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Data from: Elevated pCO2 affects tissue biomass composition, but not calcification, in a reef coral under two light regimes
Ocean acidification (OA) is predicted to reduce reef coral calcification rates and threaten the long-term growth of coral reefs under climate change. Reduced coral growth at elevated pCO2 may be buffered by sufficiently high irradiances; however, the interactive effects of OA and irradiance on other fundamental aspects of coral physiology, such as the composition and energetics of coral biomass, remain largely unexplored. This study tested the effects of two light treatments (7.5 versus 15.7 mol photons m−2 d−1) at ambient or elevated pCO2 (435 versus 957 µatm) on calcification, photopigment and symbiont densities, biomass reserves (lipids, carbohydrates, proteins), and biomass energy content (kJ) of the reef coral Pocillopora acuta from Kāne'ohe Bay, Hawai'i. While pCO2 and light had no effect on either area- or biomass-normalized calcification, tissue lipids gdw−1 and kJ gdw−1 were reduced 15% and 14% at high pCO2, and carbohydrate content increased 15% under high light. The combination of high light and high pCO2 reduced protein biomass (per unit area) by approximately 20%. Thus, under ecologically relevant irradiances, P. acuta in Kāne'ohe Bay does not exhibit OA-driven reductions in calcification reported for other corals; however, reductions in tissue lipids, energy content and protein biomass suggest OA induced an energetic deficit and compensatory catabolism of tissue biomass. The null effects of OA on calcification at two irradiances support a growing body of work concluding some reef corals may be able to employ compensatory physiological mechanisms that maintain present-day levels of calcification under OA. However, negative effects of OA on P. acuta biomass composition and energy content may impact the long-term performance and scope for growth of this species in a high pCO2 world.
Data from: Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology
The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro-ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga-Sangha Protected Areas, Central African Republic. Results show that geographical range may be an important modulator of the gut microbiomes and metabolomes of these gorilla groups. Distinctions seemed to relate to feeding behaviour, implying energy harvest through increased fruit consumption or fermentation of highly fibrous foods. These observations were supported by differential abundance of metabolites and bacterial taxa associated with the metabolism of cellulose, phenolics, organic acids, simple sugars, lipids and sterols between gorillas occupying different geographical ranges. Additionally, the gut microbiomes of a gorilla group under increased anthropogenic pressure could always be distinguished from that of all other groups. By characterizing the interplay between environment, behaviour, diet and symbiotic gut microbes, we present an alternative perspective on primate ecology and on the forces that shape the gut microbiomes of wild primates from an evolutionary context.
Data from: Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro‐organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
Data from: CO2 alters community composition and response to nutrient enrichment of freshwater phytoplankton
Nutrients can limit the productivity of ecosystems and control the composition of the communities of organisms that inhabit them. Humans are causing atmospheric CO2 concentrations to reach levels higher than those of the past millions of years while at the same time propagating eutrophication through the addition of nutrients to lakes and rivers. We studied the effect of elevated CO2 concentrations, nutrient addition and their interaction in a series of freshwater mesocosm experiments using a factorial design. Our results highlight the important role of CO2 in shaping phytoplankton communities and their response to nutrient addition. We found that CO2 greatly magnified the increase in phytoplankton growth caused by the increased availability of nutrients. Elevated CO2 also caused changes in phytoplankton community composition. As predicted from physiology and laboratory experiments, the taxonomic group that was most limited by current day CO2 concentrations, chlorophytes, increased in relative frequency at elevated CO2. This predictable change in community composition with changes in CO2 is not altered by changes in the availability of other nutrients.
Data from: Landscape composition has limited impact on local genetic structure in mountain clover, Trifolium montanum L.
