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Data from: Recent decreases in snow water storage in western North America
<p>We present long-term average and annual Snow Storage Index values over mountainous western North America, intended to represent the snow water storage capacity (and associated change) across the region. The Snow Storage Index represents the temporal phase difference between daily precipitation and surface water inputs – the sum of rainfall and snowmelt into the terrestrial systems – weighted by relative magnitudes. Different from snow water equivalent or snow fraction, the Snow Storage Index represents the degree to which the snowpack delays the timing and magnitude of surface water inputs relative to preciptiation, a fundamental component of how snow water storage influences the hydrologic cycle. Our analysis of a 64-year modeled dataset and 34-year observation dataset shows that the Snow Storage Index has decreased significantly across mountainous, western North America, due primarily to substantially earlier snowmelt and rainfall in spring months, with additional declines in winter precipitation. The Snow Storage Index and associated trends offer a new perspective on hydrologic sensitivity to climate change which have broad implications for water resources and ecosystems.</p>
Simulation code for: Clones on the run - the genomics of a recently expanded partially clonal species
<p class="MsoNormal"><span>Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasised that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (<em>Fucus vesiculosus</em>) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreased by drift following repeated bottlenecks at the expansion front. This resulted in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansions in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations. </span></p>
Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations
<p>SNP array data from our research article. It contains the SNP markers in common across the different Nile tilapia (Oreochromis niloticus) populations assessed in the study</p>
Can we collect health-related quality of life information from anticoagulated atrial fibrillation participants who have recently experienced a bleed? An observational feasibility study in primary, and secondary care and through an online forum
<p>The purpose of the study was to evaluate the feasibility of recruiting participants diagnosed with atrial fibrillation (AF) taking oral anticoagulation therapies (OACs) and recently experiencing a bleed to collect health-related quality of life (HRQoL) information.</p> <p><strong>Design</strong></p> <p>Observational feasibility study. The study aimed to determine the feasibility of recruiting participants with minor and major bleeds, the most appropriate route for recruitment and the appropriateness of the Patient Reported Outcome Measures (PROMs) selected for collecting HRQoL information in AF patients, and the preferred format of the surveys.</p> <p><strong>Setting</strong></p> <p>Primary care, secondary care, and via an online patient forum.</p> <p><strong>Participants</strong></p> <p>The study population was adult patients (≥ 18) with Atrial Fibrillation (AF) taking oral anticoagulation therapies (OATs) who had experienced a recent major or minor bleed within the last four weeks.</p> <p><strong>Primary and Secondary outcome measures</strong></p> <p>Primary outcome:</p> <p>Patient reported outcome measures (PROMs): EuroQol 5 dimensions-5 levels (EQ-5D-5L); Perception of anticoagulant treatment questionnaire, part 2 only (PACT-Q, part 2); Atrial fibrillation effect on quality of life (AFEQT)</p> <p>Secondary outcomes:</p> <p>Location of bleed; bleed severity; current treatment; patient perceptions of HRQoLin relation to bleeding events.</p> <p><strong>Results</strong></p> <p>We received initial expressions of interest from 103 participants. We subsequently recruited 32 participants to the study- 14 from primary care and 18 through the AF forum. No participants were recruited through secondary care. Despite 32 participants consenting, only 26 initial surveys were completed. We received follow-up surveys from 11 participants (8 primary care and 3 AF forum). COVID-19 had a major impact on the study. </p> <p><strong>Conclusions</strong></p> <p>Primary care was the most successful route for recruitment. Most participants recruited to the study experienced a minor bleed. Further ways to recruit in secondary care should be explored, especially to capture more serious bleeds. </p> <p><strong>Registration</strong></p> <p>The study was adopted onto the NIHR Portfolio (I.D. #47771) and registered with www.ClinicalTrials.gov (#NCT04921176) in February 2021.</p> <p>Dataset contains all anonymised data for the participants who completed the survey including demographics, details of bleeds, co-morbidities and completed patient reported outcomes</p>
Figure 4. A in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 4. A. Holotype adult Hyposmocoma desilvai sp. n., DR21D16E.1, DNA00252, reared from a "cigar" type case from Kamehamenui FR. B. Female genitalia of same specimen, slide KAA0902. C. Holotype adult H. makaohuna, DR21D16A.E3, DNA00255, reared from a "candywrapper" type case from Kamehamenui FR. D. Fe- male genitalia of same specimen, slide KAA0901. Abbreviations: pa = papilla anales, IX = segment IX.
