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Figure 2 in Dental abnormalities in Myotis riparius (Chiroptera, Vespertilionidae), with comments on its evolutionary implications
Figure 2: Polyodontia due to the presence of an extra upper incisor in Myotis riparius (DZUP-CCMZ 498) from Paraná, Brazil: (A) occlusal view; (B) lateral view.
Figure 1 in Dental abnormalities in Myotis riparius (Chiroptera, Vespertilionidae), with comments on its evolutionary implications
Figure 1: Hypodontia due to the absence of the second upper premolar (P3) in Myotis riparius (USNM 338097) from Darién, Panama.
Figure 2 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 2: Cerdocyon thous present environmental niche models result maps. (A) South model. (B) Detail of model (A) for the province of La Rioja. (C) Complete model. (D) Detail of model (C) for the province of La Rioja. The color gradient indicates the suitability values, where white represents minimum values (0–10 %) and red the maximum values (76–100 %), as detailed in the figure.
Figure 1 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 1: New records Cerdocyon thous in La Rioja. (A–C) Photograps taken near Huaco River (2020–2021). (D) C. thous skin collected by Parodi in 1929, deposited as MACN 29.882 and label information.
Figure 3 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 3: Cerdocyon thous past environmental niche models for result maps. (A) Last interglacial model. (B) Last glacial maximum model. (C) Middle Holocene model. The color gradient indicates the suitability values, where white represents minimum values (0–10 %) and red the maximum values (76–100 %), as detailed in the figure.
Data and code for: Re-drawing Köppen-Geiger classes with microclimate: implications for nature and society
<p>Data and R code for reproducing analyses and visualizations for the paper:</p> <p>Klinges, D.H., Maclean, I.M.D., Scheffers, B.R. Re-drawing Köppen-Geiger classes with microclimate: implications for nature and society. <em>Frontiers in Ecology and the Environment </em>2024 (in press)</p>
Supplementary Data for Provenance, Environments, and Tectonic Signatures of Tanjong-Sandakan Formations, Northeast Sabah, Malaysia: Implications for Sedimentology, Palynology, and Geochemistry
<p>This dataset includes supplementary sedimentary facies tables and geochemical analysis data used in the manuscript titled <strong>Provenance, Environments, and Tectonic Signatures of Tanjong-Sandakan Formations, Northeast Sabah, Malaysia: Implications for Sedimentology, Palynology, and Geochemistry</strong>.</p>
Probing Spatial Variation in AFM-Measured Adhesion: Implication of Distributed Nanoscale Charge Heterogeneity
<p><span>The adhesion forces between a microsphere and a silica substrate were measured using AFM. NaCl solutions at concentrations of 0.001 M, 0.005 M, 0.01 M, 0.05 M, and 0.1 M were used sequentially to measure the adhesion forces. </span></p>
Iron Bonding with Light Elements: Implications for Planetary Cores Beyond the Binary System
<p>X-ray Absorption Spectroscopy and DFT calculation dataset for Iron alloys at high pressures. <br><br></p> <p><strong>Abstract: </strong>Light element alloying in iron is required to explain density deficit and seismic wave velocities in Earth’s core. However, the light element composition of the Earth’s core seems hard to constrain as nearly all light element alloying would reduce the density and sound velocity (elastic moduli). The alloying light elements include oxidizing elements like oxygen and sulfur, and reducing elements like hydrogen and carbon, yet their chemical effects in alloy system are less discussed. Moreover, Fe-X-ray Absorption Near Edge Structure (Fe-XANES) fingerprints have been studied for silicate materials with ferrous and ferric ions, while not many X-ray absorption spectroscopy (XAS) studies have focused on iron alloys, especially at high pressures. To investigate the bonding nature of iron alloys in planetary interiors, we presented X-ray absorption spectroscopy of iron-nitrogen and iron-carbon alloys at high pressure up to 50 GPa. Together with existing literature on iron-carbon, -hydrogen alloys, we analyzed their edge positions and found no significant difference of degree of oxidation among these alloys. Pressure effects on edge positions were also found negligible. Our theoretical simulation of the valence state of iron, alloyed with S, C, O, N, P also showed nearly unchanged behavior under pressures up to 300 GPa. This indicates the high pressure bonding of iron alloyed with light elements closely resembles bonding at the ambient conditions. We suggest that the chemical properties of light elements constrain which ones can coexist within iron alloys.<span> </span></p>
Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon
Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometers, have become increasingly valuable in the presence of climate change, increasing hatchery production, and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive datasets from spawning populations originating from across the species? range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multi-national applications because they are easily shared, require little inter-laboratory standardization, and can be assayed through increasingly efficient technologies. Here we discuss the development of a dataset for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A dataset spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the dataset, variable linkage relationships between SNPs associated with ancestral groupings, and outlier loci with alleles associated with latitude.
