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FIGURE 2 in The genus Rhoenanthus Eaton, 1881 in China with the redescription of R hunanensis You & Gui, 1995 (Ephemeroptera: Potamanthidae)
FIGURE 2. Nymphal characters of Rhoenanthus hunanensis (digital photos). A. Habitus in dorsal view; B. Head and pronotum of another more mature nymph (dorsal view, showing mandibular tusks); C. Enlarged section of the antenna.
FIGURE 10 in The genus Rhoenanthus Eaton, 1881 in China with the redescription of R hunanensis You & Gui, 1995 (Ephemeroptera: Potamanthidae)
FIGURE 10. Selected structures of Rhoenanthus spp. (digital photos). A–C. R. sapa; D–F. R. youi; G–I. R. obscurus: A, D, G. Anterior part of body (showing the relatively length of mandibular tusks, forelegs and their setae); B, E, H. Maxilla (dorsal view); C, F, I. Labrum (ventral view).
FIGURE 6 in The genus Rhoenanthus Eaton, 1881 in China with the redescription of R hunanensis You & Gui, 1995 (Ephemeroptera: Potamanthidae)
FIGURE 6. Male structures of Rhoenanthus spp. (digital photos). A–D. Rhoenanthus hunanensis; E–F. Rhoenanthus youi: A. Forewing; B. Hindwing; C, F. Genitalia (dorsal view); D–E. Enlarged penes (ventral view).
Serological dataset and R code for: Patterns and processes of pathogen exposure in gray wolves across North America
<p>The presence of many pathogens varies in a predictable manner with latitude, with infections decreasing from the equator towards the poles. We investigated the geographic trends of pathogens infecting a widely distributed carnivore: the gray wolf (<i>Canis lupus</i>). We compiled a large serological dataset of nearly 2000 wolves from 17 study areas, spanning 80º longitude and 50º latitude. Generalized linear mixed models were constructed to predict the probability of seropositivity of four important viruses: canine adenovirus, herpesvirus, parvovirus, and distemper virus – and two parasites: <i>Neospora caninum </i>and <i>Toxoplasma gondii</i>.</p> <p>Canine adenovirus and herpesvirus were the most widely distributed pathogens, whereas <i>N. caninum</i> was relatively uncommon. Canine parvovirus and distemper had high annual variation, with western populations experiencing more frequent outbreaks than eastern populations. Seroprevalence of all infections increased as wolves aged, and denser wolf populations had a greater risk of exposure. Probability of exposure was positively correlated with human density, suggesting that dogs and synanthropic animals may be important pathogen reservoirs. Pathogen exposure did not appear to follow a latitudinal gradient, with the exception of <i>N. caninum</i>. Instead, clustered study areas were more similar: wolves from the Great Lakes region had lower odds of exposure to the viruses, but higher odds of exposure to <i>N. caninum</i> and <i>T. gondii</i>; the opposite was true for wolves from the central Rocky Mountains. Overall, mechanistic predictors were more informative of seroprevalence trends than latitude and longitude. Individual host characteristics as well as inherent features of ecosystems determined pathogen exposure risk on a large scale.</p> <p>Here we provide the serological dataset and the R code used in Brandell et al. 2021. See the README file for a description of the dataset and generalized linear mixed models (GLMM); see Brandell et al. 2021 main text and Supplementary Information for additional information about data collection and cleaning, research permits, and variable descriptions and rationales.</p>
F I G U R E 2 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 2 Bayesian phylogram of the genus Micronycteris based on a concatenated dataset of four markers (cytb, Fgb-I7, DBY5, and DBY7). Scores are Bayesian posterior probabilities (top) and bootstrap support values from maximum likelihood (bottom). Lampronycteris brachyotis was used as outgroup but is not shown. Specimen list in Table S1. Acronyms of countries: Bol: Bolivia, Bra: Brazil, Ecu: Ecuador, FGui: French Guiana, Guy: Guyana, Hon: Honduras, Per: Peru, Sur: Suriname, Tri: Trinidad and Tobago, Ven: Venezuela. Ecuadorian specimens from the western or eastern versant of the Andes are noted with W and E respectively
F I G U R E 1 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 1 Collecting localities of pale-bellied Micronycteris specimens included in this study (sequences, n = 44, and measurements, n = 114). Sampled countries are labeled
