Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
5,145
datasets available to search
ShareScore release 0.7.1
Dataset results
5,145 results for “CO₂”
Data from: Stressor dominance and sensitivity-dependent antagonism: disentangling the freshwater effects of an insecticide among co-occuring agricultural stressors
1. Pesticide concentrations are correlated with regional declines in stream invertebrate diversity. Experimental studies have identified that pesticides can have strong and persistent negative effects on aquatic ecosystems. These effects may occur at concentrations orders of magnitude lower than laboratory toxicity studies predict. Synergism among stressors is one explanation for the observed laboratory-field difference. However, the true effect of pesticides on stream invertebrates remains uncertain, given interactions between stressors and natural environmental conditions. 2. We experimentally examined multiple-stressor effects on stream invertebrate assemblages and leaf-litter breakdown using 24 independent ~900 L re-circulating outdoor mesocosms in a semi-orthogonal design. Two pulses of the pesticide malathion (C10H19O6PS2) were delivered at low and high concentrations (Pulse 1: low at 0.1 and high at 1 µg L-1¬; Pulse 2: at 2.5 and 25 µg L-1). These were crossed with a treatment mimicking the combined stressors from agricultural development; nitrogen, phosphorus and clay (kaolin) sediment (hereafter agricultural stressors). 3. Malathion degradation was rapid (<24 hr half-life) in all treatments, likely because of photolysis, hydrolysis, the presence of biofilms and sorptive processes. There were significant differences in invertebrate assemblages between treatments, where malathion contributed to 48% and 87% of deviance during Pulse 1 and 2 respectively. Malathion had strong negative effects during Pulse 2, decreasing Ephemeroptera, Plecoptera and Trichoptera abundance (P<0.05), invertebrate richness (P<0.01) and total abundance (P<0.01). 4. Despite the dominant effects of malathion on invertebrates, agricultural stressors inhibited rates of leaf litter breakdown (P<0.05), increased invertebrate densities and weakly mitigated malathion toxicity in mesocosms (e.g. PERMANOVA, P≈0.1). Malathion breakdown analysis indicated sediment addition reduced malathion concentrations through alkaline hydrolysis and sorption. Experimental assays on common taxa indicated sediment was antagonistic with malathion. 5. Pesticide effects were not synergistic with the stressors tested here. Indeed, sensitivity-dependent stressor antagonisms were observed, reinforcing a mechanistic understanding of stressor effects and interactions is important. Among aquatic stressors examined, malathion had dominant effects on invertebrate assemblages, despite rapid degradation. Our results suggest that pesticide effects may be underestimated within ecosystems, where pesticides can have severe community wide effects, but rapid pesticide breakdown and sorptive processes may conceal causal links.01-May-2019
Data from: Experimental brood enlargement differentially influences the magnitude of the corticosterone stress response in closely related, co‐occurring songbirds
1. Rearing environments can shape offspring phenotype across taxa, yet little is known about how brood size influences hypothalamic-pituitary axis functioning, whether its expression trades off with growth, and the degree to which these relationships vary between species. 2. We evaluated how brood size influenced nestling physiological (glucocorticoids) and somatic traits (growth), and the extent to which these relationships differed between two closely related, sympatric songbirds when experiencing identical rearing environments. Specifically, we used a cross-fostering approach to alter brood size and create an experimental gradient of nestmate competition, and then tested whether experimentally manipulated brood sizes resulted in nestlings with altered concentrations of corticosterone and if corticosterone responses traded off with growth. 3. Nestlings of both species experienced elevated concentrations of baseline and stressor-induced corticosterone when raised in enlarged broods, relative to control and reduced broods, but neither measurement was found to trade off with growth or be linked to survival to fledging. 4. In contrast, we found divergence in the magnitude of the corticosterone stress response between species across all brood treatments, with greater stressor-induced corticosterone concentrations found in the Violet-green Swallow (Tachycineta thalassina) relative to the closely related Tree Swallow (T. bicolor). 5. Our study demonstrated that brood size can lead to changes in offspring corticosterone concentrations in swallows, and that nestlings of sympatric species, even those that are closely related and ecologically similar, can diverge in their corticosterone stress response when experiencing identical rearing conditions. 6. We conclude that corticosterone appears to play a key role for balancing energetic demands that arise in the face of nestmate competition in Tachycineta swallows, and that elevated concentrations of corticosterone may enhance offspring survival during challenging environmental conditions, such as when brood competition is strong.
