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Data from: Demographic history of an elusive carnivore: using museums to inform management
Elusive carnivores present a challenge to managers because traditional survey methods are not suitable. We applied a genetic approach using museum specimens to examine how historical and recent conditions influenced the demographic history of Puma concolor in western and southern Texas, USA. We used 10 microsatellite loci and indexed population trends by estimating historical and recent genetic diversity, genetic differentiation, and effective population size. Mountain lions in southern Texas exhibited a 10% decline in genetic diversity, whereas diversity remained stable in western Texas. Genetic differentiation between western and southern Texas was minimal historically (FST = 0.04, P < 0.01), but increased 2-2.5 times in our recent sample. An index of genetic drift for southern Texas was 7-8 times that of western Texas, presumably contributing to the current differentiation between western and southern Texas. Furthermore, southern Texas exhibited a > 50% temporal decline in effective population size, whereas western Texas showed no change. Our results illustrate that population declines and genetic drift have occurred in southern Texas, likely because of contemporary habitat loss and predator control. Population monitoring may be needed to ensure the persistence of mountain lions in the southern Texas region. This study highlights the utility of sampling museum collections to examine evolutionary processes and inform wildlife management.
Data from: Habitat features and long-distance dispersal modify the use of social information by a long-distance migratory bird
1. The processes by which individuals select breeding sites have important consequences for individual tness as well as population- and community-dynamics. Although there is increasing evidence that many animal species use information acquired from conspecics to assess the suitability of potential breeding sites, little is known about how the use of this social information is modified by biotic and abiotic conditions. 2. We used an automated playback experiment to simulate two types of social information, post-breeding public information and pre-breeding location cues, to determine the relative importance of these cues for breeding site selection by a migratory songbird, the American redstart (Setophaga ruticilla). In addition, we used stable hydrogen isotopes to determine the dispersal status of individuals that responded to our experimental treatments and quantify whether long-distance dispersers use different social cues to select breeding sites compared to philopatric individuals. 3. We found that points that received pre-breeding location cue treatments were signi cantly more likely to be settled by redstarts than control points that received no playback. However, we found no evidence the redstarts used post-breeding public information gathered during one season to select breeding sites the following year. Breeding site habitat structure was also a strong predictor of settlement probability, indicating that redstarts modi ed the use of social information based on habitat cues. Furthermore, stable hydrogen isotope signatures from individuals that responded to location cue treatments suggest that long-distance dispersers may rely more heavily on these cues than local recruits. 4. Collectively, these results indicate that redstarts use multiple sources of information to select breeding sites, which could buffer individuals from selecting suboptimal sites when they breed in unfamiliar locations or when habitat quality becomes decoupled from social cues.
Data from: Strong evidence of an Information-Theoretical Conservation Principle linking all discrete systems
<p>Diverse discrete systems share common global properties that lack a unifying theoretical explanation. However, constraining the simplest measure of total information (Hartley-Shannon) in a statistical mechanics framework reveals a principle, the Conservation of Hartley-Shannon Information (CoHSI) that directly predicts both known and unsuspected common properties of discrete systems, as borne out in the diverse systems of computer software, proteins and music. Discrete systems fall into two categories distinguished by their structure: heterogeneous systems in which there is a distinguishable order of assembly of the system's components from an alphabet of unique tokens (e.g. proteins assembled from an alphabet of amino acids), and homogeneous systems in which unique tokens are simply binned, counted and rank ordered. Heterogeneous systems are characterized by an implicit distribution of component lengths, with sharp unimodal peak (containing the majority of components) and a power-law tail, whereas homogeneous systems reduce naturally to Zipf's Law but with a drooping tail in the distribution. We also confirm predictions that very long components are inevitable for heterogeneous systems; that discrete systems can exhibit simultaneously both heterogeneous and homogeneous behavior; and that in systems with more than one consistent token alphabet (e.g. digital music), the alphabets themselves show a power-law relationship.</p>
Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia
The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north-western and south-eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.
