmental controls and contribution to ecosystem evapotranspiration. Ecohydrology. 2020; 13:e2190.  https://doi.org/10.1002/eco.2190

opencc-zeroApr 2020View details →

Contribution of genetic versus plastic responses to adaptive patterns in a widespread butterfly along a latitudinal cline

Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. This issue is of special interest in the current era of rapidly changing climatic conditions. Here, we investigate clinal variation and plastic responses in life history, morphology, and physiology in the butterfly Pieris napi along a pan-European gradient by exposing butterflies raised in captivity to different temperatures. We found clinal variation in body size, growth rates and concomitant development time, wing aspect ratio, wing melanisation, and heat tolerance. Individuals from warmer environments were more heat-tolerant, had less melanised wings and a shorter development but still they were larger than individuals from cooler environments. These findings suggest selection for rapid growth in the warmth and for wing melanisation in the cold, and thus fine-tuned genetic adaptation to local climates. Irrespective of the origin of butterflies, the effects of higher developmental temperature were largely as expected, speeding up development, reducing body size, potential metabolic activity, and wing melanisation, while increasing heat tolerance. At least in part, these patterns likely reflect adaptive phenotypic plasticity. In summary, our study revealed pronounced plastic and genetic responses, which may indicate high adaptive capacities in our study organism. Whether this may help such species though to deal with current climate change needs further investigation, as clinal patterns have typically evolved over long periods.

opencc-by-4.0Aug 2020View details →

Contribution submitted by Antonella Garzelli for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

The European Food Safety Authority (EFSA) carried out a public consultation, from 27 February 2020 until 15 April 2020, to receive input from interested parties – organizations or private citizens - on a draft scientific opinion on the risks for animal and human health related to the presence of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products. The draft scientific opinion was prepared by the EFSA Panel on Contaminants in the Food Chain (CONTAM Panel), supported by the Working Group on Glycoalkaloids in feed and food. EFSA used the EU survey tool to receive comments on the draft scientific opinion, and the way these comments were considered for the finalisation of the opinion is described in the Technical Report available at: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2F10.2903%2Fsp.efsa.2020.EN-1905&data=02%7C01%7C%7C242adcee21744b01890408d82cba24b4%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637308525272584775&sdata=97Tc3%2FrT1SXtzIN14PCCvUv0OYyaiSO1H76iezwqvnQ%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2020.EN-1905</a>. Some contributors also attached files to the comments submitted via the EU survey tool. For transparency reasons these files are made available in the public domain as Zenodo uploads.

opencc-by-4.0Aug 2020View details →

Contribution submitted by STARCH EU for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

opencc-by-4.0Aug 2020View details →

Contribution submitted by Matthew Walker for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

opencc-zeroAug 2020View details →

Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps, and geological faults. The morphological (color pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses, and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within rivers systems and, consequently, the dynamics of gene flow between freshwater lineages/species.

opencc-zeroAug 2020View details →

Data from: Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor

Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite of efficient seed dispersal.

opencc-zeroAug 2020View details →

A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: two new species, reinstatement of Cyathea bonii, and their phylogenetic positions

Gymnosphaera represents a minor lineage within the scaly tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution area of Gymnosphaera. However, the species diversity of Gymnosphaera is currently incompletely known in mainland Asia due to lacking critical revision. Here we present new findings of species diversity and their relationships of mainland Asian Gymnosphaera based on field surveys, the examination of herbarium collections, and phylogenetic analyses of sequences of multiple chloroplast and nuclear regions. Two new species, G. saxicola from southwestern Yunnan and G. bachmaensis from central Vietnam, are established. Traditionally recognized G. podophylla is revealed to be a complex, from which G. bonii is reinstated as a distinct species. Our phylogenetic analyses identified four clades within Gymnosphaera in mainland Asia: G. denticulata clade, G. gigantea clade, G. podophylla clade, and G. salletii clade. The new species G. saxicola, which is special for its saxicolous habitat, was resolved as sister to G. austroyunnanensis in the G. salletii clade. The newly discovered G. bachmaensis, which is characterized specially by the spathulate frond, was positioned in the G. podophylla clade, being sister to G. bonii. The mountainous region from south-central Vietnam northwards to western Yunnan is a diverse center of Gymnosphaera and more species of this group are probably to be discovered there.

opencc-zeroSep 2020View details →

Simulated dataset from 'Quantifying the causal pathways contributing to natural selection'