Data from: Genetic diversity, population structure and sex-biased dispersal in three co-evolving species
Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analyzed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost's DEST), we detected strong population structuring in all species and less male-biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post-glacial colonization routes - northern populations are as variable as more southern populations. We conclude that conditions for Thompson's geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.
The spatial analysis of biological interactions: morphological variation responding to the co-occurrence of competitors and resources
By sharing geographic space, species are forced to interact with one another and the contribution of this process to evolutionary and ecological patterns of individual species is not fully understood. At the same time, species turnover makes that species composition varies from one area to another, so the analysis of biological interaction cannot be uncoupled from the spatial context. This is particularly important for clades that show high degree of specialization such as hummingbirds, where any variation in biotic pressures might lead to changes in morphology. Here, we describe the influence of biological interactions on the morphology of Hylocharis leucotis by simultaneously considering potential competition and diet resources. We characterized the extent of local potential competition and local available floral resources by correlating two measurements of hummingbird diversity, floral resources and the size of morphological space of H. leucotis along its geographic distribution. We found that H. leucotis shows an important morphological variability across its range and two groups can be recognized. Surprisingly, morphological variation is not always linked to local hummingbird richness or the phylogenetic similarity of. Only in the southern part of its distribution, H. leucotis is morphologically more variable in those communities where it coexist with closely related hummingbird species. We also found that morphological variation in H. leucotis is independent from the availability of floral resources. Our results suggest that abiotic factors might be responsible for morphological differences across populations in Hylocharis leucotis being biological interactions of minor importance.
Data from: Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot
1. Biological diversity has long been used to measure ecological health. While evidence exists from many ecosystems that declines in host biodiversity may lead to greater risk of disease emergence, the role of pathogen diversity in the emergence process remains poorly understood. Particularly, because a more diverse pool of pathogen types provides more ways in which evolutionary innovations may arise, we suggest that host–pathogen systems with high pathogen diversity are more prone to disease emergence than systems with relatively homogeneous pathogen communities. We call this prediction the diversity-emergence hypothesis. 2. To show how this hypothesis could be tested, we studied a system comprised of North American shorebirds and their associated low-pathogenicity avian influenza (LPAI) viruses. These viruses are important as a potential source of genetic innovations in influenza. A theoretical contribution of this study is an expression predicting the rate of viral subtype reassortment to be proportional to both prevalence and Simpson's Index, a formula that has been used traditionally to quantify biodiversity. We then estimated prevalence and subtype diversity in host species at Delaware Bay, a North American AIV hotspot, and used our model to extrapolate from these data. 3. We estimated that 4 to 39 virus subtypes circulated at Delaware Bay each year between 2000 and 2008, and that surveillance coverage (percentage of co-circulating subtypes collected) at Delaware Bay is only about 63·0%. Simpson's Index in the same period varied more than fourfold from 0·22 to 0·93. These measurements together with the model provide an indirect, model-based estimate of the reassortment rate. A proper test of the diversity-emergence hypothesis would require these results to be joined to independent and reliable estimates of reassortment, perhaps obtained through molecular surveillance. 4. These results suggest both that subtype diversity (and therefore reassortment) varies from year to year and that several subtypes contributing to reassortment are going undetected. The similarity between these results and more detailed studies of one host, ruddy turnstone (Arenaria interpres), further suggests that this species may be the primary host for influenza reassortment at Delaware Bay. 5. Biological diversity has long been quantified using Simpson's Index. Our model links this formula to a mechanistic account of reassortment in multipathogen systems in the form of subtype diversity at Delaware Bay, USA. As a theory of how pathogen diversity may influence the evolution of novel pathogens, this work is a contribution to the larger project of understanding the connections between biodiversity and disease.
Data from: Within guild co-infections influence parasite community membership: a longitudinal study in African Buffalo
1. Experimental studies in laboratory settings have demonstrated a critical role of parasite interactions in shaping parasite communities. The sum of these interactions can produce diverse effects on individual hosts as well as influence disease emergence and persistence at the population level. 2. A predictive framework for the effects of parasite interactions in the wild remains elusive, largely because of limited longitudinal or experimental data on parasite communities of free-ranging hosts. 3. This four year study followed a community of haemoparasites in free-ranging African buffalo (Syncerus caffer). We detected infection by 11 haemoparasite species using PCR-based diagnostic techniques, and analyzed drivers of infection patterns using generalized linear mixed models to understand the role of host characteristics and season on infection likelihood. We tested for (1) effects of co-infection by other haemoparasites (within guild) and (2) effects of parasites infecting different tissue types (across guild). 4. We found that within guild co-infections were the strongest predictors of haemoparasite infections in the buffalo; but that seasonal and host characteristics also had important effects. In contrast, the evidence for across-guild effects of parasites utilizing different tissue on haemoparasite infection was weak. 5. These results provide a nuanced view of the role of co-infections in determining haemoparasite infection patterns in free living mammalian hosts. Our findings suggest a role for interactions among parasites infecting a single tissue type in determining infection patterns.
