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Data from: A new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed models
Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics mostly uses landscape resistance surfaces and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of resistance surfaces is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix resistance surfaces were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between landscape predictor variables and genetic distances was then assessed following a mixed modeling approach to account for the non-independence of values in distance matrices. Subsequently, predictor variables were selected making use of the R_β^2 statistic. We applied LCTA and the mixed model approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis and showed that LCTA not only outperforms existing methods in a statistical way, but also provides more information about the migration ecology of the focal species. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed.
Data from: Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City
We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are "urban adapters" that occur at higher population densities as habitat fragments are reduced in area, but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in fourteen NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and BAPS. Analysis of molecular variance revealed that genetic differences between populations separated by a few km are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation-by-distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
Data from: A new ophthalmosaurid ichthyosaur from the early Cretaceous of Colombia
Cretaceous ichthyosaurs were relatively diverse in temperate latitudes, but few species have been described from the palaeotropics. Here, we describe a new ophthalmosaurid ichthyosaur, Muiscasaurus catheti gen. et sp. nov., from the Barremian–Aptian aged Paja Formation of Colombia. This species is known only from a partial skull and differs from all other ichthyosaurs in the unusual configuration of the external narial opening, slender rostrum, narrow postorbital region, and gracile dentition. It is the second ichthyosaur described from the Paja Formation, suggesting moderate taxonomic and ecological ichthyosaur diversity in the region during the Early Cretaceous.
Data from: The past ecology of Abies alba provides new perspectives on future responses of silver fir forests to global warming
Paleoecology can provide valuable insights into the ecology of species that complement observation and experiment-based assessments of climate-impact dynamics. New paleoecological records (e.g. pollen, macrofossils) from the Italian Peninsula suggest a much wider climatic niche of the important European tree species Abies alba (silver fir) than observed in its present spatial range. To explore this discrepancy between current and past distribution we analyse climatic data (e.g. temperature, precipitation, frost, humidity, sunshine) and vegetation-independent paleoclimatic reconstructions (e.g. lake levels, chironomids) and use global coupled carbon-cycle climate (NCAR CSM1.4) and dynamic vegetation (LANDCLIM) modelling. The combined evidence suggests that during the mid-Holocene (ca. 6000 years ago), prior to humanization of vegetation, A. alba formed forests under conditions that exceeded modern (1961-1990) upper temperature limit of the species by ca. 5-7 {degree sign}C (July means). Annual precipitation during this natural period was comparable to today (>700-800 mm), with drier summers and wetter winters. In the meso-mediterranean to sub-mediterranean forests A. alba co-occurred with thermophilous taxa such as Quercus ilex, Q. pubescens, Olea europaea, Phillyrea, Arbutus, Cistus, Tilia, Ulmus, Acer, Hedera helix, Ilex aquifolium, Taxus, and Vitis. Results from the last interglacial (ca. 130,000-115,000 BP), when human impact was negligible, corroborate the Holocene evidence. Thermophilous Mediterranean A. alba stands became extinct during the last 5000 years when land-use pressure and specifically excessive anthropogenic fire and browsing disturbance increased. Our results imply that the ecology of this key European tree species is not yet well understood. On the basis of the reconstructed realized climatic niche of the species, we anticipate that the future geographic range of A. alba may not contract regardless of migration success, even if climate should become significantly warmer than today with summer temperatures increasing by up to 5-7{degree sign}C, as long as precipitation does not fall below 700-800 mm/year, and disturbance (e.g. fire, browsing) does not become excessive. Our finding contradicts recent studies that projected range contractions under global-warming scenarios, but did not factor how millennia of human impacts reduced the realized climatic niche of A. alba.
Data from: A new small captorhinid reptile from the lower Permian of Oklahoma and resource partitioning among small captorhinids in the Richards Spur fauna
Two partial reptile skulls and six dentigerous fragments from the lower Permian Richards Spur locality of Oklahoma represent a new genus and species of small captorhinid reptile. Labidosauriscus richardi gen. et sp. nov. is distinguished from other captorhinids in the reduction of the height of the ridges forming the characteristic net-like, ridge-and-pit cranial sculpturing of captorhinids, and the superimposition of a system of finer pits and furrows over the primary ridge-and-pit cranial ornamentation. Labidosauriscus richardi shares with C. laticeps a post-caniniform tooth morphology characterized by convex mesial and distal carinae that form a distinctly asymmetrical apex in labial aspect. The description of L. richardi brings to six the number of captorhinid species known from the productive Richards Spur fissure-fill locality. Each of these species exhibits a distinctive post-caniniform tooth morphology (or multiplication of these teeth), which is consonant with the hypothesis of resource partitioning among the small faunivorous and omnivorous captorhinids at Richards Spur. As an 'exhumed early Permian hill,' Richards Spur provides a unique window into early reptile diversification in a distinctive upland environment that is rarely preserved in the tetrapod fossil record.
Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar 'urban adapter'. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Data from: A conifer–angiosperm divergence in the growth vs shade tolerance trade-off underlies the dynamics of a New Zealand warm-temperate rain forest
1. A central tenet of forest ecology is that succession and regeneration dynamics are driven by an interspecific trade-off between juvenile growth rates in high light and shade tolerance. There is evidence, however, that a single trade-off axis may fail to explain the dynamics of mixed conifer-angiosperm rainforests in the southern hemisphere, especially in New Zealand. 2. We tested for growth vs shade tolerance trade-offs by measuring juvenile growth of five podocarps and five broadleaved canopy angiosperms across a wide range of light environments in a New Zealand warm-temperate rainforest. The light compensation point of growth was used as a measure of species light requirements, which we then compared with height growth in 10% light, approximating the environments encountered beneath small tree-fall gaps. 3. Despite considerable overlap between the ranges of both growth rates and compensation points found in the two lineages, major axis tests showed that the growth vs shade tolerance trade-off differed significantly between podocarp and angiosperm species. At a common compensation point, angiosperms were faster-growing than podocarps in 10% light. However, juveniles of these angiosperm species were notably scarce in the more open environments associated with forest margins. 4. Synthesis. A conifer–angiosperm divergence in the growth vs shade tolerance trade-off may explain long-standing problems of the dynamics of these forests. Although juveniles of most lowland podocarps can tolerate considerable shade, the more vigorous response of broadleaved angiosperms to small canopy openings enables them to out-compete podocarps in old-growth stands. The greater abundance of podocarp juveniles on forest margins cannot be attributed to them outcompeting angiosperm species where light is abundant, and is likely to reflect superior resistance to frost and/or drought. The drivers of the dynamics of New Zealand's podocarp–broadleaved forests therefore differ appreciably from those ascribed to tropical and north-temperate forests.
Data from: New record of Egertonia (Elopiformes, Phyllodontidae) from the Late Cretaceous of South India
We report a new occurrence of the phyllodontid teleost fish Egertonia from the Late Cretaceous Kallamedu Formation of the Cauvery Basin, South India. This is the oldest occurrence of Phyllodontidae in India, and only the second Cretaceous Gondwanan occurrence of this genus, following a toothplate previously described from the Late Cretaceous Maevarano Formation, Madagascar. The presence of phyllodontid fish supports a fluvial–deltaic or brackish environment for the lower part of the Kallamedu Formation, a rich deposit including typically Gondwanan taxa, such as simosuchid crocodiles, bothremydid turtles and abelisaurid dinosaurs, as well as an anomalous troodontid dinosaur. Egertonia adds another taxon of primarily Laurasian distribution to the Kallamedu fauna and further expands the list of taxa known from the Late Cretaceous of both India and Madagascar, strengthening the degree of faunal similarity between the two landmasses in the latest Cretaceous.
Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites
We used a high density SNP array to genotype 75 P. falciparum isolates recently collected from Senegal and The Gambia in order to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors.
Data from: Genetic evidence of a population bottleneck and inbreeding in the endangered New Zealand sea lion, Phocarctos hookeri
The New Zealand sea lion (NZSL) is of high conservation concern due to its limited distribution and its declining population size. Historically it occupied most of coastal New Zealand, but is now restricted to a few coastal sites in southern mainland New Zealand and the sub-Antarctic Islands. NZSLs have experienced a recent reduction in population size due to sealing in the 1900s, which is expected to have resulted in increased inbreeding and a loss of genetic variation, potentially reducing the evolutionary capacity of the species and negatively impacting on its long-term prospects for survival. We used 17 microsatellite loci, previously shown to have cross-species applications in pinnipeds, to determine locus- and population-specific statistics for 1205 NZSLs from seven consecutive breeding seasons. We show that the NZSL population has a moderate level of genetic diversity in comparison to other pinnipeds. We provide genetic evidence for a population reduction, likely caused by historical sealing, and a measure of allele sharing/parental relatedness (internal relatedness, IR) that is suggestive of increased inbreeding in pups that died during recent epizootic episodes. We hypothesise that population bottlenecks and non-random mating have impacted on the population genetic architecture of NZSLs, affecting its population recovery.
