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FIGURE 19 in Taxonomic evaluation of the Grallaria rufula (Rufous Antpitta) complex (Aves: Passeriformes: Grallariidae) distinguishes sixteen species
FIGURE 19. Map showing the taxonomy and distribution of the Grallaria rufula complex as revised herein, Part 1: populations formerly ascribed to G. rufula. Solid circles represent sectors (Isler 1997) that contain locations of genetic samples used in a companion paper (Chesser et al. 2020) and stars that are sectors containing locations where specimens have been collected or vocalizations recorded. Sectors may contain more than one genetic or vocal sample or specimen. Lines encompass sectors attributed to the same taxon and are not projections of geographic range. Some sectors are placed away from boundary lines (country boundaries, coasts) for clarity which results in discrepancies with geographic range projections which can be found in the companion paper (Chesser et al. 2020).
Distinguishing Between Shock Darkening and Space Weathering Trends in Ordinary Chondrite Reflectance Spectra
<p>The data file contains raw spectra of Chelyabinsk meteorite IM, SD, and SW series as described in the linked journal publication.</p>
Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony
Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance and sPCA were used to characterize spatio-temporal genomic variation using 1370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over > 140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.
FIGURE 3. M in Revision of the Metallactus generosus species-group with a preliminary evaluation of the effectiveness of the endophallus morphology in distinguishing critical sibling species (Coleoptera: Chrysomelidae: Cryptocephalinae)
FIGURE 3. M. nigroplagiatus new species: a–b: habitus (lectotype, from type locality); c–e: median lobe of aedeagus in ventral (c), dorsal (d) and lateral (e) view [0.7 mm]; f: sclerites of endophallus in lateral view [0.5 mm]; g: spermatheca [0.4 mm]; h: antenna [1.6 mm]. scI–IV: sclerites I–IV of endophallus; ds: dorsal spicule. Square brackets: length of scale segment.
FIGURES 1–2. Metallactus generosus Suffrian, 1866 in Revision of the Metallactus generosus species-group with a preliminary evaluation of the effectiveness of the endophallus morphology in distinguishing critical sibling species (Coleoptera: Chrysomelidae: Cryptocephalinae)
FIGURES 1–2. Metallactus generosus Suffrian, 1866 (1), M. argentinensis Jacoby, 1907 (2): 1a–b: habitus; 1c–e: median lobe of aedeagus in ventral (c), dorsal (d) and lateral (e) view [0.8 mm]; 1f: sclerites of endophallus in lateral view [0.4 mm]; 1g: spermatheca [0.6 mm]; 1h: antenna [1.6 mm]. 2a–b: habitus; 2c–e: median lobe of aedeagus in ventral (c), dorsal (d) and lateral (e) view [0.8 mm]; 2f: sclerites of endophallus in lateral view [0.5 mm]; 2g: spermatheca [0.4 mm]; 2h: antenna [1.5 mm]. 1a–b: lectotype; 2a–b: lectotype. scI–IV: sclerites I–IV of endophallus; ds: dorsal spicule; sd: setose depression. Square brackets: length of scale segment.
FIGURE 8 in Revision of the Metallactus generosus species-group with a preliminary evaluation of the effectiveness of the endophallus morphology in distinguishing critical sibling species (Coleoptera: Chrysomelidae: Cryptocephalinae)
FIGURE 8. Sclerites of endophallus of Metallactus luniger Suffrian, 1866 (a), M. crassicollis Suffrian, 1866 (b), M. sekerkai Sassi, 2015 (c), M. agonista Suffrian, 1866 (d), M. corruptus Suffrian, 1866 (e), M. albipes Suffrian, 1866 (f), M. longicornis Sassi, 2018 (g), M. kollari (Perty, 1832) (h). scI–IV: sclerites I–IV of endophallus. Only the sclerites discussed in the text have been highlighted with abbreviations. Not to same scale.
FIGURES 5–7. Distribution maps for Metallactus generosus species-group. M. generosus Suffrian, 1866 in Revision of the Metallactus generosus species-group with a preliminary evaluation of the effectiveness of the endophallus morphology in distinguishing critical sibling species (Coleoptera: Chrysomelidae: Cryptocephalinae)
FIGURES 5–7. Distribution maps for Metallactus generosus species-group. M. generosus Suffrian, 1866 (5); M. argentinensis Jacoby, 1907 (6); M. nigroplagiatus new species (7). Grey square: hypothetical location for specimen labelled from 'Brazil'.