Data from: Population structure of riverine and coastal dolphins Sotalia fluviatilis and Sotalia guianensis: PATTERNS of nuclear and mitochondrial diversity AND implications for conservation
Coastal and freshwater cetaceans are particularly vulnerable due to their proximity to human activity, localized distributions and small home ranges. These species include Sotalia guianensis, found in the Atlantic and Caribbean coastal areas of central and South America, and Sotalia fluviatilis, distributed in the Amazon River and tributaries. We investigated the population structure and genetic diversity of these two species by analyses of mtDNA control region and 8-10 microsatellite loci. MtDNA analyses revealed strong regional structuring for S. guianensis (i.e. Colombian Caribbean vs. Brazilian Coast, FST= 0.807, ΦST = 0.878, P <0.001) especially north and south of the Amazon River mouth. For S. fluviatilis, population structuring was detected between the western and eastern Amazon (i.e. Colombian Amazon vs. Brazilian Amazon, FST= 0.085, ΦST = 0.277, P <0.001). Haplotype and nucleotide diversity were higher for S. fluviatilis. Population differentiation was supported by analysis of the microsatellite loci (S. guianensis, northern South America vs. southern South America FST= 0.275, Jost´s D = 0.476, P<0.001; S. fluviatilis, western and eastern Amazon FST= 0.197, Jost´s D = 0.364, P<0.001). Most estimated migration rates in both species overlapped with zero, suggesting no measurable migration between most of the sampling locations. However, for S. guianensis, there was measurable migration in neighboring sampling locations. These results indicate that the small home ranges of these species may act to restrict gene flow between populations separated by relatively short distances, increasing the risk of extirpation of some localized populations in the future if existing threats are not minimized.
Data from: Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation
Once widely distributed throughout Africa, cheetahs (Acinonyx jubatus) occur today within fragmented populations and are listed as vulnerable by the IUCN. Botswana currently hosts the second largest cheetah population throughout the species' range. This study initiated a molecular genetic survey of wild Botswana cheetah populations. It focused on the relatedness within presumed social groups using 14 microsatellite markers and revealed a higher proportion of unrelated male coalitions than was expected. Based on the unrelated cheetahs only, the estimation of the genetic variation corresponded with results from recent studies on different African populations. The analysis of unrelated individuals indicated limited genetic differentiation between cheetahs from different regions of Botswana. This suggests that the Botswana cheetah population might represent a unique panmictic population as long as sufficient levels of gene flow are maintained within the distribution range. This baseline information will now be incorporated to develop management strategies and set priorities for cheetah conservation in Botswana.
Data from: Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot
The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.
Data from: Manipulation of habitat isolation and area implicates deterministic factors and limited neutrality in community assembly
Theory predicts deterministic and stochastic factors will contribute to community assembly in different ways: environmental filters should regulate those species that establish in a particular area resulting in the ecological requirements of species being the primary driver of species distributions, while chance and dispersal limitation should dictate the likelihood of species reaching certain areas with the ecology of species being largely neutral. These factors are specifically relevant for understanding how the area and isolation of different habitats or islands interact to affect community composition. Our review of the literature found few experimental studies have examined the interactive effect of habitat area and isolation on community assembly, and the results of those experiments have been mixed. We manipulated the area and isolation of rock 'islands' created de novo in a grassland matrix to experimentally test how deterministic and stochastic factors shape colonizing animal communities. Over 64 weeks, the experiment revealed the primacy of deterministic factors in community assembly, with habitat islands of the same size exhibiting remarkable consistency in community composition and diversity, irrespective of isolation. Nevertheless, tangible differences still existed in abundance inequality among taxa: large, near islands had consistently higher numbers of common taxa compared to all other island types. Dispersal limitation is often assumed to be negligible at small spatial scales, but our data shows this not to be the case. Furthermore, the dispersal limitation of a subset of species has potentially complex flow-on effects for dictating the type of deterministic factors affecting other colonising species.
