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FIGURES 16–18 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 16–18. Habitats of Adelphydraena species. 16–17. Collecting locality of Adelphydraena orchymonti, in Venezuela, Amazonas prov., Cerro Cuau env. 18. Collecting locality of Adelphydraena spangleri, in Venezuela, Bolívar prov., La Gran Sabana, Yaro Parú. Photos. by F. Čiampor.
FIGURES 11–12. 11. Adelphydraena spinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 11–12. 11. Adelphydraena spinosa n. sp., spermatheca and terminal abdominal segments. 12. Adelphydraena surinamensis n. sp., spermatheca and terminal abdominal segments.
FIGURES 5–6. 5 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 5–6. 5. Adelphydraena spangleri Perkins, non-type aedeagus and last tergites. 6. Adelphydraena surinamensis n. sp., holotype aedeagus and last tergite.
FIGURES 9–10. 9. Adelphydraenaspinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 9–10. 9. Adelphydraenaspinosa n. sp., holotypeaedeagus. 10. Adelphydraenaorchymonti Perkins, non-type, aedeagus.
Data from: Demographic responses of rare forest plants to multiple stressors: the role of deer, invasive species and nutrients
Forest ecosystems in eastern North America face multiple threats or stressors including plant and animal invasions and increased white-tailed deer (Odocoileus virginianus) herbivory. While each stressor may have independent detrimental effects on native biota, stressors often co-occur and are likely to have interactive effects. Despite recognition that concurrent processes drive plant demographic responses, few studies evaluate independent and combined effect of stressors. Using a network of 12 sites that varied in non-native plant cover and introduced earthworm density and biomass we experimentally assessed effects of deer exclusion (30 x 30 m paired plots), slug exclusion and nutrient addition on survival, growth and fecundity of four rare forest understorey plant species (Aristolochia serpentaria L., Agrimonia rostellata Wallr., Carex retroflexa Muhl. ex Willd, and Trillium erectum L). We found that single and combined effects of stressors were species-specific and varied according to plant stage and demographic parameter. Interactions were prevalent among all studied stressors and, for most cases, did not follow predicted responses. We found detrimental deer herbivory effects on reproductive A. rostellata and non-consumptive effects on A. serpentaria and T. erectum. Negative deer effects follow underlying predictions, and override effects of other stressors, even when other concurrent processes are at play. Contrary to expectations, we did not find negative effects of non-native plants. Earthworms had positive effects on A. rostellata and C. retroflexa (especially when deer were excluded), but negative effects on T. erectum. Slug effects were dependent on other stressors, especially on interactions with non-native plants and earthworms. Nutrient addition had a negative effect on survival of A. serpentaria and T. erectum, but positive effects on C. retroflexa and T. erectum growth. Synthesis: We found prevalent but unpredictable interactions among all study factors and plant species. Negative direct and indirect deer effects overrode impacts of all other stressors we investigated. A multi-factor approach is critical to predict plant responses to concurrent environmental forces. Assessment of combined effects should form an essential component of subsequent research on plant demography and management of declining species.
Data from: Species but not genotype diversity strongly impacts the establishment of rare colonisers
1. Understanding species coexistence and regulation of biodiversity are major research challenges, yet there is no consensus on the effects of diversity on diversity, including their mediation through plant–plant interactions. 2. We examined how the diversity of recipient communities impacted on the establishment of colonising species. We ran a greenhouse-based community experiment, creating artificial arable crop communities with varying levels of barley genotype and weed species diversity, analysed with structural equation modelling of responses across trophic levels. 3. Colonising arable weed species establishment was significantly reduced when the recipient communities' weed species richness, but not barley genotype richness, increased. Recipient plant communities with higher species richness occupied more total niche space and showed stronger competition with colonising species. In contrast, recipient plant communities with higher genotype richness, even though they had slightly greater niche space occupancy, had no significant effects on the colonisation of additional species. 4. Responses were species-specific: colonising common weed species establishment was less affected by the recipient plant communities than that of colonising rare weed species. Strong responses of colonising rare species were related to the abiotic rather than the biotic environment created by the recipient communities. The stronger response of colonising rare species suggests greater niche overlap with and competitive inferiority to the recipient plant community, whereas the relative independence of colonising common species indicates less niche overlap and/or competitive equality or superiority. 5. We observed a negative species diversity effect on colonising species, with the effect size increasing with increasing rarity of the colonising species. This differential responsiveness of colonising rare and common arable weed species to the presence of and diversity in the recipient arable plant communities may be crucial in understanding rarity and may result from differential evolutionary pathways in response to interactions.
Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition
Plant and soil communities are tightly linked, but the mechanisms by which the invasion of an exotic plant and the resulting shifts in plant diversity and productivity influence soil bacterial community structure remain poorly understood. We investigated the effects of invasive smooth brome (Bromus inermis) on grassland soil bacterial community structure using massively-parallel sequencing of the 16S rRNA gene to determine bacterial community richness, evenness, composition, and beta diversity (UniFrac indices) of soils collected along a gradient of smooth brome abundance. We evaluated several hypotheses including: a) that the declines in native plant diversity associated with smooth brome invasion would cause declines in bacterial community diversity, and b) that mechanisms driving smooth brome effects on bacterial community structure involved altered soil edaphic properties rather than preferential invasion in areas of high soil nitrogen and distinct soil microbial communities. Smooth brome invasion led to increased soil nitrogen, soil carbon and root biomass. Bacterial evenness and bacterial richness increased with increasing smooth brome cover, while bacterial beta diversity declined. We found no evidence of a dominant direct link between the alteration of soil edaphic properties by brome and the changes in the soil bacterial community. Rather, the main controls on the soil bacterial community were direct effects of pH and smooth brome that could not be linked to the edaphic changes. The most important effect of brome on the bacterial community was the selective suppression of dominant bacterial species, which allowed rarer bacteria to increase in relative abundance. Synthesis: Here we show that plant community composition influences bacterial community structure at a very fine scale, but that these changes are not due to altered soil total nitrogen or carbon content. The dominant direct effect of smooth brome invasion on soil communities suggests non-edaphic, i.e. inter and intra-trophic, interactions among smooth brome and non-bacterial components of the soil ecosystem are key drivers of soil community structure. Some of the data in this repository were also reported in the following paper: Piper, C.L., Lamb, E.G. & Siciliano, S.D. (In Press) Smooth brome changes gross soil nitrogen cycling processes during invasion of a rough fescue grassland. Plant Ecology. doi:10.1007/s11258-014-0431-y
Data from: Non-random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi-natural grasslands
1. Although biodiversity loss is a critically important topic, our understanding of how both land abandonment and land-use intensification in semi-natural grasslands alters the community diversity and assembly mechanisms is very limited. Large-scale economic drivers of land-use change might inadvertently result in the loss of vulnerable species and reduce ecosystem services provisioning. 2. In this study, we assessed non-random community change by examining patterns of low-abundance species loss, and community assembly in semi-natural grasslands due to land abandonment and intensification in southwest Japan. We analyzed relationships between evolutionary distinctiveness and abundance for each species. In addition, we used metrics of species and phylogenetic diversity and phylogenetic structure to assess patterns of non-random biodiversity loss due to both abandoned and intensified land-use. 3. We demonstrated that low-abundance species were more evolutionarily distinct compared to high-abundance (i.e., dominant) species. Furthermore, land-use intensification resulted in further declines in low-abundance species, whereas land abandonment resulted in declines in all species, regardless of their initial abundance. 4. We found that both forms of land-use change (abandonment and intensification) resulted in non-random patterns of community change, with traditional land-use maintaining the highest biodiversity and land-use change coinciding with decreased species and phylogenetic diversity measures. Intensified land-use caused phylogenetic community structure to be more closely related than expected by chance, whereas the metrics of how distant species are from one another on average based on phylogenetic tree (i.e., mean pairwise phylogenetic distance) did not change from land abandonment. 5. Synthesis and applications. We show that the loss of phylogenetic diversity, and especially of low-abundance species with high value of phylogenetic distinctiveness, resulted in non-random community disassembly. Our results argue that in order to maintain biodiversity in these semi-natural grasslands, traditional management practices should be encouraged over intensification and simple abandonment. Government agencies should adopt policies or provide incentives that encourage the maintenance of traditional practices in rural Japan, and elsewhere where the combination of land consolidation and abandonment are important conservation issues.
Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan
1. To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics. 2. The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real-time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species. 3. In environmental samples, we detected mtDNA of the endemic species at 25 sites and mtDNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey. 4. Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide-ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species.
Data from: The contribution of rare species to community phylogenetic diversity across a global network of forest plots
Niche differentiation has been proposed as an explanation for rarity in species assemblages. Testing this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal and that common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six forests but is rejected in nine forests, and that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.
Data from: Assessing species boundaries and the phylogenetic position of the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae), using coalescent-based methods
Delimiting species and clarifying phylogenetic relationships are the main goals of systematics. For species with questionable taxonomic status, species delimitation approaches using multi-species coalescent models with multiple loci are recommended if morphological data are unavailable or unhelpful. Moreover, these methods will also reduce subjectivity based on genetic distance or requirement of monophyletic genetic lineages. We determine the validity and phylogenetic position of a rare and long controversial species of Chinese reptile, the Szechwan ratsnake (Euprepiophis perlacea), using multi-locus data from multiple individuals and coalescent-based approaches. Species were first delimited using Bayesian Phylogenetics & Phylogeography (BP&P), Brownie and Bayes Factor model comparison approaches, while relationships among species were estimated using species tree inference in *BEAST. Results indicate that Euprepiophis perlacea is a distinct species sister to Euprepiophis mandarinus. Despite gene tree discrepancy, the coalescent model-based approaches used here demonstrate the taxonomic validity and the phylogenetic position of Euprepiophis perlacea. These approaches objectively test the validity of questionable species diagnoses based on morphological characters and determine their phylogenetic position.