Data from: Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding
Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS), we evaluated 1170 of these advanced lines in two environments, drought (2014, 2015) and heat (2015). A portable phenotyping system called 'Phenocart' was used to measure normalized difference vegetation index and canopy temperature simultaneously while tagging each data point with precise GPS coordinates. For genomic profiling, genotyping-by-sequencing (GBS) was used for marker discovery and genotyping. Several GS models were evaluated utilizing the 2254 GBS markers along with over 1.1 million phenotypic observations. The physiological measurements collected by HTP, whether used as a response in multivariate models or as a covariate in univariate models, resulted in a range of 33% below to 7% above the standard univariate model. Continued advances in yield prediction models as well as increasing data generating capabilities for both genomic and phenomic data will make these selection strategies tractable for plant breeders to implement increasing the rate of genetic gain.
Data from: True colors: commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential
<p>Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANEL<sup>TM</sup> data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e<sup>-7</sup> and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to trace the mode by which characteristics have spread across breeds during historical breed formation; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.</p>
Data from: Remotely sensed data informs red list evaluations and conservation priorities in southeast Asia
The IUCN Red List has assessed the global distributions of the majority of the world's amphibians, birds and mammals. Yet these assessments lack explicit reference to widely available, remotely-sensed data that can sensibly inform a species' risk of extinction. Our first goal is to add additional quantitative data to the existing standardised process that IUCN employs. Secondly, we ask: do our results suggest species of concern—those at considerably greater risk than hitherto appreciated? Thirdly, these assessments are not only important on a species-by-species basis. By combining distributions of species of concern, we map conservation priorities. We ask to what degree these areas are currently protected and how might knowledge from remote sensing modify the priorities? Finally, we develop a quick and simple method to identify and modify the priority setting in a landscape where natural habitats are disappearing rapidly and so where conventional species' assessments might be too slow to respond. Tropical, mainland Southeast Asia is under exceptional threat, yet relatively poorly known. Here, additional quantitative measures may be particularly helpful. This region contains over 122, 183, and 214 endemic mammals, birds, and amphibians, respectively, of which the IUCN considers 37, 21, and 37 threatened. When corrected for the amount of remaining natural habitats within the known elevation preferences of species, the average sizes of species ranges shrink to <40% of their published ranges. Some 79 mammal, 49 bird, and 184 amphibian ranges are <20,000km2—an area at which IUCN considers most other species to be threatened. Moreover, these species are not better protected by the existing network of protected areas than are species that IUCN accepts as threatened. Simply, there appear to be considerably more species at risk than hitherto appreciated. Furthermore, incorporating remote sensing data showing where habitat loss is prevalent changes the locations of conservation priorities.
Data from: Environmental DNA reveals that rivers are conveyer belts of biodiversity information
DNA sampled from the environment (eDNA) is a useful way to uncover biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land–water interface. Using an eDNA metabarcode approach, we detect 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with the classical community assessments by integrating biodiversity information over space. In addition, we demonstrate that many terrestrial species are detected; thus suggesting eDNA in river water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess the total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.
Data from: Towards a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)
Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N=274). These SNPs were variable both in wild (HE=0.107) and domestic cats (HE=0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise FCT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average FCT>0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest FCT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.
Data from: Biogeographic dating of speciation times using paleogeographically informed processes
Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth's history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
Data from: Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus
A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely un-investigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6,172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3,256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
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: Does wildlife resource selection accurately inform corridor conservation?