Semi-dry grasslands in the European Alps have been increasingly fragmented over the last 150 years. Few studies have investigated the implications of landscape configuration for genetic structure and gene flow among remnant habitat patches. Conservation management of semi-dry grassland plants rarely accounts for possible effects of major landscape elements; such as forest patches, as barriers to gene flow and dispersal via seed and pollen, despite their potential importance for biodiversity conservation. Using 1,416 individuals from 61 sampling sites across two valleys in South-Eastern Switzerland and AFLP fingerprints we applied a spatial strip and a circle approach to determine the impact of different landscape elements on genetic differentiation in the semi-dry grassland herb Trifolium montanum (mountain clover). Overall genetic differentiation among sampling sites was low (overall FST = 0.044). Forest area had no effect on gene flow at the landscape scale but area of semi-dry grassland, the potential habitat of T. montanum, road area and altitude influenced genetic differentiation among sampling sites. The observed pattern of genetic differentiation suggests that a future increase in forest area, due to land use abandonment, at least in the short term, are unlikely to directly impact patterns of genetic variation in T. montanum.
Data from: Taxonomic and phylogenetic determinants of functional composition of Bolivian bat assemblages
Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.
Data from: Re-growing a tropical dry forest: functional plant trait composition and community assembly during succession
A longstanding goal of ecology and conservation biology is to understand the environmental and biological controls of forest succession. However, the patterns and mechanisms that guide successional trajectories, especially within tropical forests, remain unclear. We collected leaf functional trait and abiotic data across a 110-year chronosequence within a tropical dry forest in Costa Rica. Focusing on six key leaf functional traits related to resource acquisition and competition, along with measures of forest stand structure, we propose a mechanistic framework to link species composition, community trait distributions, and forest structure. We quantified the community-weighted trait distributions for specific leaf area, leaf dry matter concentration, leaf phosphorus concentration, leaf carbon to nitrogen ratio, and leaf stable isotopic carbon and nitrogen. We assessed several prominent hypotheses for how these functional measures shift in response to changing environmental variables (soil water content, bulk density and pH) across the chronosequence. Increasingly, older forests differed significantly from younger forests in species composition, above ground biomass and shifted trait distributions. Early stages of succession were uniformly characterized by lower values of community-weighted mean specific leaf area, leaf stable nitrogen isotope, and leaf phosphorus concentration. Leaf dry matter concentration and leaf carbon to nitrogen ratio were lower during earlier stages of succession, and each trait reached an optimum during intermediate stages of succession. The leaf carbon isotope ratio was the only trait to decrease linearly with increasing stand age indicating reduced water use efficiency in older forests. However, in contrast to expectations, community-weighted trait variances did not generally change through succession, and when compared to null expectations were lower than expected. The observed directional shift in community-weighted mean trait values is consistent with the 'productivity filtering' hypothesis where a directional shift in water and light availability shifts physiological strategies from 'slow' to 'fast'. In contrast to expectations arising from niche based ecology, none of the community trait distributions were over-dispersed. Instead, patterns of trait dispersion are consistent with the abiotic filtering and/or competitive hierarchy hypotheses.
Data from: Edge-mediated compositional and functional decay of tree assemblages in Amazonian forest islands after 26 years of isolation
1.Islands formed upstream of mega hydroelectric dams are excellent experimental landscapes to assess the impacts of habitat fragmentation on biodiversity. We examined the effects of plot-, patch- and landscape-scale variables on the patterns of floristic diversity across 34 forest islands that had experienced 26 years of isolation since the creation of the 4,437 km2 Balbina Hydroelectric Reservoir of central Brazilian Amazonia. In addition, three undisturbed continuous forest sites in neighbouring mainland areas were also sampled across a comparable elevational gradient. 2.We identified all live trees ≥10 cm DBH at species level within a total of 87 quarter-hectare forest plots and conducted a comprehensive compilation of functional attributes of each tree species. We then examined species-area relationships (SARs) and the additional effects of patch and landscape scale metrics on patterns of tree assemblage heterogeneity, both in terms of taxonomic and functional diversity. 3.Despite a clearly positive SAR, edge-mediated forest disturbance was the single most important driver of species composition and abundance within islands. Our results suggest that non-random floristic transitions within island plots followed a predictable pattern, with different life-history traits either penalizing or rewarding local persistence of different functional groups. Distance to edges mediated the probability of tree mortality induced by windfalls and episodic surface fires, clearly resulting in faster species turnover and unidirectional changes in guild structure within small islands where light-wooded fast-growing pioneers largely replaced heavy-wooded species of the old-growth flora. 3.Synthesis ─ Following a simultaneous 26-year post-isolation history, we disentangle the effects of habitat loss and insularization on tree assemblages within a large set of Amazonian 'true' forest islands, of variable sizes, sharing a uniform open-water matrix. Area effects are expressed via a response to edge effects, with trees in smaller islands being more vulnerable to edge-related surface fires and windthrows. Additionally, forest edge effects can be a powerful driver of non-random floristic transitions across islands within the Balbina archipelago via a process of rapid pioneer proliferation, drastically affecting both the taxonomic and functional composition of insular tree communities. Finally, our results indicate that detrimental effects of forest fragmentation induced by hydroelectric dams are considerably stronger than those of forest patches embedded within a terrestrial vegetation matrix.
