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Data from: Conservation planning for offsetting the impacts of development: a case study of biodiversity and renewable energy in the Mojave Desert
Balancing society's competing needs of development and conservation requires careful consideration of tradeoffs. Renewable energy development and biodiversity conservation are often considered beneficial environmental goals. However, the direct footprint and disturbance of renewable energy can displace species' habitat and negatively impact populations and communities if sited without ecological consideration. To mitigate residual impacts, offsets have emerged as a potentially useful tool after trying to avoid, minimize, or restore affected sites. Yet where many species or many sites are involved, the problem of efficiently designing a set of offset sites becomes increasingly complex. Spatial conservation prioritization tools are designed to handle this problem, but have seen little application to offset siting and analysis. To address this need we designed an offset siting support tool for the Desert Renewable Energy Conservation Plan (DRECP) of California, and present a case study of hypothetical impacts from solar development in the Western Mojave subsection. We compare two offset scenarios designed to mitigate a hypothetical 15,331 ha derived from proposed utility-scale solar energy development (USSED) projects. The first prioritizes offsets based precisely on impacted features, while the second offsets impacts based on the potential to maximize biodiversity conservation gains in the region. The two methods only agree on 28% of their prioritized sites and differ in meeting species-specific offset goals. Differences between the two scenarios highlight the importance of clearly specifying choices and priorities for offset siting and mitigation in general. Similarly, the effects of background climate and land use change may lessen the durability or effectiveness of offsets if not considered. Our offset siting support tool was designed specifically for the DRECP area, but with minor code modification could work well in other offset analyses, and provide continuing support for a potentially innovative mitigation solution to environmental impacts.
Data from: How does spatial resolution affect model performance? A case for ensemble approaches for marine benthic mesophotic communities
Aim: To investigate how changing grid size can alter model predictions of the distribution of mesophotic taxa and how it affects different modelling methods. Location: Ningaloo Marine Park, Western Australia. Taxon: Benthic mesophotic taxa: corals, macroalgae, and sponges. Methods: We determined the distributions of the major benthic taxonomic groups: corals, macroalgae, and sponges, using a number of modelling techniques and an ensemble using the 'sdm' R package. A range of grid sizes were used (10 m, 50 m, 100 m, and 250 m) to identify how model predictions were altered. Models were evaluated using the area under the curve of a receiver operator characteristic plot (AUC) and the true skill statistic (TSS) using a spatially independent dataset. Results: Grid size had a large effect on model performance across the taxonomic groups. Model outputs were compared to null surfaces and 88.8% of models performed significantly better than null. Distribution of corals was best predicted using the finest grid size (10 m) regardless of modelling method, although a model ensemble produced the best results (AUC = 0.80, TSS = 0.52). Macroalgae and sponges were better predicted at coaster grids sizes (250 m). Again, ensembles performed well for both macroalgae (AUC = 0.83, TSS = 0.63) and sponges (AUC = 0.88, TSS = 0.66). Model ensembles maintained high accuracy across grid sizes and were consistently the best, or second-best, performing method. Main Conclusions: This study has shown how grid size should be considered when producing distribution models. Identifying the most relevant grid size and being aware of the influence it may have will provide more accurate predictions of the distributions of taxa. Ensemble methods maintained good performance across scenarios and thus provide a useful tool for conservation and management especially where single modelling methods showed high levels of variability.
ACS - case study, simulation data
<p>These data refer to the simulations carried out to verify the ability of this plant to provide flexibility as market services </p>
Data from: The evolution of chemical defenses along invasion routes: Harmonia axyridis Pallas (Coccinellidae: Coleoptera) as a case study
The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey & Nötzold, 1995) postulates that escaping from coevolved enemies increases invaders fitness by energy reallocation from defenses and immunity to growth and reproduction. In this context, we evaluated the evidence of evolutionary change in invasive populations of Harmonia axyridis Pallas (Coccinellidae: Coleoptera). We measured egg defenses – cocktail of hydrocarbons on the egg's surface flagging egg toxicity, and the concentration of the main alkaloid harmonine - in individuals from three populations along the invasion route (Japan: native, USA: introduced more than 30 years ago, South Africa: introduced in the early 2000s) in a common garden experiment. Our results support the EICA hypothesis: we found changes along the invasion route in the profiles of the hydrocarbons coating the eggs' surface, and a decrease in the concentration of harmonine in eggs from the most recent invasive South African population compared to the long established in the USA and the native Japanese ones.