Data from: A native parasitic plant and soil microorganisms facilitate a native plant co-occurrence with an invasive plant
Invasive plants often interact with antagonists that include native parasitic plants and pathogenic soil microbes, which may reduce fitness of the invaders. However, to date, most of the studies on the ecological consequences of antagonistic interactions between invasive plants and the resident biota focused only on pairwise interactions. A full understanding of invasion dynamics requires studies that test the effects of multiple antagonists on fitness of invasive plants and co-occurring native plants. Here, we used an invasive plant Mikania micrantha, a co-occurring native plant Coix lacryma-jobi, and a native holoparasitic plant Cuscuta campestris to test whether parasitism on M. micrantha interacts with soil fungi and bacteria to reduce fitness of the invader and promote growth of the co-occurring native plant. In a factorial set up, M. micrantha and C. lacryma-jobi were grown together in pots in the presence versus absence of parasitism on M. micrantha by C. campestris, and in the presence versus absence of full complements of soil bacteria and fungi. Fungicide and bactericide were used to suppress soil fungi and bacteria, respectively. Findings show that heavy parasitism by C. campestris caused the greatest reduction in M. micrantha biomass when soil fungi and bacteria were suppressed. In contrast, the co-occurring native plant C. lacryma-jobi experienced the greatest increase in biomass when grown with heavily parasitized M. micrantha and in the presence of a full complement of soil fungi and bacteria. Taken together, our results suggest that selective parasitism on susceptible invasive plants by native parasitic plants and soil microorganisms may diminish competitive ability of invasive plants and facilitate native plant co-existence with invasive plants.
Data from: Taxonomic and functional diversity of the co-flowering community differentially affect Cakile edentula pollination at different spatial scales
1. The number of co-flowering species, floral density and floral trait diversity can be major determinants of pollinator-mediated plant-plant interactions in a community. However, evaluation of how each one of these co-flowering components affects the pollination success of a single focal plant species, and how these effects vary at different spatial scales, is lacking. 2. Here we evaluated the effects of functional diversity (flower morphology and colour), taxonomic diversity (reflecting potential sampling effects) and flower density (conspecific and heterospecific), on the pollinator environment (i.e. visitation rate and pollinator diversity), and pollination success (i.e. pollen load size and number of pollen tubes per style) of Cakile edentula (Brassicaceae). We applied structural equation models (SEM's) at the floral-neighbourhood (plot level) and community-wide scales to uncover the factors that mediate co-flowering community effects on C. edentula pollination success. 3. We found that co-flowering community effects at the community level are more important than fine-scale floral-neighbourhood differences in mediating plant pollination success in our study species. Increasing plant functional diversity decreased pollinator visitation rate but increased the diversity of pollinator functional groups visiting C. edentula flowers. Taxonomic diversity negatively affected pollinator diversity suggesting that other unmeasured floral traits may be relevant or that single-species effects (sampling effects) may be important. Overall, our results suggest that functional floral trait diversity in a community may be the most important factor influencing pollination success of species in a community. We also found evidence for intra- and interspecific pollinator competition mediated by flower density but none of these effects seemed to have a significant impact on pollination success. 4. This study is an important step towards understanding the complexity of co-flowering community effects on the pollination success of individual plant species at multiple spatial scales. This study further reveals the potential importance of plant functional diversity in a community in helping predict competitive and facilitative interactions in co-flowering communities. 5. Synthesis. Floral density, taxonomic and functional co-flowering diversity are important drivers of pollination success in flowering plants. The effects of the co-flowering diversity on the pollination success of plant species can largely depend on the spatial scale being studied. Only evaluating the outcomes of pollinator-mediated plant-plant interactions at multiple stages of the pollination process can lead to a complete understanding of their ecological consequences in nature.