Data from: Taxonomic composition and body-mass distribution in the terminal Pleistocene mammalian fauna from the Marmes site, southeastern Washington state, U.S.A.
Mean adult body mass of mammal taxa is a fundamental ecological variable. Variability in the distributions of body masses of a mammal fauna suggest variability in habitat structure. Mammal remains from the Marmes archaeological site in southeastern Washington State date between 13,200 and 10,400 b.p., during the Pleistocene–Holocene transition (PHT). Known environmental history prompts the expectations that the Marmes PHT mammal remains should represent greater species richness and a larger array of body-mass sizes than modern faunas in the Marmes locale and in open shrub-steppe habitats, and lower species richness and a smaller array of body-mass sizes than modern faunas in closed forest habitats; species richness and the array of body-mass sizes should be similar to that for a mixed habitat of cool shrub-steppe with scattered conifers. The Marmes PHT cenogram meets these expectations. Body-mass clumps displayed by the Marmes PHT mammal fauna fall between those of closed forests and open shrub-steppe habitats in terms of clump richness and breadth, and in terms of gap width. Marmes PHT body-mass clumps are very similar to those for the mixed habitat. Cenograms and body-mass clumps confirm conclusions drawn 40 years ago that the Marmes PHT habitat was much like that of today but cooler and with more plant biomass and greater structural diversity than today.
Data from: Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae sensu lato during colonization in the laboratory
The gut microbiota is known to play a role in the mosquito vectors' life history, which is a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared Anopheles gambiae s.l. mosquitoes continuously hatched in water from the field breeding habitats. Pupae and late instars were obtained from the field and reared, and the emerged adults were blood fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F0 (emerging from field-caught pupae and larvae), F5, and F10 were dissected out and genomic DNA were extracted for 16S metagenomic sequencing. The sequences were compared to investigate the diversity, and bacteria compositional differences using ANCOM and correlation clustering methods. Less than 10% of the bacteria families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F10 mosquitoes during lab colonization (Shannon-Weaver; p-value< 0.05), 50% of bacteria genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water. The study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.
Data from: Personality composition is more important than group size in determining collective foraging behaviour in the wild
Describing the factors that shape collective behaviour is central to our understanding of animal societies. Countless studies have demonstrated an effect of group size in the emergence of collective behaviours, but comparatively few have accounted for the composition/diversity of behavioural phenotypes, which is often conflated with group size. Here, we simultaneously examine the effect of personality composition and group size on nest architecture and collective foraging aggressiveness in the social spider Stegodyphus dumicola. We created colonies of two different sizes (10 or 30 individuals) and four compositions of boldness (all bold, all shy, mixed bold and shy, or average individuals) in the field and then measured their collective behaviour. Larger colonies produced bigger capture webs, while colonies containing a higher proportion of bold individuals responded to and attacked prey more rapidly. The number of attackers during collective foraging was determined jointly by composition and size, although composition had an effect size more than twice that of colony size: our results suggest that colonies of just 10 bold spiders would attack prey with as many attackers as colonies of 110 'average' spiders. Thus, personality composition is a more potent (albeit more cryptic) determinant of collective foraging in these societies.