Figure 3. A in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 3. A. Paratype adult of Hyposmocoma kukilakila sp. n., DR21D16B.E1, DNA00228, reared from a "tiny burrito" type case from Kamehamenui FR. B. Female genitalia of same specimen, slide KAA0899. C. Male genitalia, tegumen, ventral view, paratype slide KAA0960. D. Male genitalia, valvae and aedeagus, slide KAA0960, digitally dissected partial valvae with spurs intact below, paratype slide KAA0959. E. Pleural lobes on sternite VIII, slide KAA0959. F. Sternite sclerotization and protruding sternite hook on segment VII, slide KAA0959. Abbreviations: lb = left brachium, rb = right brachium, st = sterigma, sp = spur, la = left anellus lobe, ph = phallus, ra = right anellus lobe, ss = sternite sclerotization, rsh = right sternite hook.
Figure 6 in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 6. Larval cases of the new species, all to same scale. A. Hyposmocoma makaohuna, rearing lot DR21D16A, B. H. kamehamenui, rearing lot DR21D16B, C. H. desilvai, larval case of holotype (note case openings on both ends), D. H. starrorum, rearing lot DR21E1A (single case opening), E. H. kukilakila, rearing lot DR21D16B.
Figure 2 in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 2. Hyposmocoma starrorum sp. n. A. Holotype adult male DR21E1A.E8, DNA00319, reared from a "burrito" type case from Kamehamenui FR. B. Female genitalia, slide KAA0898. C. Male holotype genitalia, valvae and tegumen (right bra- chium folded over right valva), slide KAA0897. D. Phallus and ductus ejaculatorius, slide KAA0897. E. Sternite hooks on segment VII, slide KAA0897. F. Pleural lobes on sternite VIII. Abbreviations: sp = spur, la = left anellus lobe, ra = right anellus lobe, lb = left brachium, rb = right brachium, cp = costal process, o = ostium, st = sterigma, lsh = left sternite hook, rsh = right sternite hook.
Figure 1 in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 1. Map of East Maui with the 3,433 acres of Kamehamenui Forest Reserve indicated in red. Map tiles by Stamen Design, under CC BY 3.0. Data by Open- StreetMap, under ODbL.
Figure 5. A in Five New Species of Hawaiian Endemic Fancy Case Caterpillars from a Recently Established Forest Reserve on Maui (Cosmopterigidae: Hyposmocoma)
Figure 5. A. Holotype adult of H. kamehamenui, DR21D16B.E2, DNA00249, reared from a "burrito" type case from Kamehamenui FR. B. Male genitalia of same speci- men, tegumen and brachia, lateral view, slide KAA0900. C. Phallus, same specimen. D. Valvae, same specimen. E. Pleural lobes, same specimen. Abbreviations: rb = right brachium, t = tegumen, sp = spur, ph = phallus.
Higher plant colonisation and lower resident diversity in grasslands more recently abandoned from agriculture
<p>1. Rates of species colonisation and extirpation are increasing in plant communities worldwide. Colonisation could potentially help compensate for, or compound, resident diversity loss that results from global environmental change. 2. We use a multifactorial seed addition grassland experiment to examine relationships between plant colonisation, resident species diversity and key community assembly factors over three years. By manipulating colonist seed rate, imposing disturbance and examining abundance and diversity impacts of 14 formerly absent sown colonists in communities that varied in successional stage and time since agricultural abandonment, we were able to disentangle effects of global change factors (species introduction, novel disturbance and land use change) that are usually confounded. 3. Evidence suggested that cover abundance of sown colonists was most strongly influenced by successional stage of recipient communities, though number of growing seasons was also important for the group of seven colonists with resource conservative "slow" life history traits. Colonist type, seed rate and disturbance had weaker relationships with colonist cover. 4. Factors affecting sown colonist cover were highly conditional. A negative relationship between plot-level disturbance and colonist cover in early successional communities meant that, despite a positive relationship in late succession, colonisation was negatively related to disturbance overall, defying theoretical expectations. 5. Non-sown resident diversity was negatively related to colonist cover and positively related to successional stage. Resource acquisitive colonists with "fast" life history traits appeared to limit cover of "slow colonists" when the two groups were sown together, likely reflecting niche pre-emption. 6. Communities at earlier stages of succession had lower resident diversity and experienced higher levels of colonisation than communities at later stages of succession. Elevated colonisation and lower resident diversity both appeared to be symptoms of human-induced land use change. However, results suggested that resource competition from plant colonists may also limit resident diversity in grasslands abandoned from agriculture more recently. Synthesis: Our findings point to the importance of resource availability and competition on plant colonisation and colonist impacts on residents. Although colonisation is potentially a source of biodiversity in the short-term, our results suggest that plant colonists that reach high abundance may be a further threat to resident plant diversity in secondary grasslands recovering from a recent history of agriculture.</p>