Data from: Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia)
Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesised to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesised to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra-pair reproduction and male within-pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate non-zero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modelled as direct and associative genetic effects on offspring paternity respectively, in free-living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, while substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra-pair reproduction is facilitated by genetic covariance with male within-pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.
Data from: Non-random associations of maternally transmitted symbionts in insects: the roles of drift versus co-transmission and selection
Virtually all higher organisms form holobionts with associated microbiota. To understand the biology of holobionts we need to know how species assemble and interact. Controlled experiments are suited to study interactions between particular symbionts, but they can only inform about a tiny portion of the diversity within each species. Alternatively, interactions can be inferred from associations among symbionts in the field that are more or less frequent than expected under random assortment. However, random assortment may not be a valid null hypothesis for maternally transmitted symbionts in finite populations, where drift alone can result in associations. Here we report results from a European field survey of endosymbionts in the pea aphid (Acyrthosiphon pisum), and we develop a model to study the effect of drift on symbiont associations under different population sizes, considering varying rates of horizontal and maternal transmission. The model showed that even though horizontal transmissions and maternal transmission failures randomise symbiont associations, drift can induce significant departures from random assortment, at least in moderate-sized populations. Based on these results, we carefully interpret our field survey and we re-visit the association between Spiroplasma and Wolbachia in Drosophila neotestacea reported by Jaenike et al. (2010). For this and for several significant associations between symbionts in European pea aphids we conclude that under reasonable assumptions of effective population size, they are indeed likely to be maintained by biased co-transmission or selection. Our study shows that formulating appropriate null expectations can strengthen the biological inference from co-occurrence patterns in the field.
Data from: Sources of (co)variation in alternative siring routes available to male great tits (Parus major)
Males of socially monogamous species can increase their siring success via within-pair and extra-pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five-year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as "interactive phenotypes" arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra-pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra-pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multi-level structure of male fertilization routes when studying the evolution of male mating strategies.
Data from: Soil biota and chemical interactions promote co-existence in co-evolved grassland communities
1. Plant populations can exhibit local adaptation to their abiotic environment, such as climate and soil properties, as well as biotic components such as the chemical signatures of dominant plant species and mutualistic and pathogenic microbial populations. While patterns of local adaptation in individual species are widely recorded, the importance of microevolutionary processes for plant community assembly and function is poorly understood. 2. Here we examined how a history of long-term co-existence, and thus potential for local co-adaptation, influenced the process of plant community assembly. Soil inocula and seeds of eight plant species were collected from three calcareous grasslands with a long history of grazing within a single geographical region. Mesocosm communities were established using local genotypes from a single site or an artificial mixture of genotypes from two different sites. To investigate the role of root exudates and local ("home") and non-local ("away") soil biota as mediators of plant species co-existence, the population origin treatment was combined with the addition of activated carbon, which is known to adsorb exudates from soil, and sterilisation of soil inocula. Individual-, species- and mesocosm-level responses were measured over the course of three growing seasons. 3. We found that root exudates promoted seedling survival, species co-existence and productivity in assemblages of genotypes originating from the same community but had a weak impact in mixed, novel communities. Soil biota promoted the growth of subordinate forbs and restrained the growth of dominant graminoids, particularly in communities composed of local genotypes. The effects of population origin were significant in the first two years of the experiment but were not detectable in the third year when interbreeding and new seedling establishment took place. Plant genotypes coupled with "home" microbial inoculum experienced a stronger reduction in growth compared with genotypes exposed to "away" inoculum, indicating that plants experienced home-field disadvantage in interactions with soil biota. 4. Synthesis. Our study demonstrates that the mechanisms of initial grassland community assembly depend on community history, with belowground chemical interactions and plant interactions with soil biota becoming stronger drivers of dynamics in established and potentially co-evolved communities.
Data from: Ecological co-associations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle
Ecologically interacting species may have phylogeographic histories that are shaped both by features of their abiotic landscape, and by biotic constraints imposed by their co-association. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species. This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of co-distributed free-living animals (e.g., herpetofauna and small mammals). Thus, 'plant-like' patterns should be discernible in host-specific insect herbivores. Here we investigate the population history of a monophagous bark beetle, Araptus attenuatus, and consider drivers of phylogeographic patterns in light of previous work on its host plant, Euphorbia lomelii. Based on mitochondrial and nuclear markers, we found that the evolutionary history of A. attenuatus exhibits similarities to host plant that are attributable to both biotic and abiotic processes. Southward range expansion and recent colonization of continental Sonora peninsula appear to be unique to this taxon pair, and likely reflect influences of the host plant. On the other hand, abiotic factors with landscape-level influences on suites of co-distributed taxa, such as Plio- and Pleistocene-aged marine incursions in the region, also left genetic signatures in beetle populations. Superimposed on these similarities, bark beetle-specific patterns and processes were also evident. Taken together, this work illustrates that the evolutionary history of species-specific insect herbivores may represent a mosaic of influences, including—but not limited to—those imposed by the host plant.