Evaluating landscape connectivity and identifying and protecting corridors for animal movement have become central challenges in applied ecology and conservation. Currently, resource selection analyses are widely used to focus corridor planning where animal movement is predicted to occur. An animal's behavioural state (e.g. foraging, dispersing) is a significant determinant of resource selection patterns, yet has largely been ignored in connectivity assessments. We review 16 years of connectivity studies employing resource selection analysis to evaluate how researchers have incorporated animal behaviour into corridor planning, and highlight promising new approaches for identifying wildlife corridors. To illustrate the importance of behavioural information in such analyses, we present an empirical case study to test behaviour-specific predictions of connectivity with long-distance dispersal movements of African wild dogs Lycaon pictus. We conclude by recommending strategies for developing more realistic connectivity models for future conservation efforts. Our review indicates that most connectivity studies conflate resource selection with connectivity requirements, which may result in misleading estimates of landscape resistance, and lack validation of proposed connectivity models with movement data. Our case study shows that including only directed movement behaviour when measuring resource selection reveals markedly different, and more accurate, connectivity estimates than a model measuring resource selection independent of behavioural state. Synthesis and applications. Our results, using African wild dogs as a case study, suggest that resource selection analyses that fail to consider an animal's behavioural state may be insufficient in targeting movement pathways and corridors for protection. This failure may result in misidentification of wildlife corridors and misallocation of limited conservation resources. Our findings underscore the need for considering patterns of animal movement in appropriate behavioural contexts to ensure the effective application of resource selection analyses for corridor planning.
Data from: Nest fidelity is driven by multi-scale information in a long-lived seabird
Although the reproductive success of most organisms depends on factors acting at several spatial scales, little is known about how organisms are able to synthesize multi-scale information to optimize reproduction. Using longitudinal data from a long-lived seabird, Monteiro's storm-petrel, we show that average breeding success is strongly related to oceanic conditions at the population level, and we postulate that (i) individuals use proximal information (their own reproduction outcome in year t) to assess the qualities of their mate and nest and to decide to retain them or not in year t + 1; (ii) the intensity of these responses depends on the quality of the oceanic environment in year t, which affects the predictability of reproduction outcome in year t + 1. Our results confirm that mate and nest fidelities are higher following successful reproduction and that the relationship between the success of a given pair and subsequent nest fidelity is stronger in years with unfavourable oceanic conditions, suggesting that individuals rely on distant information to modulate their use of proximal information and adjust their breeding strategy.
Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)
This investigation establishes the first sequence-based phylogenetic hypothesis of species relationships in the Coca family (Erythroxylaceae). We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that Neotropical Erythroxylum are monophyletic within the Paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense but relationships within this "coca" clade remain equivocal, suggesting a more complicated origin than Plowman's single-domestication hypothesis. Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.
Data from: Spatial dynamics of habitat use informs reintroduction efforts in the presence of an invasive predator
1. Islands experience major impacts from introduced species, especially nocturnal predators. The Brown Treesnake (Boiga irregularis) extirpated almost the entire native avifauna on Guam shortly after introduction. Reintroductions from neighboring islands can restore bird communities but will take place in heavily managed units where snake populations can be controlled. Yet reintroductions often proceed without relevant biological information such as nocturnal habitat and space use when nocturnal predators are present. To guide efforts, we studied diurnal and nocturnal habitat and space use by the avian frugivore community on the nearby island of Saipan where the snake is absent. 2. Using radio telemetry and a Bayesian framework, we first compared data typically accessible to resource managers (diurnal home range [DHR] and habitat selection) and which often forms the basis of reintroduction plans. We contrast this with data on nocturnal habitat use that is often not available but relevant when nocturnal predation threat is high. 3. DHR size varied within and among species with Micronesian Starlings (Aplonis opaca) having DHRs at least 45 ha larger than other species. For all species, night roost locations were generally spatially clustered within a DHR and covered a smaller spatial extent. Two species had higher probabilities of roosting outside DHR boundaries but, when outside, roosts were often within 200 m of the DHR boundary. All species selected forested habitats during day and night, with some species choosing native forest over non-native habitat. 4. Synthesis and applications If individuals roosted randomly throughout DHR's, landscape-level suppression of B. irregularis might be the only viable option for reintroductions of some species. However, individuals of all species showed clustered roosting and high site fidelity. If site fidelity is common, then individuals that roost within fenced areas where snake populations are severely reduced or eliminated will experience high survivorship even if DHRs extend into surrounding unprotected matrix. There was large overlap in habitat selection during day and night indicating managed areas should be composed of native forest with non-native forests of secondary importance. In systems with nocturnal predators, understanding variability in diurnal and nocturnal habitat use could lead to better informed decisions.