This dataset (Antechinus.csv) relates to the worked example in the appendix of the paper: Henshaw JM, Morrissey MB, Jones AG (2020). Quantifying the causal pathways contributing to natural selection. Evolution (doi:10.1111/evo.14091) The worked example concerns a hypothetical study of female antechinus. These are small carnivorous marsupials that use torpor to reduce energy consumption from late summer to early winter. They reproduce once per year in late winter or early spring, following which most individuals die. We suppose that researchers tracked female antechinus from mid summer to the end of the breeding season. They recorded the animals' body size, their date of last torpor, whether they survived to breed, their number of mates, and their fecundity. I simulated the dataset resulting from this hypothetical study in Wolfram Mathematica (see Methods below). In the above paper, we analyse the causal structure of natural selection in this dataset (the R code for the causal analysis is included here as 'AntechinusAnalysis.R'). The variables in the dataset are: body size in unspecified units (BodySize); the date of last torpor (TorporDate), standardized as the number of days before/after an unspecificed reference date; whether the individual survived to breed, given as a binary variable (Survival); an individual's number of mates (Mates); and her fecundity (Fecundity).

Figs 65-69 in Contribution to the Palaearctic species of Mesochorus G (Hymenoptera, Ichneumonidae, Mesochorinae): 1. The M. fulvus-group

Figs 65-69: Mesochorus caucasicus nov.sp. ♀ (holotypus): (65) face, (66) propodeum, (67) hind claw, (68) head, (69) ovipositor sheaths.

Figs 56-59 in Contribution to the Palaearctic species of Mesochorus G (Hymenoptera, Ichneumonidae, Mesochorinae): 1. The M. fulvus-group

Figs 56-59: Mesochorus lapponator nov.sp. ♀ (holotypus): (56) face, (57) head, (58) ovipositor sheaths, (59) hind claw.

Figs 25-28 in Contribution to the Palaearctic species of Mesochorus G (Hymenoptera, Ichneumonidae, Mesochorinae): 1. The M. fulvus-group

Figs 25-28: Mesochorus fulvoides nov.sp. ♀ (holotypus): (25) face; (26) head, (27) hind claw, (28) ovipositor sheaths.

Figs 1-4 in Contribution to the Palaearctic species of Mesochorus G (Hymenoptera, Ichneumonidae, Mesochorinae): 1. The M. fulvus-group

Figs 1-4: Mesochorus agnellonis SCHWENKE ♀ (holotypus): (1) face, (2) propodeum, (3) distal fore tarsomere, (4) ovipositor sheaths.

opencc-zeroSep 2019View details →

Data from: Contributions of bats to the local economy through durian pollination in Sulawesi, Indonesia

Durian is economically important for local livelihoods in Indonesia. Our study investigated the identity of pollinators of semi-wild durian, and subsequently estimated the economic contribution of these pollination services. We conducted pollination exclusion experiments and deployed camera traps at durian trees from October 2017 to January 2018 in an area where the local economy depends on durian production in West Sulawesi, Indonesia. Durian flowers in the experiment that were accessible to bats had significantly higher fruit set compared to flowers that were completely closed to animal visitors or those that could only be visited by insects, suggesting that bats were the primary durian pollinator. The small, highly nectarivorous cave nectar bat (Eonycteris spelaea) visited more inflorescences (n = 25) and had visits of much longer duration (X ̅ = 116.87 sec/visit) than the two species of flying foxes: Pteropus alecto (n = 7 inflorescences visited,X ̅ = 11.07 sec/visit) and Acerodon celebensis (n = 6 inflorescences visited,X ̅ = 11.60 sec/visit). Visits by large and small bats were influential in differentiating successful durian fruit production from unsuccessful. Using a bioeconomic approach, we conservatively estimate that bat pollination services are valued at ~$117/ha/fruiting season. By demonstrating an ecological link between bats and the local economy, this research provides an urgent message for Southeast Asian governments regarding the need to promote bat conservation in order to increase the production of durian grown under semi-wild conditions.

opencc-zeroSep 2020View details →

Data from: Terrestrial contributions to Afrotropical aquatic food webs: the Congo River case

1. Understanding the degree to which aquatic and terrestrial primary production fuel tropical aquatic food webs remains poorly understood, and quantifying the relative contributions of autochthonous and allochthonous inputs is methodologically challenging. Carbon and nitrogen stable isotope ratios (δ13C, δ15N) can provide valuable insights about contributions of terrestrial resources and trophic position respectively, but this approach has caveats when applied in typical complex natural food webs. 2. Here, we used a combination of C, N, and H (δ2H) stable isotope measurements and Bayesian mixing models to estimate the contribution of terrestrial (allochthonous) and aquatic (autochthonous) inputs to fish and invertebrate communities in the Congo River (and some tributaries). 3. Overall, our results show that we gained power to distinguish sources by using a multiple tracer approach and we were able to discriminate aquatic vs. terrestrial sources (esp. including hydrogen isotopes). Fish δ2H values were clearly correlated with their food preferences and revealed a high level of variation in the degree of allochthony in these tropical aquatic communities. 4. At the community level, it is clear that terrestrial C3 plants are an important source fueling the Congo River food web. However, in order to better constrain source contribution in these complex environments will require more robust constraints on stable isotope values of algal and methane-derived C sources.