Data from: Scale-dependent shifts in the species composition of flower visitors with changing floral density
Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects of floral density on visitation to the annual composite Holocarpha virgata at both patch (4 m(2)) and site (12.6 ha) spatial scales. The species composition of flower visitors changed with floral density, and did so in different ways at the two scales. At the site scale, average floral density within patches of H. virgata or within patches of all summer-flowering species combined had a significant positive effect on per-flowerhead visitation by the long-horned bee Melissodes lupina and no significant effects on visitation by any other taxa. At the patch scale, per-flowerhead visitation by honeybees significantly increased whereas visitation by M. lupina often decreased with increasing floral density. For both species, responses to patch-scale floral density were strongest when site-scale floral density was high. The scale-dependence of flower visitor responses to floral density and the interactions between site- and patch-scale effects of floral density observed in this study underscore the importance of improving our understanding of pollinators' responses to floral density at population scales.
Data from: Linking habitat composition, local population densities and traffic characteristics to spatial patterns of ungulate-train collisions
1. Total length of railways worldwide exceeds 1 million kilometres and recent railway development directly impacts wildlife because of animal-train collisions. Few studies, however, have analysed factors driving ungulate-train collisions. 2. We analysed over 3500 ungulate-train collisions including roe deer, red deer, wild boar, and moose collected in 2012-2015 in Poland. We compared train traffic characteristics (e.g. traffic intensity, speed, rail curvature), land-use and habitat characteristics (e.g. share of forests and build-up areas) and local ungulate population densities at collision sites and random sites distributed along the rail network. 3. Forest coverage generally increased, while urban areas decreased ungulate collision risk. Local density of ungulate species was strongly positively related to the relative collision risk in all four ungulate species, but above certain densities, the risk levelled off for all four species. 4. Train speed and train traffic intensity were positively associated with elevated collision risk in all four species, but the latter in a non-linear manner reached an asymptote at the level of ca. 10 trains per day. Rail curvature also increased probability of collisions with roe deer and red deer and possibly also wild boar. 5. Mortality rate of ungulates on railways in Poland is estimated to be 0.13-0.42% of annual hunting bags of studied species assuming that only one individual is killed at each occasion and ignoring undetected collisions. These values are expected to increase in near future due to increasing train speed in Central European countries. 6. Synthesis and applications. Ungulate-train collisions spots are characterised by surrounding forest, rail curvature, high train speed, and a moderate to high train traffic intensity. To reduce collision risk in a cost-effective way, we suggest to prioritise mitigation actions at sections of the railway characterized by those factors, e.g. by fencing and various warning devices. Due to nonlinear correlation between collision risk and population density, reducing density of ungulates will most likely reduce collision risk only marginally, and only in regions of low population densities where collision risk is relatively low anyway.
Data from: Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations
Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (Fst = 0.32) was more than twice as high as that of the young trees naturally established around native adults (Fst = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity.
Data from: Sea buckthorn berries (Hippophae rhamnoides L.) predict size and composition of a great tit population (Parus major L.).
In seasonal environments variation in food abundance in the non-breeding season is thought to affect songbird population dynamics. In a unique tit-sea buckthorn berry system we can estimate the berry abundance and both the tit consumption and population dynamics. Six hundred nest boxes were available to great and blue tits (Cyanistes caeruleus) for breeding in spring and roosting in winter. We followed the dynamics including the recapture histories of individually marked great tits from 2008-2013. In each year we estimated 1) the winter sea buckthorn berry availability, 2) an index of berry consumption in December based on the colour of the faeces of roosting birds, 3) the number of breeding great and blue tits, 4) both recapture probability and the return rate of the great tits and 5) immigration rates. December berry abundance positively predicted the number of breeding pairs of both species in the subsequent season and great tit return rates in the second half of the winter. There was support for a sex specific berry effect on the adult return rate in the great tit: female return rate was associated less strongly to berry abundance than male return rate. This skewed the sex ratio of the local breeders in the following breeding season. Intriguingly, annual berry consumption in December was not related to berry abundance, and individuals consuming more berries tended to have slightly lower return rates. Reproductive rate was not related to berry abundance. There was hardly support for a relation between immigration rates of first year breeders and berry abundance. Taken together these results imply that berry stock not only affected population size but also the population composition through sex specific exchange with the surroundings. Since population density covaried with berry abundance, density dependent effects provide an alternative explanation for the patterns observed.