F I G U R E 5 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 5 Dorsal, ventral, anterior, and posterior views of the cranium, and lateral views of the cranium and mandible of Micronycteris schmidtorum from Ecuador (TTU 103196). Scale bar = 5 mm
S u m m a r y s t a t i s t i c s in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
S u m m a r y s t a t i s t i c s (m e a n, s t a n d a r d d e v i a t i o n, s a m p l e s i z e, a n d r a n g e) o f t h e c r a n i a l m e a s u r e m e n t s o f t h e p a l e - b e l - l i e d s p e c i e s o f m i c r o ny c te r i s
F I G U R E 4 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 4 Chromosomes of (a) Micronycteris tresamici sp. nov. (b) M. simmonsae sp. nov. (c) M. minuta Northern South America, and (d) M. minuta from the literature (Baker, 1979)
F I G U R E 7 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 7 Dorsal, ventral, anterior, and posterior views of the cranium, and lateral views of the cranium and mandible of Micronycteris simmonsae sp. nov. (TTU 103201, holotype). Scale bar = 5 mm
F I G U R E 6 in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
F I G U R E 6 Dorsal, ventral, anterior, and posterior views of the cranium, and lateral views of the cranium and mandible of Micronycteris tresamici sp. nov. (TTU 103880, holotype). Scale bar = 5 mm
Supplementary material 1 from: Gómez-Domínguez H, Ortiz-Rodríguez AE, Velasco-Espino D, Hernández-Burguete R (2021) Taxonomic updates in Amphitecna (Bignoniaceae): A new Mexican species and the re-establishment of the giant-leaved A. megalophylla. PhytoKeys 171: 75-90. https://doi.org/10.3897/phytokeys.171.55397
Figure S1. Cophenetic correlation between clustering results from eight different linkage algorithms and Gower similarity index.
Data from: PolyPatEx: an R package for paternity exclusion in autopolyploids
Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species and several software packages exist for elucidating paternity in diploids, however these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and a lack of available software. We introduce PolyPatEx, an R package for paternity exclusion analysis using microsatellite data in autopolyploid, monoecious or dioecious/bisexual species with a ploidy of 4n, 6n or 8n. Given marker data for a set of offspring, their mothers, and a set of candidate fathers, PolyPatEx uses allele matching to exclude candidates whose marker alleles are incompatible with the alleles in each offspring-mother pair. PolyPatEx can analyse marker data sets in which allele copy numbers are known (genotype data) or unknown (allelic phenotype data) – for data sets in which allele copy numbers are unknown, comparisons are made taking into account all possible genotypes that could arise from the compared allele sets. PolyPatEx is a software tool that provides population geneticists with the ability to investigate the mating patterns of autopolyploids using paternity exclusion analysis on data from codominant markers having multiple alleles per locus.
Data from: Multi-DICE: R package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest, and composite likelihood optimization. Here, we introduce the R package Multi-DICE, a wrapper program that exploits existing simulation software for straight-forward and flexible execution of hierarchical model-based inference using the aSFS, which is derived from genomic-scale data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding event pulses, and specifying flexible hyperprior distributions. In sum, Multi-DICE provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a valuable tool for comparative phylogeography and population genomics.
Data from: The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events
There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site–leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.
Data from: Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers
Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity management units and genetic structure. Here we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait South China Sea and Northwest Pacific Ocean). In R. stylosa the genetic break was located more eastward between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves especially relating to replanting efforts and the definition of ESUs in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species determine their respective genetic structure and avoid artificially promoting hybridization in mangrove restoration programmes.