FIGURE 4. Frontal view. Metallactus generosus Suffrian, 1866 in Revision of the Metallactus generosus species-group with a preliminary evaluation of the effectiveness of the endophallus morphology in distinguishing critical sibling species (Coleoptera: Chrysomelidae: Cryptocephalinae)
FIGURE 4. Frontal view. Metallactus generosus Suffrian, 1866 (a); M. argentinensis Jacoby, 1907 (b); M. nigroplagiatus new species (c).
Data from: Trait-mediated community assembly: distinguishing the signatures of biotic and abiotic filters
Conflicting hypotheses predict how traits mediate species establishment and community assembly. Traits of newly establishing individuals are predicted to converge, or be more similar to the resident, preexisting community, when the biotic or abiotic environment favors a single best phenotype, but are predicted to diverge when trait differences reduce competitive interactions. We tested these competing hypotheses using transplant seedlings in an old-field environment, and assessed the contribution of inter- and intra-specific transplant trait variation to community-level patterns. Using a soil moisture gradient and resident plant removals, we determined when traits of newly-establishing plants converge or diverge from the resident community by calculating community weighted mean traits for transplant and resident communities. We saw evidence of environmentally- and competitively-driven trait shifts that resulted in both trait convergence and divergence from the resident community, whose traits reflect the combined effects of both drivers. Leaf dry matter content (LDMC) of transplants diverged in the presence of competition, whereas plant height and stem-specific density (SSD) showed the opposite pattern, converging with the resident community in their presence. Specific leaf area (SLA) shifted with competition but did not reflect resident community SLA. All transplant traits were influenced by soil moisture, often in an interaction with competition, indicating that the strength of convergence or divergence is contingent on the abiotic environment. Intraspecific differences in transplant traits among treatments were evident in three of four traits; intraspecific height and SLA trends mirrored transplant community-level trends, whereas intraspecific shifts in SSD were distinct from community-level trends. Our study shows competition between plant species may cause traits of newly establishing plants to converge with the resident community, as frequently as it selects for trait divergence. These opposing effects of competition suggest that it plays a pervasive role in both intraspecific and species-level trait differences among communities.
Data from: An extensive suite of functional traits distinguishes wet and dry Hawaiian forests and enables prediction of species vital rates
1. The application of functional traits to predict and explain plant species' distributions and vital rates has been a major direction in functional ecology for decades, yet numerous physiological traits have not yet been incorporated into the approach. 2. Using commonly measured traits such as leaf mass per area (LMA) and wood density (WD), and additional traits related to water transport, gas exchange and resource economics, including leaf vein, stomatal, and wilting traits, we tested hypotheses for Hawaiian wet montane and lowland dry forests (MWF and LDF respectively): (1) forests would differ in a wide range of traits as expected from contrasting adaptation; (2) trait values would be more convergent among dry than wet forest species due to the stronger environmental filtering; (3) traits would be inter-correlated within "modules" supporting given functions; (4) relative growth rate (RGR) and mortality rate (m) would correlate with a number of specific traits, with (5) stronger relationships when stratifying by tree size, and (6) RGR and m can be strongly explained from trait-based models. 3. The MWF species' traits were associated with adaptation to high soil moisture and nutrient supply and greater shade tolerance whereas the LDF species' traits were associated with drought tolerance. Thus, on average, MWF species achieved higher maximum heights than LDF species and had leaves with larger epidermal cells, higher maximum stomatal conductance and CO2 assimilation rate, lower vein lengths per area, higher saturated water content and greater shrinkage when dry, lower dry matter content, higher phosphorus concentration, lower nitrogen to phosphorus ratio, high chlorophyll to nitrogen ratio, high carbon isotope discrimination, high stomatal conductance to nitrogen ratio, less negative turgor loss point, and lower WD. Functional traits were more variable in the MWF than LDF, were correlated within modules, and predicted species' RGR and m across forests, with stronger relationships when stratifying by tree size. Models based on multiple traits predicted vital rates across forests (R2 = 0.70-0.72; P < 0.01). 4. Our findings are consistent with a powerful role of broad suites of functional traits in contributing to forest species' distributions, integrated plant design, and vital rates.
Data from: Distinguishing the victim from the threat: SNP‐based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration
The degree of introgressive hybridisation between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here we use a 35-SNP-marker test, designed to assess hybridisation between wildcat and domestic cat populations in Scotland, to assess a database of 265 wild-living and captive cat samples, and test the assumptions of the test using 3097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridised, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage disequilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone are poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.