Data from: Searching for diamonds in the apomictic rough: a case study involving Boechera lignifera (Brassicaceae)
The genus Boechera is one of the most difficult species complexes in North America, with about 70 sexual diploids and hundreds of apomictic taxa representing diverse combinations of nearly every known sexual genome. In this study, we set out to clarify the taxonomy of Boechera lignifera, which currently includes a small number of sexual diploid populations in addition to the widespread apomictic diploid upon which the name is based. Using data from cytological studies, microsatellite DNA analyses, geography, and morphology, we demonstrate that the apomictic populations are genetically quite divergent from the sexual diploids. We propose the name Boechera kelseyana to accommodate the sexual diploid taxon, which occurs entirely south of the geographic range of B. lignifera. Boechera kelseyana is consistently separable from B. lignifera based on pollen and seed morphology, the length and proximal orientation of fruiting pedicels, differences in the branching and orientation of trichomes on the lowers stems, and the number of flowers and cauline leaves on unbranched fertile stems.
Data from: A novel case of autogamy and cleistogamy in Dendrobium wangliangii: a rare orchid distributed in the dry-hot valley
Dendrobium wangliangii is an epiphytic orchid distributed in the Jinshajiang dry-hot valley in Luquan County, Yunnan Province, China. Most Dendrobium spp. typically have a low fruit set, but this orchid shows a higher fruit set under natural conditions despite the lack of effective pollinators. The pollination biology of the critically endangered D. wangliangii was investigated in this study. A fruit set rate of 33.33±4.71% was observed after bagging treatment in 2017 and a high fruit set rate (65.72±4.44% in 2011; 50.79±5.44% in 2017) was observed under natural conditions, indicating that D. wangliangii is characterized by spontaneous self-pollination. The anther cap prevented the growing pollinium, thus the pollinium slid down and reached the stigmatic cavity, leading to autogamous self-pollination. Specifically, 51.50% of 162 unopened flowers (total 257 flowers) of this Dendrobium species under extreme water-deficit conditions developed into fruits, suggesting the presence of cleistogamy in D. wangliangii. Here, cleistogamy may represent the primary mode of pollination for this orchid. Spontaneous self-pollination and specific cleistogamous autogamy could represent major adaptions to the drought and pollinator-scarce habitat in the Jinshajiang dry-hot valley.
Data from: Finding politically feasible conservation policies: the case of wildlife trafficking
Conservation management is of increasing importance in ecology as most ecosystems nowadays are essentially managed ones. Conservation managers work within a political-ecological system when they develop and attempt to implement a conservation plan that is designed to meet particular conservation goals. In this article, we develop a decision support tool that can identify a conservation policy for a managed wildlife population that is both sustainable and politically feasible. Part of our tool consists of a simulation model composed of interacting influence diagrams. We build, fit, and use our tool on the case of rhino horn trafficking between South Africa and Asia. Using these diagrams, we show how a rhino poacher's belief system can be modified by such a policy and locate it in a perceived risks-benefits space before and after policy implementation. We statistically fit our model to observations on group actions and rhino abundance. We then use this fitted model to compute a politically feasible conservation policy.
Data from: Undocumented beetle diversity in the Southeastern United States: a case study of the minute clubbed beetles (Coleoptera: Monotomidae)
Studies of the saproxylic and predatory beetle family Monotomidae (Coleoptera: Cucujoidea) in the southeastern USA increased the known diversity for the family in the state of Georgia by one genus and nine species. Online records of Monotomidae from Georgia increased from 0 to 885. This work highlights the lack of basic diversity information about small beetles that inhabit wood, leaf litter, and other decaying plant matter in this region.
Data from: Toward a mechanistic understanding of human-induced rapid environmental change: a case study linking energy development, nest predation, and predators
1. Demographic consequences of human-induced rapid environmental change (HIREC) have been widely documented for many populations. The mechanisms underlying such patterns, however, are rarely investigated and yet are critical to understand for effective conservation and management. 2. We investigated the mechanisms underlying reduced avian nest survival with intensification of natural gas development, an increasing source of HIREC globally. We tested the hypothesis that energy development increased the local activity of important nest predator species thereby elevating nest predation rates. During 2011–2012, we surveyed predators and monitored 668 nests of Brewer's sparrows Spizella breweri, sagebrush sparrows Artemisiospiza nevadensis and sage thrashers Oreoscoptes montanus breeding at twelve sites spanning a gradient of habitat loss from energy development in western Wyoming, USA. 3. Nine species, representing four mammalian and three avian families, were video-recorded depredating eggs and nestlings. Important nest predator species differed across songbird species, despite similar nesting habitats. Approximately 75% of depredation events were by rodents. 4. Consistent with our predictions, detections of most rodent nest predators increased with surrounding habitat loss due to natural gas development, which was associated with increased probability of nest predation for our three focal bird species. 5. An altered nest predator assemblage was therefore at least partly responsible for elevated avian nest predation risk in areas with more surrounding energy development. 6. Synthesis and applications. We demonstrate one mechanism, i.e. the local augmentation of predators, by which human-induced rapid environmental change (HIREC) can influence the demography of local populations. Given the accelerating trajectory of global energy demands, an important next step will be to understand why the activity and/or abundance of rodent predators increased with surrounding habitat loss from energy development activities.
Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai'i
Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawai'i. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawa'i. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D-statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the State of Hawai'i. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a local scale relevant to biocultural conservation initiatives.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Data from: Assessing reproductive behavior important to fisheries management: a case study with red drum, Sciaenops ocellatus
Spawning site selection and reproductive timing affect stock productivity and structure in marine fishes but are poorly understood. Traditionally, stock assessments measure reproductive potential as spawning stock biomass or egg production and do not include other aspects of reproductive behavior. Red drum make an excellent case study to assess these other aspects, as (1) they are highly fecund, pelagic spawners, like most exploited marine fishes; (2) their life cycle is delineated between nursery (estuarine) and adult (coastal and offshore) habitat; and (3) they are managed at these two spatial scales. This study was conducted from August 2012 to December 2013 and integrates data from multiple methods and spatial scales. Aerial surveys were used for large-scale monitoring of aggregations off two known estuarine nursery areas, Tampa Bay and Charlotte Harbor, Florida, USA. Capture-based sampling in Tampa Bay coastal (n = 2581) and estuarine waters (n = 158) was used to assess reproductive state and to confirm coastal spawning. To assess spatial dynamics, we acoustically tagged two population components in the Tampa Bay system, subadults from the estuary (n = 20) and adults from the coastal spawning site (n = 60). Behavioral plasticity was seen in subadult recruitment to coastal habitat, with some subadults maturing and recruiting before or during the spawning season and others (14 of 20 acoustically tagged fish) recruiting at the end of the 2012 spawning season. Both adults and recruited subadults (n = 29) were consequently detected in the Charlotte Harbor array, 132 km to the south. Spawning-site fidelity to the Tampa Bay spawning site occurred at both the population and individual scales. Aggregations consistently occurred in Tampa Bay coastal waters during the spawning season, and approximately two-thirds of tagged adults returned in the 2013 spawning season. A similar proportion of subadults returned to the Tampa Bay spawning site, exhibiting natal homing. However, these first-time spawners arrived later than repeat spawners and were detected over shorter time periods. This study, and others like it, demonstrates how integrating data from individuals tracked over space and time with more traditional population-based sampling is changing our understanding of ecological processes that affect marine fish productivity and our ability to manage for sustainablity.
Data from: Morphological vs. molecular delineation of taxa across montane regions in Europe: the case study of Gammarus balcanicus Schäferna, 1922 (Crustacea: Amphipoda)
Mountainous areas are characterized by substantial biodiversity and endemicity due to their complex geological history and habitat fragmentation. Hence, it can be assumed that particularly high species richness can be found in organisms with limited dispersal capabilities that inhabit mountain streams. A number of scientific papers focus on molecular phylogeography or traditional taxonomy of species or species groups inhabiting such habitats. However, there is a lack of studies that integrate morphological and molecular data to identify and delineate cryptic species. For practical reasons, uncovering cryptic diversity is crucial in taxa used in biomonitoring. Distinct species, hard to separate based on morphology only, may have different tolerance ranges towards a variety of factors. Thus, our goal is to combine the two approaches to reveal potential patterns of diversification within a species widely distributed across European mountains: the amphipod crustacean Gammarus balcanicus. The data were obtained from 13 populations spread across the range of the species. Individuals were initially ascribed to G. balcanicus based on conventional fauna key morpho-anatomical diagnostic features and were further analysed for 23 additional features to explore any putative diversification. Morphometric data were analysed with use of the multiple correspondence analysis and anova. Molecular distances were calculated for 551-bp-long COI sequences. Test for isolation by distance was performed for both morphological and molecular data. The morphometric studies showed that some of the analysed features differed significantly between populations, although there was only a weak correlation between the morphological divergence and the between-population geographical distances. Moreover, high morphological diversity was present within sites. A set of 42 COI haplotypes was identified among the 135 individuals sequenced. No haplotype was shared among populations. The molecular p-distances within the nine localities presenting more than one haplotype were either almost null (ca. <0.003 for 7 localities) or relatively low (ca. 0.01–0.02 for 2 localities). In opposite, the molecular p-distances between localities were mostly at a high level (94% of pairwise comparisons being >0.14), similar as between other well-defined species of the genus Gammarus. Surprisingly, G. balcanicus appears to be polyphyletic based on topology of the neighbour-joining tree. The level of genetic distance between localities was not correlated with their geographical proximity. Globally, combining spatial patterns of morphological versus molecular divergence indicates a high level of cryptic diversity within a species conventionally defined based upon fauna key morphological features. In this context, the name G. balcanicus should be applied only to the population from locus typicus, while the other populations represent a number of putative distinct species. We may expect that such phenomenon would apply also to other animal taxa with conserved morphology, which are widespread over different mountain ranges in Europe.