Data from: Plant population success across urban ecosystems – a framework to inform biodiversity conservation in cities
1. In a rapidly urbanising world, the ability of plant species to survive and build self-sustaining populations in urban environments is increasingly important for biodiversity conservation. Yet the contribution of cities to biodiversity conservation remains unclear because ecologists have studied biodiversity patterns, largely without considering the population establishment of plants and the ways in which different kinds of urban ecosystems harbour native and endangered plant species. These limitations can mislead conservation policies for cities. 2. To better-understand how urban ecosystems can contribute to biodiversity conservation, we propose a framework that links the population status (casual or established) of plant species with ecosystem novelty and highlights barriers to population establishment in different types of urban ecosystems, from natural remnants to novel ecosystems. 3. To quantify the relative importance of natural remnants vs. human-shaped ecosystems for the conservation of self-sustaining urban plant populations we re-analyse a unique dataset from a metropolitan region in Europe with information on the population status of 1199 plant species. 4. Results demonstrate that urban ecosystems harbour many established native and endangered species although a considerable share (37%) of species of conservation concern are confined to natural remnants. In hybrid and immature novel ecosystems, high species numbers reflect many species with only casual populations. The role of novel ecosystems as habitats for native and endangered plant species increases as novel ecosystems mature. 5. Synthesis and applications. General information about plant species richness in urban environments may mislead conservation policies as different kinds of urban ecosystems can play different roles in harbouring species of conservation concern. Moreover, presence-absence data can mask establishment failures of species. This proposed framework helps to distinguish between casual and established populations of plant species, and highlights barriers to population persistence in urban ecosystems; reflecting different land uses and land use histories over time. Revealing the role of natural remnants vs. hybrid vs. novel ecosystems as habitats for species of conservation concern illustrates opportunities for biodiversity conservation in all urban ecosystems and can support setting priorities for conservation.
Data from: How lovebirds maneuver through lateral gusts with minimal visual information
Flying birds maneuver effectively through lateral gusts, even when gust speeds are as high as flight speeds. What information birds use to sense gusts and how they compensate is largely unknown. We found that lovebirds can maneuver through 45-degree lateral gusts similarly well in forest, lake, and cave-like visual environments. Despite being diurnal and raised in captivity, the birds fly to their goal perch with only a dim point light source as a beacon, showing that they do not need optic flow or a visual horizon to maneuver. To accomplish this feat, lovebirds primarily yaw their bodies into the gust while fixating their head on the goal using neck angles of up to 30 degrees. Our corroborated model for proportional yaw reorientation and speed control shows how lovebirds can compensate for lateral gusts informed by muscle proprioceptive cues from neck twist. The neck muscles not only stabilize the lovebirds' visual and inertial head orientations by compensating low-frequency body maneuvers, but also attenuate faster 3D wingbeat-induced perturbations. This head stabilization enables the vestibular system to sense the direction of gravity. Apparently, the visual horizon can be replaced by a gravitational horizon to inform the observed horizontal gust compensation maneuvers in the dark. Our scaling analysis shows how this minimal sensorimotor solution scales favorably for bigger birds, offering local wind angle feedback within a wingbeat. The way lovebirds glean wind orientation may thus inform minimal control algorithms that enable aerial robots to maneuver in similar windy and dark environments.
Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach using SDMs based on marsh bird monitoring program data collected by citizen scientists and other participants following protocols specifically designed to maximize detections of species of interest at locations representative of the species range. We then used the SDMs to refine isotopic assignments of breeding areas of autumn-migrating and wintering Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow Rails (Coturnicops noveboracensis) based on feathers collected from individuals caught at various locations in the United States from Minnesota south to Louisiana and South Carolina. Sora were assigned to an area that included much of the western U.S. and prairie Canada, covering parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were assigned to a broad area along Hudson and James Bay in northern Manitoba and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and Michigan, including parts of the Mississippi and Atlantic Flyways. Virginia Rails were from several discrete areas, including parts of Colorado, New Mexico, the central valley of California, and southern Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study demonstrates extensive data from organized citizen science monitoring programs are especially useful for improving isotopic assignments of migratory connectivity in birds, which can ultimately lead to better informed management decisions and conservation actions.
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.