Data from: Experimental rewilding enhances grassland functional composition and pollinator habitat use
1. Semi-natural grasslands are rich in biodiversity and thus important habitats for conservation, yet subjected to rapid declines due to agricultural intensification or abandonment. Promoting a more diverse mammalian herbivore community, including large and megaherbivores, may result in positive cascade effects for biodiversity and ecosystem functioning. Therefore, reintroducing an ecologically functional substitute of an extinct large herbivore could mitigate current biodiversity declines and foster semi-natural grassland conservation. 2. To test this hypothesis, we set up a 3-year rewilding experiment where 12 feral horses were introduced in three 10-hectare enclosure replicates (four horses per enclosure). We used community-weighted mean plant functional traits to elucidate plant community changes induced by grazing through time. We additionally investigated the effects of the experimental treatment on insect pollinated plants and on pollinator habitat use. 3. The grassland community exerted a mixed tolerance/avoidance response to grazing. This resulted in plant functional compositional changes which favoured prostrate plant species with higher specific leaf area, characteristic of ruderal communities. 4. Plant species richness was higher in grazed compared to ungrazed areas. Butterfly and bumblebee habitat use, as well as feeding and resting activities were also higher in grazed areas. Moreover, the number of pollinators increased with plant species richness. 5. Synthesis and applications. This study demonstrates that to enhance the diversity of a given herbivore community with an ecologically functional substitute of extinct wild horses can have significant effects on the functional composition of grasslands, mitigate plant species declines, and boost pollinator habitat use. Thus, rewilding interventions with large herbivores may offset current biodiversity declines by maintaining important functional links between plants and pollinators in grassland ecosystems.
Data from: Impacts of landscape composition, marginality of distribution, soil fertility, and climatic stability on the patterns of woody plant endemism in the Cerrado
Aim: Although various theories have been proposed to explain the outstanding endemism of plants in the Cerrado, four hypotheses about the mechanisms of diversification and distribution are most supported: (1) plateau/valley, (2) stable/unstable climate, (3) core/peripheral distribution, and (4) soil fertility. The first argues that plateaus harbor more ancient lineages than valleys and therefore presents higher endemism. The second theory suggests that climatic stable environments maintained more paleoendemic species. The third scenario attributes the distribution of endemism to gradients of conditions available to locally adapted species and predicts higher endemism in nuclear than in marginal areas. The last theory suggests that lower fertility soils account for higher endemism due to the habitat specialization of its species. We compared endemism patterns with the predictions of each theory to discuss their importance. Location: Brazil. Time period: Quaternary. Major taxa studied: Angiosperms. Methods: We mapped the endemism using records of 311 plant species of the Cerrado and applied spatial analysis and distribution models to summarize the importance of each predictor of endemism. Results: We identified 28 areas in which the higher endemism of Cerrado plants were concentrated and presented a map of its distribution. We found correlations among endemism, climate stability, elevation, and marginality, which supported the plateau/valley, core/peripheral, and stable/unstable hypotheses. No association between soil fertility and endemism was detected. We propose that plateaus are more stable climatic environments, and this characteristic along with their elevation and centrality are predictive of endemism. Main conclusions: We concluded that most of the endemism is concentrated in overlapping areas of stability of species, which are concentrated in higher elevation central regions. Soil fertility was not linked to endemism. We recommend that central plateaus in the Cerrado require special attention in conservation to optimize the protection of endemic species in the biome.
Data from: Long-term genetic monitoring reveals contrasting changes in the genetic composition of newly established populations of the intertidal snail Bembicium vittatum
Newly established populations are susceptible to founder events that reduce genetic variation. This may be counterbalanced by gene flow after populations become established or founders coming from genetically different populations. However, initial gains in genetic diversity may be short-lived if there is limited mixing between lineages and subsequent inbreeding or if one lineage sweeps to fixation through selection or genetic drift. Here, we report on the genetic changes taking place within two newly established populations of intertidal snail over a 15-year period (~ 10 generations). Each translocation was set up using multiple, genetically distinct source populations. Our data show that higher levels of variation in the translocated populations compared to the source populations were maintained over time for both nuclear (microsatellite) and mitochondrial genes. Small changes in allele and haplotype frequencies were observed in the source populations and in one of the translocated populations, but marked changes were evident in the other, where there was a dramatic shift towards the genetic make-up of one of the source populations. These genetic changes occurred despite relatively large numbers of founders (200- 374 adults) and no evidence of the population experiencing a severe reduction in effective population size. Our study shows that the genetic composition of newly established populations can vary greatly over time and that genetic outcomes can be highly variable, and significantly different to expectations, even when they are established using high numbers of individuals and involve source populations from the same geographic regions.