Data from: Plant-mycorrhizal fungus co-occurrence network lacks substantial structure
The interactions between plants and arbuscular mycorrhizal fungi (AMF) maintain a crucial link between macroscopic organisms and the soil microbial world. These interactions are of extreme importance for the diversity of plant communities and ecosystem functioning. Despite this importance, only recently has the structure of plant–AMF interaction networks been studied. These recent studies, which used genetic data, suggest that these networks are highly structured, very similar to plant–animal mutualistic networks. However, the assembly process of plant–AMF communities is still largely unknown, and an important feature of plant–AMF interactions has not been incorporated: they occur at an extremely localized scale. Studying plant–AMF networks in a spatial context seems therefore a crucial step. This paper studies a plant–AMF spatial co-occurrence network using novel methodology based on information theory and a unique set of spatially explicit species-level data. We apply three null models of which only one accounts for spatial effects. We find that the data show substantial departures from null expectations for the two non-spatial null models. However, for the null model considering spatial effects, there are few significant co-occurrences compared with the other two null models. Thus, plant–AMF spatial co-occurrences seem to be mostly explained by stochasticity, with a small role for other factors related to plant–AMF specialization. Furthermore, we find that the network is not significantly nested or modular. We conclude that this plant–AMF spatial co-occurrence network lacks substantial structure and, therefore, plants and AMF species do not track each other over space. Thus, random encounters seem more important in the first step of the assembly of plant–AMF communities.
Data from: Buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts
Symbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long-term obligate interactions. Recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement and/or supplementation of an obligate symbiosis by an additional bacterium has occurred during the history of many insect groups. Yet, the factors favoring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a "ménage à trois", in which Buchnera is complemented by a co-symbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species confirm that these co-resident symbionts fulfill essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that co-symbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.
Data from: Dynamic species co-occurrence networks require dynamic biodiversity surrogates
In conservation it is inevitable that surrogates be selected to represent the occurrence of hard–to–find species and find priority locations for management. However, species co–occurrence can vary over time. Here we demonstrate how temporal dynamics in species co–occurrence influence the ability of managers to choose the best surrogate species. We develop an efficient optimisation formulation that selects the optimal set of complementary surrogate species from any co–occurrence network. We apply it to two Australian datasets on successional bird responses to disturbances of revegetation and fire. We discover that a surprisingly small number of species are required to represent the majority of species co–occurrences at any one time. Because co–occurrence patterns are temporally dynamic, the optimal set of surrogates, and the number of surrogates required to achieve a desired surrogacy power, depend on sampling effort and the successional state of a system. Overlap in optimal sets of surrogates for representing 70% of co–occurring species ranges from zero to 57% depending on when the surrogacy decision is made. Surrogate sets representing early successional communities over–estimate the power of surrogacy decisions at later times. Our results show that in dynamic systems, optimal surrogates might be selected in different ways: (1) use short–term monitoring to choose a larger number of static less–informative surrogates; (2) use long–term monitoring to choose a smaller number of static high–power surrogates that may poorly represent early successional co–occurrence; (3) develop adaptive surrogate selection frameworks with high short–term and long–term surrogacy power that update surrogate sets and capture temporal dynamics in species co–occurrence. Our results suggest vigilance is needed when selecting surrogates for other co–occurring species in dynamic landscapes, as selected surrogates from one time may have reduced effectiveness at a different time. Ultimately, decisions that fail to acknowledge dynamic species co–occurrence will lead to uninformative or redundant surrogates.