Data from: Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: implications for vector control
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine scale spatial resolution of genetic structure of G. f. fuscipes from 42 sampling sites from the northern region of Uganda where a merger of the two disease belts is feared. Based on microsatellite analyses, we found that G. f. fuscipes in northern Uganda are structured into three distinct genetic clusters with varying degrees of interconnectivity among them. Based on genetic assignment and spatial location, we grouped the sampling sites into four genetic units corresponding to northwestern Uganda in the Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage, western Uganda in the Victoria Nile drainage, and a transition zone between the two northern genetic clusters characterized by high level of genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm model as most consistent with tsetse genotypes in these admixed samples. Results of mtDNA analyses revealed the presence of 30 haplotypes representing three main haplogroups, whose location broadly overlaps with the microsatellite defined clusters. Migration analyses based on microsatellites point to moderate migration among the northern units located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga drainages, but not between the northern units and the Victoria Nile drainage in the west. Effective population size estimates were variable with low to moderate sizes in most populations and with evidence of recent population bottlenecks, especially in the northeast unit of the Lake Kyoga drainage. Our microsatellite and mtDNA based analyses indicate that G. f. fuscipes movement along the Achwa and Okole rivers may facilitate northwest expansion of the Rhodesiense disease belt in Uganda. We identified tsetse migration corridors and recommend a rolling carpet approach from south of Lake Kyoga northward to minimize disease dispersal and prevent vector re-colonization. Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control.
Data from: Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: implications for the conservation and management of Vulnerable Marine Ecosystems
Deep-sea stony corals, which can be fragile, long-lived, late to mature and habitat-forming, are defined as vulnerable marine ecosystem indicator taxa. Under United Nations resolutions these corals require protection from human disturbance such as fishing. To better understand the vulnerability of stony corals (Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) to disturbance within the New Zealand region, and to guide marine protected area design, genetic structure and connectivity were determined using microsatellite loci and DNA sequencing. Analyses compared population genetic differentiation between two biogeographic provinces, amongst three sub-regions (north-central-south), and amongst geomorphic features. Extensive population genetic differentiation was revealed by microsatellite variation, whilst DNA sequencing revealed very little differentiation. For G. dumosa, genetic differentiation existed amongst regions and geomorphic features, but not between provinces. For M. oculata, only a north-central-south regional structure was observed. For S. variabilis, genetic differentiation was observed between provinces, amongst regions and amongst geomorphic features. Populations on the Kermadec Ridge were genetically different from Chatham Rise populations in all three species. A significant isolation-by-depth pattern was observed for both marker types in G. dumosa, and also in ITS of M. oculata. An isolation-by-distance pattern was revealed for microsatellite variation in S. variabilis. Medium to high levels of self-recruitment were detected in all geomorphic populations, and rates and routes of genetic connectivity were species-specific. These patterns of population genetic structure and connectivity at a range of spatial scales indicate that flexible spatial management approaches are required for the conservation of deep-sea corals around New Zealand.
Data from: Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation
Ecological selection against hybrids between populations occupying different habitats might be an important component of reproductive isolation during the initial stages of speciation. The strength and directionality of this barrier to gene flow depends on the genetic architecture underlying divergence in ecologically relevant phenotypes. We here present line cross analyses of inheritance for two key foraging-related morphological traits involved in adaptive divergence between stickleback ecotypes residing parapatrically in lake and stream habitats within the Misty Lake watershed (Vancouver Island, Canada). One main finding is striking genetic dominance of the lake phenotype for body depth. Selection associated with this phenotype against first and later generation hybrids should therefore be asymmetric, hindering introgression from the lake to the stream population but not vice versa. Another main finding is that divergence in gill raker number is inherited additively and should therefore contribute symmetrically to reproductive isolation. Our study suggests that traits involved in adaptation might contribute to reproductive isolation qualitatively differently, depending on their mode of inheritance.