opencc-zeroOct 2020View details →

Data from: Spontaneous forest regrowth in South-West Europe: consequences for nature's contributions to people

Context European forests are expanding and becoming denser following the widespread abandonment of farmland and rural areas. Yet, little is known about the goods and services that spontaneous forest regrowth provide to people. Aims We assessed the changes in nature's contributions to people (NCP) from spontaneous forest regrowth, i.e. forest expansion and densification, in South-West Europe. Methods We investigated 65 forest plots in four different landscapes with contrasting ecological and societal contexts. Two landscapes are located in rural areas undergoing human exodus and forest expansion and densification; the other two, in peri-urban areas with intense land use and forest densification but negligible expansion. For each forest plot, we estimated variables related to ten out of the 18 main NCP defined by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). Regulating and material NCP were addressed using variables measured in the field as proxies. Non-material NCP were studied through stakeholder interviews. Results Our results show across the cases that forest expansion and densification is generally associated with greater climate regulation and energy provision. Changes in other NCP, especially in non-material ones, were strongly context-dependent. The social perception of spontaneous forest regrowth was primarily negative in rural areas and more positive in peri-urban landscapes. Conclusion Passive restoration through spontaneous forest expansion and densification can enhance regulating and material NCP, especially when adaptive management is applied. To optimise NCP and to increase the societal awareness of and interest in spontaneous forest regrowth, the effects of this process should be analysed in close coordination with local stakeholders to unveil and quantify the many and complex trade-offs involved in rural or peri-urban social perceptions.

opencc-zeroOct 2020View details →

Recent warming reduces the reproductive advantage of large size and contributes to evolutionary downsizing in nature

Body size is a key functional trait that is predicted to decline under warming. Warming is known to cause size declines via phenotypic plasticity, but evolutionary responses of body size to warming are poorly understood. To test for warming-induced evolutionary responses of body size and growth rates, we used populations of mosquitofish ( Gambusia affinis ) recently established (less than 100 years) from a common source across a strong thermal gradient (19–33°C) created by geothermal springs. Each spring is remarkably stable in temperature and is virtually closed to gene flow from other thermal environments. Field surveys show that with increasing site temperature, body size distributions become smaller and the reproductive advantage of larger body size decreases. After common rearing to reveal recently evolved trait differences, warmer-source populations expressed slowed juvenile growth rates and increased reproductive effort at small sizes. These results are consistent with an adaptive basis of the plastic temperature–size rule, and they suggest that temperature itself can drive the evolution of countergradient variation in growth rates. The rapid evolution of reduced juvenile growth rates and greater reproduction at a small size should contribute to substantial body downsizing in populations, with implications for population dynamics and for ecosystems in a warming world.

opencc-zeroOct 2020View details →

The contribution of the edaphic factor as a driver of recent plant diversification in a Mediterranean biodiversity hotspot

1. The high diversification rates of plant lineages in the Mediterranean Basin hotspot have been linked to a complex interaction of climatic stressors, geographic isolation and soil type, but the question remains as to which of these factors has been the most significant environmental driver of recent speciation. 2. Here, we draw on distributional data for the entire endemic flora of the Iberian Peninsula, together with DNA-based phylogenies and spatial phylogenetic methods, to explore patterns of relative phylogenetic endemism at different spatial resolutions and phylogenetic scales (superclades) and assess how environmental factors contribute to explain these patterns. 3. We found that recent diversification of angiosperms as a whole, and particularly of eudicots, has been boosted by environmental stressors including high values of soil pH and dry-seasonal climatic conditions, while diversification of monocots has not been associated with soil conditions but with high elevation and less seasonal climate. 4. Synthesis. These results provide robust insights into the environmental factors driving recent plant diversification in the Mediterranean Basin, including a role of soil properties that had not been quantified before. The contrasting environmental drivers of diversification in Eudicots and Monocots highlight the importance of analyzing spatial phylogenetic patterns at multiple phylogenetic scales to get a better understanding of the processes that shape biodiversity.