Data from: Population genetics of Setaria viridis, a new model system
An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production, and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a world-wide sample of more than 200 S. viridis accessions, using the genotyping by sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate, and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modeled demographic history and show signal of recent population decline in one subgroup. Finally we show linkage disequilibrium decay is rapid (less then 45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genome-wide association studies.
Data from: What can multiple phylogenies say about the latitudinal diversity gradient? A new look at the tropical conservatism, out-of-the-tropics, and diversification rate hypotheses
We reviewed published phylogenies and selected 111 phylogenetic studies representing mammals, birds, insects, and flowering plants. We then mapped the latitudinal range of all taxa to test the relative importance of the tropical conservatism, out of the tropics, and diversification rate hypotheses in generating latitudinal diversity gradients. Most clades originated in the tropics, with diversity peaking in the zone of origin. Transitions of lineages between latitudinal zones occurred at 16–22% of the tree nodes. The most common type of transition was range expansions of tropical lineages to encompass also temperate latitudes. Thus, adaptation to new climatic conditions may not represent a major obstacle for many clades. These results contradict predictions of the tropical conservatism hypothesis (i.e., few clades colonizing extratropical latitudes), but support the out-of-the-tropics model (i.e., tropical originations and subsequent latitudinal range expansions). Our results suggest no difference in diversification between tropical and temperate sister lineages; thus, diversity of tropical clades was not explained by higher diversification rates in this zone. Moreover, lineages with latitudinal stasis diversified more compared to sister lineages entering a new latitudinal zone. This preserved preexisting diversity differences between latitudinal zones and can be considered a new mechanism for why diversity tends to peak in the zone of origin.
Data from: Below-ground causes and consequences of woodland shrub invasions: a novel paired-point framework reveals new insights
1. Confirming the impacts of invasive plants is essential for prioritizing management efforts, but is challenging, especially if impacts occur below ground and over long periods as hypothesized for woodland shrub invasions. 2. For this reason, we developed a novel "paired-point" framework capable of detecting the below-ground impacts of slow-growing invasive plants from short-term datasets in an investigation into the below-ground consequences of European buckthorn Rhamnus cathartica L. (hereafter buckthorn) invasions into Chicago-area woodlands. We measured differences between the members of 97 pairs of buckthorn-invaded and buckthorn-free points in ten below-ground response variables (RVs) that buckthorn is hypothesized to alter (listed below). We then modelled these differences (ΔRVs) in response to the severity of the invasion found at each invaded point. A relationship (linear or non-linear) between a ΔRV and severity, i.e. slope ≠ 0, suggests a buckthorn-induced change. An intercept (value of ΔRV where severity = 0) different from zero suggests a pre-existing difference. 3. Relating differences to an invasion gradient rather than simply noting their presence provided evidence that the higher levels of moisture, pH, total C, total N, NH4+-N, and Ca2+ in invaded soils pre-date and possibly promote invasion (particularly Ca2+), and that neither earthworm biomass nor soil C:N ratios are associated with buckthorn invasion, all of which suggest buckthorn to be less of a "driver" of below-ground change than hypothesized. We did, however, find evidence that buckthorn establishes in areas having greater leaf-litter mass and higher rates of decomposition, and then proceeds to accelerate decomposition further and to alter spring soil NO3--N levels. 4. Synthesis and applications. Our findings suggest that decisions regarding regional buckthorn management should be less driven by concerns about buckthorn's below-ground impacts, and that greater consideration of how variation in below-ground factors relates to invader establishment is needed, rather than simply assuming this variation to be invader-induced. This latter consideration can help to design better-targeted monitoring programs, limiting the further spread of woodland invaders. These insights illustrate the utility of the paired-point framework both for investigating below-ground causes and consequences of slow-growing invasive plants and for guiding the management of these invasions.
Data from: Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara desert
The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.