Data from: Mitochondrial genetic structure and matrilineal origin of white sharks, Carcharodon carcharias, in the Northeastern Pacific: implications for their conservation
White sharks (Carcharodon carcharias, WS henceforth) are globally and regionally threatened. Understanding their patterns of abundance and connectivity, as they relate to habitat use, is central for delineating conservation units and identifying priority areas for conservation. We analyzed mitochondrial data to test the congruence between patterns of genetic connectivity and of individual movements in the Northeastern Pacific (NEP) and to trace the matrilineal origin of immature WS from coastal California and Baja California to adult aggregation areas. We analyzed 186 mitochondrial control region sequences from sharks sampled in Central California (CC; n = 61), Southern California Bight (SCB; n = 25), Baja California Pacific coast (BCPC; n = 9), Bahía Vizcaíno (BV; n = 39), Guadalupe Island (GI; n = 45), and the Gulf of California (GC; n = 7). Significant mitochondrial differentiation between adult aggregation areas (CC, GI) revealed two reproductive populations in the NEP. We found general concordance between movement patterns of young and adult WS with genetic results. Young sharks from coastal California and Baja California were more likely born from females from GI. Mitochondrial differentiation of young-of-the-year from SCB and BV suggests philopatry to nursery areas in females from GI. These results provide a genetic basis of female reproductive behavior at a regional scale and point to a preponderance of sharks from GI in the use of the sampled coastal region as pupping habitat. These findings should be considered in Mexican and US management and conservation strategies of the WS NEP population.
Data from: Impact of habitat fragmentation on the spatial structure of the Eastern Arc Forests in East Africa: implications for biodiversity conservation
The Eastern Arc Mountains in Tanzania and Kenya are one of 35 global biodiversity hotspots. The Eastern Arc forests are, as are many other tropical biodiversity hotspots, highly fragmented. Understanding the impact of habitat fragmentation (i.e., habitat loss and subdivision) on the spatial structure of the Eastern Arc forests is important because forest spatial structure highly influences species richness, persistence, and extinction debt. Here we examine the impact of habitat fragmentation on the spatial structure of the Eastern Arc forests at a patch scale using very high resolution aerial imagery having a spatial resolution of 0.5–1.5 m. Forest area across the 13 Eastern Arc Mountains is 405,852 ha and is distributed into 311 fragments ≥ 10 ha in size with a median fragment size of 84 ha. The 18 largest forest fragments in the Eastern Arc Mountains contain greater than three-quarters of total forest area. Average fragment isolation, as assessed by median distance to nearest fragment and median distance to the nearest larger fragment, is 867 and 1533 m, respectively. Of total forest area, 14% is < 100 m from the forest edge and 33% is < 300 m from the forest edge. Establishing forested linkages among the largest and closest forest fragments through forest regeneration and protection of secondary regenerating forest as well as providing protected area status to the remaining non-protected forest including unprotected smaller forest fragments are important to enhancing the long-term persistence of many plant and animal species here.
Data from: Synchrotron-X-ray absorption spectroscopy of melanosomes in vertebrates and cephalopods: implications for the affinity of Tullimonstrum
Screening pigments are essential for vision in animals. Vertebrates utilise melanins bound in melanosomes as screening pigments, whereas cephalopods are assumed to use ommochromes. Preserved eye melanosomes in the controversial fossil Tullimonstrum (Mazon Creek, Illinois) display size-and/or shape-specific are present in geometrically distinct layers that resemble tissue-specific melanosome populations considered unique to the vertebrate eye. Here, we show that extant cephalopod eyes also show tissue-specific size- and/or shape-specific partitioning of melanosomes; these differ from vertebrate melanosomes in the relative abundance of trace metals and in the binding environment of Cu. Chemical signatures of melanosomes in the eyes of Tullimonstrum more closely resemble those of modern cephalopods than those of vertebrates, suggesting that an invertebrate affinity for Tullimonstrum is plausible. Melanosome chemistry may thus provide insights into the phylogenetic affinities of enigmatic fossils where melanosome size and/or shape is are equivocal.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.