Data from: How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa
Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pleistocene glaciation–deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study we estimated time-calibrated phylogenetic/phylogeographic patterns in lizards of the Liolaemus lineomaculatus group, and related them to historical Miocene-to-Pleistocene events of Patagonia and the previously proposed phylogeographic patterns. Individuals from 51 localities were sequenced for the mitochondrial marker (cyt-b) and a sub-sample of individuals from each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one slow evolving mitochondrial gene (12S). Our analyses revealed strong phylogeographic structure among lineages and, in most cases, no signal of population changes through time. The lineomaculatus group is composed of three strongly supported clades (lineomaculatus, hatcheri and kolengh+silvanae), and divergence estimates suggested their origins associated with the oldest known Patagonian glaciation (7-5 Ma); subsequent diversification within the lineomaculatus clade coincided with the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade includes nine strongly structured genetically and geographically lineages and five of them are interpreted candidate species. Our findings suggest that some Liolaemus lineages have persisted in situ in multiple refugia through several glaciation-deglaciation cycles in southern Patagonia without demographic fluctuations. We also provide qualitative evidence of some shared phylogeographic breaks and refugia among plants, rodents, and lizards.
Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts
Global climate change is known to affect the assembly of ecological communities by altering species' spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species' temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon groups from 329 local meteorological observatories across China. We show that widespread shifts in phenology have resulted in community-wide changes in the temporal overlap between taxa that are dominated by extensions, and that these changes are largely due to taxa's altered span of temporal occurrence rather than the degree of synchrony in phenological shifts. Importantly, our findings also suggest that climate change may have led to less phenological mismatch than generally presumed, and that the context under which to discuss the ecological consequences of phenological shifts should be expanded beyond asynchronous shifts.
Data from: Transcriptomic responses to conspecific and congeneric competition in co-occurring Trifolium
Species coexistence requires differential response to inter- and intraspecific competition, typically conceptualized as niche differentiation. Coexistence of close relatives therefore poses an interesting scenario with regards to niche differentiation since these species generally have many traits in common due to shared ancestry. Native Californian Trifolium assemblages are locally diverse and represent a unique system for understanding competitive interactions among close relatives. We conducted two similar greenhouse studies in which Trifolium fucatum was grown alone, with a conspecific competitor, and with a congeneric competitor (Trifolium macraei). In the first study, we assessed biomass production in T. fucatum, and in the second study we conducted an RNAseq analysis of T. fucatum roots to test for differentially expressed genes that may mediate competitive interactions and potentially coexistence. Compared to plants grown alone, competition (i.e. growth in the same pot) with a conspecific resulted in a greater reduction in biomass than competition with a congener, as predicted by theory. However, competition with a congener resulted in twice as many differentially expressed genes as competition with a conspecific. Annotations of identified genes differentiating congeneric from conspecific competition suggest several functions attributed to interactions with third-party organisms, including nodulation with rhizobial mutualists, and defence responses against pathogens and herbivores. In addition, salt-responsive genes and an iron transporter were differentially expressed in congeneric competition, and comparisons of sodium and iron concentrations in field soils where these species are found showed that T. fucatum occurs in higher sodium and iron microsites than T. macraei. Thus, the transcriptome highlighted abiotic niche axes worth pursuing in future ecological experiments as potential mediators of coexistence. We also found a subset of genes that responded similarly to both congeneric and conspecific competition in both direction and magnitude, indicating some conserved responses to competition, regardless of neighbour identity. Synthesis. Transcriptomic analyses represent novel tools for identifying the molecular mechanisms underlying interactions among species. Working iteratively with ecological experimentation and observation, transcriptomes may allow us to identify novel dimensions of the n-dimensional niche that determine species' distributions and their ability to coexist.
Data from: Species discrimination of co-occurring small fossil mammals: a case study of the Cretaceous-Paleogene multituberculate genus Mesodma
The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear and geometric morphometrics on 86 p4s representing four Cretaceous-Paleogene (K-Pg) species of Mesodma that are common in deposits of the western interior of North America. Although Mesodma has been extensively discussed in the literature, these four species overlap considerably in p4 size and shape, making species-level identifications challenging. Using linear measurements, landmarks, and semilandmarks, we quantified p4 size and shape to understand morphological variation across the genus and uncover practical sources of morphological differentiation among the species represented here. Our results indicate (1) size is more important than shape for identifying p4s of Mesodma species; p4 shape varies across the genus, but cannot be used alone to identify isolated p4s to species; (2) M. garfieldensis and M. thompsoni cannot be distinguished from each other using p4 size or shape; we therefore subsume M. garfieldensis within M. thompsoni; and (3) M. formosa increased in size across the K-Pg boundary. In light of these results, we recommend that taxonomic diagnoses relying on isolated teeth incorporate quantitative analyses of morphology whenever possible to increase the accuracy of species-level identifications and paleofaunal studies that employ them.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.