Data from: Polyphyly of Mesadenus (Orchidaceae, Spiranthinae) and a new genus from the Espinhaço Range, Southeastern Brazil
Mesadenus displays an odd disjunction, with most species found in the southeastern USA, the Caribbean, and Mexico south to El Salvador, and two outliers occurring in southeastern Brazil. A recent molecular phylogenetic study showed that, as currently delimited, Mesadenus is polyphyletic, and further study of this little-known genus is required. Here we assessed relationships in Mesadenus and to other genera conducting a cladistic parsimony analysis of nucleotide sequences of nuclear (ITS) and plastid DNA (matK-trnK, trnL-trnF) for an enlarged sample of taxa, including five out of six currently accepted species of Mesadenus and representatives of nearly all (36 out of 41) genera of Spiranthinae, plus suitable outgroups. Detailed comparison of vegetative and floral attributes of relevant taxa was also conducted. Our results confirm polyphyly of Mesadenus and support creation of a new genus, Espinhassoa, to include Brazilian 'Mesadenus' glaziovii and 'M.' rhombiglossus (as Espinhassoa glaziovii and E. rhombiglossa, respectively). An identification key, descriptions, and illustrations of the two species herein included in Espinhassoa are provided.
Data from: Establishing a community-wide DNA barcode library as a new tool for arctic research
DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.
Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation
Among the World's most challenging environments for plant life is the Atacama Desert, an arid zone extending over 1300 km and from sea level to 2000/3000 m along the southwestern Andean foothills. Plants there and in the adjacent Mediterranean zone exhibit striking adaptations, and we here use a species-rich such group to address the question whether adaptations arose in parallel, at different times, or simultaneously. Answering this type of question has been a major concern of evolutionary biology over the past few years, with a growing consensus that lineages tend to be conservative in their vegetative traits and niche requirements. Combined nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900 aligned nucleotides) yielded a fossil-calibrated phylogeny that includes 43 of the 54 species of Oxalis occurring in Chile. Distribution models (SDMs) for these species that included precipitation, temperature, fog and/or vegetation types and the phylogeny were used to reconstruct ancestral habitat preferences, relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we used a background sample from 1224 Chilean Oxalis collections to correct models for collecting effort. Models with just 10 of 19 bioclim parameters did as well as more parameter-rich models. Results reveal that the Oxalis flora of Chile consists of seven distant lineages that originated at different times prior to the last Andean uplift pulse and some of which had features pre-adapting them to seasonally arid or xeric conditions. The Mediterranean core zone, south of the Atacama, offered an ecological refuge for insufficiently arid-adapted species and harbors a mix of ancient and young groups. There is no evidence of rapid adaptive radiation.
Data from: Jerzego, a new hisponine jumping spider from Borneo (Araneae: Salticidae)
A new genus and species of hisponine jumping spider from Sarawak, Jerzego corticicola Maddison sp. nov. are described, representing one of the few hisponine jumping spiders known from Asia, and the only whose male is known. Although similar to the primarily-Madagascan genus Hispo in having an elongate and flat body, sequences of 28s and 16sND1 genes indicate that Jerzego is most closely related to Massagris and Tomomingi, a result consistent with morphology. Females of Jerzego and other genera of Hisponinae were found to have an unusual double copulatory duct, which appears to be a synapomorphy of the subfamily. Two species are transferred from Hispo, Jerzego bipartitus (Simon) comb. nov. and Jerzego alboguttatus (Simon) comb. nov. Diagnostic illustrations and photographs of living spiders are provided.
Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their monotypic genera, due to their distinctive morphology. We apply the recently resurrected genus Clanga for the spotted eagles (previously Aquila spp.) to resolve the paraphyly of the genus Aquila such that the clade including the Booted Eagle (H. pennatus), Little Eagle (H. morphnoides), Pygmy Eagle (H. weiskei), Ayres's Eagle (H. ayresii) and Wahlberg's Eagle (H. wahlbergi) can remain in the genus Hieraaetus. The Rufous-bellied Eagle should be retained in the genus Lophotriorchis. For consistency in English names, we recommend that the term "hawk-eagles" be used only for the species in the genera Nisaetus and Spizaetus. We suggest following new or modified English names: Cassin's Eagle (Aquila africana), Bonaparte's Eagle (A. spilogaster), Ayres's Eagle (Hieraaetus ayresii), and Black-and-chestnut Hawk-Eagle (Spizaetus isidori).
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.