Data from: An unfavorable body composition is common in early arthritis patients: a case control study
Background. An unfavorable body composition is often present in chronic arthritis patients. This unfavorable composition is a loss of muscle mass, with a stable or increased (abdominal) fat mass. Since it is unknown when this unfavorable composition develops, we compared body composition in disease-modifying antirheumatic drugs (DMARD)-naive early arthritis patients with non-arthritis controls and explored the association, in early arthritis patients, with disease activity and traditional cardiovascular risk factors. Methods. 317 consecutive early arthritis patients (84% rheumatoid arthritis according to 2010 ACR/EULAR criteria) and 1268 age-/gender-/ethnicity-matched non-arthritis controls underwent a Dual-energy X-ray absorptiometry scan to assess fat percentage, fat mass index, fat mass distribution and appendicular lean (muscle) mass index. Additionally, disease activity, health assessment questionnaire (HAQ), acute phase proteins, lipid profile and blood pressure were evaluated. Results. Loss of muscle mass (corrected for age suspected muscle mass) was 4-5 times more common in early arthritis patients, with a significantly lower mean appendicular lean mass index (females 6% and males 7% lower, p<0.01). Patients had more fat distributed to the trunk (females p<0.01, males p=0.07) and females had a 4% higher mean fat mass index (p<0.01). An unfavorable body composition was associated with a higher blood pressure and an atherogenic lipid profile. There was no relationship with disease activity, HAQ or acute phase proteins. Conclusion. Loss of muscle mass is 4-5 times more common in early arthritis patients, and is in early arthritis patients associated with a higher blood pressure and an atherogenic lipid profile. Therefore, cardiovascular risk is already increased at the clinical onset of arthritis making cardiovascular risk management necessary in early arthritis patients.
Data from: Environmental drivers of soil phosphorus composition in natural ecosystems
Abstract. Soil organic and inorganic phosphorus (P) compounds can be influenced by distinctive environmental properties. This study aims to analyze soil P composition in natural ecosystems, relating organic (inositol hexakisphosphate, DNA and phosphonates) and inorganic (orthophosphate, polyphosphate and pyrophosphate) compounds with major temporal (weathering), edaphic and climatic characteristics. A dataset including 88 sites was assembled from published papers that determined soil P composition using one-dimensional liquid state 31P nuclear magnetic resonance spectroscopy of NaOH-EDTA extracts of soils. Bivariate and multivariate regression models were used to better understand the environmental properties influencing soil P. In bivariate relationships, trends for soil P compounds were similar for mineral and organic layers but with different slopes. Independent and combined effects of weathering, edaphic and climatic properties of ecosystems explained up to 78% (inositol hexakisphosphates) and 89% (orthophosphate) of variations in organic and inorganic P compounds across the ecosystems, likely deriving from parent material differences. Soil properties, particularly pH, total carbon, and carbon-to-phosphorus ratios, over climate and weathering mainly explained the P variation. We conclude that edaphic and climatic drivers regulate key ecological processes that determine the soil P composition in natural ecosystems. These processes are related to the source of P inputs, primarily determined by the parent material and soil forming factors, plant and microbe P cycling, the bio-physico-chemical properties governing soil phosphatase activity, soil solid surface specific reactivity, and P losses through leaching, and finally the P persistence induced by the increasing complexity of organic and inorganic P compounds as the pedogenesis evolves. Soil organic and inorganic P compounds respond differently to combinations of environmental drivers, which likely indicates that each P compound has specific factors governing its presence in natural ecosystems.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.