Data from: When a clonal genome finds its way back to a sexual species: evidence from ongoing but rare introgression in the hybridogenetic water frog complex
Besides several exceptions, asexual metazoans are usually viewed as ephemeral sinks for genomes, which become 'frozen' in clonal lineages after their emergence from ancestral sexual species. Here, we investigated whether and at what rate the asexuals are able to introgress their genomes back into the parental sexual population, thus more or less importantly affecting the gene pools of sexual species. We focused on hybridogenetic hybrids of western Palaearctic water frogs (Pelophylax esculentus), which originate through hybridization between P. ridibundus and P. lessonae, but transmit only clonal ridibundus genome into their gametes. Although usually mating with P. lessonae, P. esculentus may upon mating with P. ridibundus or another hybrid produce sexually reproducing P. ridibundus offspring with the introgressed ex-clonal genome. We compared the rate of nuclear amplified fragment length polymorphism (AFLP) and mitochondrial introgression in two types of populations, that is, those where P. ridibundus occurs in isolation and those where it lives with the hybridogens. Although significant differentiation (Φpt) between sexual and clonal ridibundus genomes suggested limited gene flow between sexuals and hybridogens, a non-negligible (~5%) proportion of P. ridibundus bore introgressed mtDNA and AFLP markers. Whereas transfer of mtDNA was exclusively unidirectional, introgression of nuclear markers was bidirectional. The proportion of introgressed P. ridibundus was highest in syntopic populations with P. esculentus, proving an ongoing and site-specific interspecific genetic transfer mediated by hybridogenetic hybrids. It turns out that asexual hybrids are not just a sink for genes of sexual species, but may significantly influence the genetic architecture of their sexual counterparts.
Data from: Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designed group-specific primer set and next-generation sequencing for the detection of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada; the Grand River and the Sydenham River. Out of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.
Data from: Persistently rare species experience stronger negative frequency dependence than common species: a statistical attractor that is hard to avoid
Aim: Why are so many species rare, yet persistent? Possibly, rare species experience strong negative frequency dependence (NFD, i.e. strong intraspecific competition relative to interspecific competition), which both makes them rare and buffers them against extinction. A second, not mutually exclusive, possibility is that rare species that experience weak NFD go extinct quickly due to demographic and environmental stochasticity. Both possibilities predict that persistent rare species will experience stronger NFD than common ones. Yenni et al. (2017) confirmed this prediction in a range of mostly-terrestrial communities. Here we test that prediction in lake zooplankton, and explore its theoretical basis. Location: 53 temperate lakes Time period: 1970-2011 Major taxa studied: Cladocerans, copepods Methods: We used long-term time series data to estimate the covariance between strength of NFD and mean frequency (relative abundance) for crustacean zooplankton. We used a randomization test to ask whether the covariance between NFD and mean frequency is stronger than expected, given sampling error. We also calculated the covariance between NFD and mean frequency in simulated communities from three different ecological models. Results: Rare species experience significantly stronger NFD than common species in over half of the communities. The distribution of associations between NFD and rarity is skewed towards weak associations, which always occur in communities with high evenness. All three theoretical models reproduce these empirical results, even though they are based on different mechanisms (demographic or environmental stochasticity, and mathematical constraints on possible NFD-frequency relationships). Main conclusions: Rare species typically experience stronger NFD than common ones because there are many different ecological scenarios in which they will do so, and only a few scenarios in which they won't. Like several other macroecological patterns, the tendency for rare species to experience stronger NFD than common ones is a "statistical attractor" that is hard to avoid.
FIGURES 8–15 in New or rare Madagascar tiger beetles— 9. Two new species of the genus Physodeutera Lacordaire, with revised keys to the species of subgenera Diarrhiza Jeannel and Minideutera Moravec (Coleoptera: Cicindelidae)
FIGURES 8–15: characters of Physodeutera. Figs. 8–12: Ph. (Diarrhiza) murzini sp. n.: 8 — male labrum (holotype); 9 — female labrum (allotype); 10 — male pronotum (holotype); 11 — male elytron (holotype); 12 — female elytron (allotype). Figs. 13–15: Ph. (Minideutera) kamilmoraveci sp. n.(male, holotype): 13 — labrum; 14 — pronotum; 15 — elytron.
FIGURES 1415 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURES 1415. Eustigmaeus brevivestitus sp. n., male (allotype). 14 left tibia, tarsus and apotel I, paraxially; 15 aedagus, lateral view.
FIGURES 1112 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURES 1112. Eustigmaeus brevivestitus sp. n., female (holotype). 11 genital region. 12 right chelicera and palp, dorsal view.
FIGURES 89 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURES 89. Eustigmaeus brevivestitus sp. n., female (holotype). 8 dorsal view; 9 opisthosomal seta c.
FIGURES 57 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURES 57. Eustigmaeus formosus sp. n., female (holotype). 5 genital region; 6 palp (right); 7 right leg I, paraxial view.
FIGURES 13 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURES 13. Eustigmaeus formosus sp. n., female (holotype). 1 dorsal view; 2 aspidosomal seta be; 3 opisthosomal seta e.
ScienceDex guides
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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.