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae
PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species' biogeographic histories and possible links between diversification and Pleistocene glaciations. METHODS: A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.
Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)
Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
Data from: Thelomma ocellatum, a range extension to the Yukon Territory and case study in the use of molecular data to recognize asexually reproducing crustose lichens
An unusual sterile, asexually reproducing crustose lichen was encountered during fieldwork in the Yukon Territory of Canada. Genus and family level placement of the taxon were precluded by a lack of both sexual characters and any non-sexual characters that would have suggested an unambiguous generic affiliation. Examination of mtSSU and nrITS sequence data of the taxon revealed it to be a member of the Caliciaceae, with a sister relationship to the genus Tholurna. Subsequent molecular phylogenetic analyses of mtSSU sequence data suggested conspecificity with Thelomma ocellatum, one of the few calicioid lichens that reproduce asexually via lichenized diaspores. Comparison of the material from the Yukon with reference specimens and descriptions of T. ocellatum confirmed the identification of these populations, which extend the known distribution of T. ocellatum considerably northward in North America.
Data from: Are landscape attributes a useful shortcut for classifying vegetation in the tropics? A case study of La Amistad International Park
Effective vegetation classification schemes identify the processes determining species assemblages and support the management of protected areas. They can also provide a framework for ecological research. In the tropics, elevation-based classifications dominate over alternatives such as river catchments. Given the existence of floristic data for many localities, we ask how useful floristic data are for developing classification schemes in species-rich tropical landscapes and whether floristic data provide support for classification by river catchment. We analyzed the distribution of vascular plant species within 141 plots across an elevation gradient of 130 to 3200 m asl within La Amistad National Park. We tested the hypothesis that river catchment, combined with elevation, explains much of the variation in species composition. We found that annual mean temperature, elevation, and river catchment variables best explained the variation within local species communities. However, only plots in high-elevation oak forest and Páramo were distinct from those in low- and mid-elevation zones. Beta diversity did not significantly differ in plots grouped by elevation zones, except for low-elevation forest, although it did differ between river catchments. None of the analyses identified discrete vegetation assemblages within mid-elevation (700–2600 m asl) plots. Our analysis supports the hypothesis that river catchment can be an alternative means for classifying tropical forest assemblages in conservation settings.
Data from: Continental-scale patterns of pathogen prevalence: a case study on the corncrake
Pathogen infections can represent a substantial threat to wild populations, especially those already limited in size. To determine how much variation in the pathogens observed among fragmented populations is caused by ecological factors, one needs to examine systems where host genetic diversity is consistent among the populations, thus controlling for any potentially confounding genetic effects. Here, we report geographic variation in haemosporidian infection among European populations of corncrake. This species now occurs in fragmented populations, but there is little genetic structure and equally high levels of genetic diversity among these populations. We observed a longitudinal gradient of prevalence from western to Eastern Europe negatively correlated with national agricultural yield, but positively correlated with corncrake census population sizes when only the most widespread lineage is considered. This likely reveals a possible impact of local agriculture intensity, which reduced host population densities in Western Europe and, potentially, insect vector abundance, thus reducing the transmission of pathogens. We conclude that in the corncrake system, where metapopulation dynamics resulted in variations in local census population sizes, but not in the genetic impoverishment of these populations, anthropogenic activity has led to a reduction in host populations and pathogen prevalence.
Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. Results: Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. Discussion: Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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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.