Data from: An R package for analyzing survival using continuous-time open capture-recapture models
Capture–recapture software packages have proven to be very powerful tools for analysing factors affecting survival in wild populations. However, all such packages are limited to discrete-time protocols. Appropriate survival analysis tools are still lacking for data acquired from continuous-time protocols. We have developed a statistical method and propose an r package for analysing such data based on an extension of classical survival analysis models incorporating an inhomogeneous Poisson process for modelling capture histories. First, data were simulated from a continuous-time protocol. These data were used to (i) compare survival estimation biases of discrete- and continuous-time approaches and (ii) investigate the performance and accuracy of our r package for four types of covariates: factors varying between individuals (like sex), in time (like climatic factors), both in time and between individuals (like physical condition) and age (as a categorical factor). Secondly, the r package has been applied to a real data set for survival analysis of cats in the Kerguelen archipelago (regrouping 682 cats over 20 years) as an illustrative example. Results of the simulated data analysis show that the method performs better than its discrete-time counterpart for analysing data acquired from continuous-time protocols. It provides unbiased parameter estimates for all parameters except those that vary both in time and between individuals – which is not surprising, since in our case, these factors were not updated in continuous time (i.e. only upon capture). When applied to the Kerguelen cat data set, the results suggest that survival is lower in juveniles than in adults and subadults, varies between study sites and increases with physical condition, and this latter effect being more important in females than in males. Sex, season, temporal linear trend in survival and the NDVI vegetation index were also tested but were not found to be significant. However, confidence intervals were too large (due to a low recapture rate) for excluding such effects. Further analyses are still needed for rigorous covariate testing in this context. In conclusion, continuous-time approaches – such as that presented in this paper – should be preferred when data acquired from continuous-time protocols is analysed.
Data from: Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R. grassei
Social insects exhibit remarkable variation in their colony breeding structures, both within and among species. Ecological factors are believed to be important in shaping reproductive traits of social insect colonies, yet there is little information linking specific environmental variables with differences in breeding structure. Subterranean termites (Rhinotermitidae) show exceptional variation in colony breeding structure, differing in the number of reproductives and degree of inbreeding; colonies can be simple families headed by a single pair of monogamous reproductives (king and queen) or they can be extended families headed by multiple inbreeding neotenic reproductives (wingless individuals). Using microsatellite markers, we characterized colony breeding structure and levels of inbreeding in populations over large parts of the range of the subterranean termites Reticulitermes flavipes in the USA and R. grassei in Europe. Combining these new data with previous results on populations of both species, we found that latitude had a strong effect on the proportion of extended-family colonies in R. flavipes and on levels of inbreeding in both species. We examined the effect of several environmental variables that vary latitudinally; while the degree of inbreeding was greatest in cool, moist habitats in both species, seasonality affected the species differently. Inbreeding in R. flavipes was most strongly associated with climatic variables (mean annual temperature and seasonality), whereas nonclimatic variables, including the availability of wood substrate and soil composition, were important predictors of inbreeding in R. grassei. These results are the first showing that termite breeding structure is shaped by local environmental factors and that species can vary in their responses to these factors.
Data from: SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness
Stable isotope mixing models (SIMMs) are an important tool used to study species' trophic ecology. These models are dependent on, and sensitive to, the choice of trophic discrimination factors (TDF) representing the offset in stable isotope delta values between a consumer and their food source when they are at equilibrium. Ideally, controlled feeding trials should be conducted to determine the appropriate TDF for each consumer, tissue type, food source, and isotope combination used in a study. In reality however, this is often not feasible nor practical. In the absence of species-specific information, many researchers either default to an average TDF value for the major taxonomic group of their consumer, or they choose the nearest phylogenetic neighbour for which a TDF is available. Here, we present the SIDER package for R, which uses a phylogenetic regression model based on a compiled dataset to impute (estimate) a TDF of a consumer. We apply information on the tissue type and feeding ecology of the consumer, all of which are known to affect TDFs, using Bayesian inference. Presently, our approach can estimate TDFs for two commonly used isotopes (nitrogen and carbon), for species of mammals and birds with or without previous TDF information. The estimated posterior probability provides both a mean and variance, reflecting the uncertainty of the estimate, and can be subsequently used in the current suite of SIMM software. SIDER allows users to place a greater degree of confidence on their choice of TDF and its associated uncertainty, thereby leading to more robust predictions about trophic relationships in cases where study-specific data from feeding trials is unavailable. The underlying database can be updated readily to incorporate more stable isotope tracers, replicates and taxonomic groups to further increase the confidence in dietary estimates from stable isotope mixing models, as this information becomes available.
Supplementary material 1 from: Mesibov R (2020) A second remarkable case of parapatry in a Tasmanian millipede genus (Diplopoda, Polydesmida, Dalodesmidae). In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 89-101. https://doi.org/10.3897/zookeys.930.38031
Specimen data for Tasmaniosoma armatum Verhoeff, 1936, T. clarksonorum Mesibov, 2010, T. orientale Mesibov, 2010 and specimens not yet identifiable as T. armatum or T. orientale
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.