Data from: Accelerating local extinction associated with very recent climate change
<p>Climate change has already caused local extinction in many plants and animals, based on surveys spanning many decades. As climate change accelerates, the pace of these extinctions may also accelerate, potentially leading to large-scale, species-level extinctions. We tested this hypothesis in a montane lizard. We resurveyed 18 mountain ranges in 2021–2022 after only ~7 years. We found rates of local extinction among the fastest ever recorded, which have tripled in the past ~7 years relative to the preceding ~42 years. Further, climate change generated local extinction in ~7 years similar to that seen in other organisms over ~70 years. Yet, contrary to expectations, populations at two of the hottest sites survived. We found that genomic data helped predict which populations survived and which went extinct. Overall, we show the increasing risk to biodiversity posed by accelerating climate change, and the opportunity to study its effects over surprisingly brief timescales.</p>
Host-associated genetic differentiation and origin of a recent host shift in the generalist parasitic weed Phelipanche ramosa
<p>The branched broomrape, <em>Phelipanche ramosa</em> (L.) Pomel, is a parasitic weed that can infest several crops, notably tobacco, hemp and tomato. In western France, it has recently adapted to a new host, oilseed rape. We collected <em>P. ramosa</em> samples from fields cultivated with six different crops across Europe. Data from SSR markers and DNA sequences showed strong host-associated genetic differentiation.</p> <p>File SSRdata-Pramosa1611.txt contains sampling locations, host crops and microsatellite genotypes.</p> <p>Files BO1aligned.fas, ITSaligned.fas, RPL16aligned.fas and trnKtrnQaligned.fas contain aligned DNA sequences.</p>
FIGURE 7 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 7 Enlarged section of the Maximum-likelihood phylogenetic reconstruction of fig. 6, with all COI sequences shown for the sericatus group, i.e., P. thebeatles, P. medius, and P. sericatus. Colours match those in fig. 5.
FIGURE 4 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 4 Dorsal (perpendicular to the surface of the aedeagus between the orifice and the apex) and lateral views of the apices of the aedeagi of members of the Ptomaphagus sericatus complex. a: P. medius from Oegstgeest, the Netherlands, dorsal (a) and lateral (b) views. b: P. sericatus from Les Arnoulats, France, dorsal (c) and lateral (b) views. c: P. thebeatles from Amsterdam, the Netherlands, dorsal (e) and lateral (f) views. (Images derived from topotypical material, not from the holotype itself.).
FIGURE 2 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 2 Neotype of P. sericatus from Kiev, Ukraine: a, habitus; b, aedeagus, dorsal view (angle of view somewhat more rostral than in fig. 4); c, aedeagus, lateral view; d, genital segment; e, labels.
FIGURE 3 Antennomeres 1-7 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 3 Antennomeres 1-7 for members of the Ptomaphagus sericatus complex. a: P. sericatus, female (a) and male (b) from Les Arnoulats, France. b: P. thebeatles, female (c) from Middelburg, the Netherlands, and male (d) from Schiedam, the Netherlands. After Schilthuizen, 1989. c: P. medius, female (e) from Nieuw & St. Joostland, the Netherlands, and male (f) from Oostvoorne, the Netherlands. After Schilthuizen, 1989.
FIGURE 5 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 5 Distribution map of the specimens studied for this paper (the extralimital specimens of P. medius in Canada have not been included). The white arrows point at records that we interpret as recent range expansions.
FIGURE 6 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)
FIGURE 6 Maximum-likelihood phylogenetic reconstruction, based on COI sequences, of P. thebeatles, P. medius, P. sericatus, and other members of the subgenus Ptomaphagus s. str., rooted with P. (Adelops) hatchi. Multiple sequences per species have been collapsed. Support values are given only for branches with>80% bootstrap percentage.
Figure 7 in Annotated checklist for fishes of the Main Nile Basin in the Sudan and Egypt based on recent specimen records (2006-2015)
Figure 7. – Males of Micropanchax species from the Nile. A-B: Micropanchax cf. or sp. aff. loati, Taraq Island, Lower Nile (9 Apr. 2008); C: Poropanchax cf. or sp. aff. normani., White Nile at Kosti (23 Jan. 2006).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.