Data from: Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides an excellent case study to examine. To examine contemporary hybridization between the two species, we developed a panel of 310 ancestry-informative SNPs from a population transcriptomic study. Hybridization rates were examined on 449 individuals sampled in eight sites from the sympatric range and five sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one-first-generation hybrid and no other genotype compatible with recent backcrosses. Despite the almost lack of contemporary hybridization, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of shared polymorphisms compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasize efficient reproductive barriers preventing hybridization between introduced and native species, which suggests hybridization should not impede too much the expansion and the establishment of the non-native species in its introduction range.
Data from: Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison
Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.
Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World "mallards" (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes, regions that may have been involved in the diversification of species in this recent radiation.
Data from: Which traits do observers use to distinguish Batesian mimics from their models?
Batesian mimicry, in which a harmless mimic resembles a more aversive model, can encompass a wide range of morphological traits, but the resemblance is never perfect. Previous studies have used abstract "prey" designs to show that differences in certain traits may not be relevant to mimicry if they are not perceived or recognized by a predator. Here, we extend these results by examining how human "predators" respond to realistic variation in traits of aposematic wasps and their hoverfly mimics. We measured the ability of humans to discriminate between images of wasps and hoverflies in which only certain traits were visible, to determine the contributions of those traits to discrimination decisions. We found that shape is a particularly useful and easily learnt trait for separating the 2 taxa. Subjects did not successfully discriminate on the basis of abdominal patterns, despite those containing useful information. Color similarity between wasps and hoverflies is relatively high in comparison with other traits, suggesting that selection has acted more strongly on color. Our findings demonstrate the importance of consideration of natural variation in the traits of prey and their salience to predators for understanding the evolution of prey defenses.
Data from: Distinguishing migration events of different timing for wild boar in the Balkans
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimation analysis. Results: Both microsatellite and SNP data analyses detected genetic structure caused by historic events and support the existence of three groups in the studied area. A hybrid zone between two of the groups was also detected. We also showed that genome-wide SNP data analysis can identify recent events in bottlenecked populations. Main conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp when populations contracted to different refugia. Our findings strengthened the evidence that the southern Balkan area was a glacial refugium including further local smaller refugia. Genome-wide genotyping inferred a recent population expansion that can mimic a 'refugium within refugium' scenario. It seems that microsatellite data tend to overestimate genetic structure when genetic drift happens in bottlenecked populations over a short distance. Therefore, genome-wide SNPs are more powerful at inferring phylogeography in natural populations, resolving inconsistencies from mitochondrial and microsatellite data sets.
Data from: Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases
Diapause is a deep resting stage facilitating temporal avoidance of unfavourable environmental conditions that is used by many insects to adapt their life cycle to seasonal variation. Although considerable work has been invested in trying to understand each of the major diapause stages (induction, maintenance and termination), we know very little about the transitions between stages, especially diapause termination. Understanding diapause termination is critical for modelling and predicting spring emergence and winter physiology of insects, including many pest insects. In order to gain these insights we investigated metabolome dynamics across diapause development in pupae of the butterfly Pieris napi, which exhibits adaptive latitudinal variation in the length of endogenous diapause that is uniquely well characterized. By employing a time-series experiment we show that the whole-body metabolome is highly dynamic throughout diapause and differs between pupae kept at a diapause-terminating (low), or at a diapause-maintaining (high) temperature. We show major physiological transitions through diapause, separated temperature-dependent from temperature-independent processes and identified significant patterns of metabolite accumulation and degradation. Together the data show that while the general diapause phenotype (suppressed metabolism, increased cold tolerance) is established in a temperature-independent fashion, diapause termination is temperature-dependent and requires a cold signal. This revealed several metabolites that are only accumulated in diapause terminating conditions and degraded in a temperature-unrelated fashion during diapause termination. In conclusion, our findings indicate that some metabolites, in addition to functioning as e.g. cryoprotectants, are candidates for having regulatory roles as metabolic clocks or time-keepers during diapause.
FIGURE 4 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 4. Dendrogram (K2P) for An. neivai specimens from Colombia, Panama, with other Kerteszia and Nyssorhynchus species (based on a 535 bp COI alignment. Branch support was provided by bootstrap resampling (10000 replicates).
FIGURE 5 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 5. Haplotype network for An. neivai collected in Colombia and Panama (based on a 535 bp COI alignment).
FIGURE 2 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 2. Genetic differences (K2P) among An. neivai collected specimens (A) and against other species from Kerteszia (B) and Nyssorhynchus from NCBI (C).
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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.