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3,507 results for “Species identification”
Data from: Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and fecal DNA
There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids.
Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK
<p>One of the most foundational aspects of ecological studies and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of proof of principle experiments to characterize SHERLOCK's ability to accurately, sensitively, and rapidly distinguished three fish species (two with protected status and one non-native) co-occurring in the San Francisco Estuary which are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining its rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.</p>
Data from: Evolution of wing shape in hornets: why is the wing venation efficient for species identification?
Wing venation has long been used for insect identification. Lately, the characterization of venation shape using geometric morphometrics has further improved the potential of using the wing for insect identification. However, external factors inducing variation in wing shape could obscure specific differences, preventing accurate discrimination of species in heterogeneous samples. Here, we show that interspecific difference is the main source of wing shape variation within social wasps. We found that a naive clustering of wing shape data from taxonomically and geographically heterogeneous samples of workers returned groups congruent with species. We also confirmed that individuals can be reliably attributed to their genus, species and populations on the basis of their wing shape. Our results suggested that the shape variation reflects the evolutionary history with a potential influence of other factors such as body shape, climate and mimicry selective pressures. However, the high dimensionality of wing shape variation may have prevented absolute convergences between the different species. Wing venation shape is thus a taxonomically relevant marker combining the accuracy of quantitative characters with the specificity required for identification criteria. This marker may also highlight adaptive processes that could help understand the wing's influence on insect flight.
Data from: Accuracy of identifications of mammal species from camera trap images: a northern Australian case study
Camera traps are a powerful and increasingly popular tool for mammal research, but like all survey methods, they have limitations. Identifying animal species from images is a critical component of camera trap studies, yet while researchers recognize constraints with experimental design or camera technology, image misidentification is still not well understood. We evaluated the effects of a species' attributes (body mass and distinctiveness) and individual observer variables (experience and confidence) on the accuracy of mammal identifications from camera trap images. We conducted an Internet‐based survey containing 20 questions about observer experience and 60 camera trap images to identify. Images were sourced from surveys in northern Australia and included 25 species, ranging in body mass from the delicate mouse (Pseudomys delicatulus, 10 g) to the agile wallaby (Macropus agilis, >10 kg). There was a weak relationship between the accuracy of mammal identifications and observer experience. However, accuracy was highest (100%) for distinctive species (e.g. Short‐beaked echidna [Tachyglossus aculeatus]) and lowest (36%) for superficially non‐distinctive mammals (e.g. rodents like the Pale field‐rat [Rattus tunneyi]). There was a positive relationship between the accuracy of identifications and body mass. Participant confidence was highest for large and distinctive mammals, but was not related to participant experience level. Identifications made with greater confidence were more likely to be accurate. Unreliability in identifications of mammal species is a significant limitation to camera trap studies, particularly where small mammals are the focus, or where similar‐looking species co‐occur. Integration of camera traps with conventional survey techniques (e.g. live‐trapping), use of a reference library or computer‐automated programs are likely to aid positive identifications, while employing a confidence rating system and/or multiple observers may lead to a collection of more robust data. Although our study focussed on Australian species, our findings apply to camera trap studies globally.
Data from: Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens
The first step in many community ecology studies is to produce a species list from a sample of individuals. Community ecologists now have two viable ways of producing a species list: morphological and barcode identification. In this study, we compared the taxonomic resolution gained by a combined use of both methods and tested whether a change in taxonomic resolution significantly impacted richness estimates for benthic macroinvertebrates sampled from ten lakes in Sequoia National Park, USA. Across all lakes, 77 unique taxa were identified and 42% (32) were reliably identified to species using both barcode and morphological identification. Of the 32 identified to species, 63% (20) were identified solely by comparing the barcode sequence from cytochrome oxidase I to the Barcode of Life reference library. The increased resolution using a combined identification approach compared to identifications based solely on morphology resulted in a significant increase in estimated richness within a lake at the order, family, genus and species levels of taxonomy (P < 0.05). Additionally, young or damaged individuals that could not be identified using morphology were identified using their COI sequences to the genus or species level on average 75% of the time. Our results demonstrate that a combined identification approach improves accuracy of benthic macroinvertebrate species lists in alpine lakes and subsequent estimates of richness. We encourage the use of barcodes for identification purposes and specifically when morphology is insufficient, as in the case of damaged and early life stage specimens of benthic macroinvertebrates.
Data from: Hybridization relics complicate barcode-based identification of species in earthworms
Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference dataset including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and non-matching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 non-matching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae.
Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications
Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.
FIGURES 6A–C. Eucyclops torresphilipi n in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURES 6A–C. Eucyclops torresphilipi n. sp. adult male (allotype) from Chiapas, Mexico. A) habitus, dorsal view; B) left antennule showing armature; C) fifth pedigerous and genital doublesomites, lateral view, showing sixth legs (only setal armature represented).
FIGURES 5A–D. Eucyclops torresphilipi n in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURES 5A–D. Eucyclops torresphilipi n. sp. adult female from Chiapas, Mexico. A) coxal plate of second swimming leg, caudal view; B) two terminal segments of endopod of fourth swimming legs; C) fourth swimming legs; D) coxal plate of third swimming leg, caudal view; E) coxal plate of fourth swimming leg, caudal view; F) labrum; G) fifth leg; H) fourth swimming leg, distal segment of exopod.
FIGURES 4A–E. Eucyclops torresphilipi n in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURES 4A–E. Eucyclops torresphilipi n. sp. adult female from Chiapas, Mexico. A) first swimming leg showing coxal plate; B) second swimming leg; C) third swimming leg.
FIGURES 3A–E. Eucyclops torresphilipi n in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURES 3A–E. Eucyclops torresphilipi n. sp. adult female from Chiapas, Mexico. A) mandible; B) maxillule and maxillular palp; C) maxilla; D) antenna; E) maxilliped.
FIGURES 2A–G. Eucyclops torresphilipi n in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURES 2A–G. Eucyclops torresphilipi n. sp.. adult female from Chiapas, Mexico. A) antennule; B) habitus, dorsal view; C) fifth pedigerous and genital doublesomites, ventral view; D) caudal rami, dorsal view; E) urosome, dorsal view, another specimen.
FIGURE 1 in A new species of Eucyclops Claus (Copepoda: Cyclopoida) from Southeast Mexico with a key for the identification of the species recorded in Mexico
FIGURE 1. Location of the surveyed area in southern Chiapas, Mexico. The type locality of Eucyclops torresphilipi n. sp. is indicated by a solid square.
FIGURE 7 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 7. Larva of Inaequalium maranguapense sp. n. a: cephalic fan, row of microtrichia of primary ray; b: mandible, arrow points to mandibular process; c–d: labral sclerite, arrow points to one of the apical teeth; e: detail of thoracic proleg; arrow points to lateral sclerite.
FIGURE 3 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 3. Female of Inaequalium maranguapense sp. n. a: detail of wing chaetotaxy; b: legs; c: tarsal claws; d: spermatheca; e: gonapophyses; f: genital fork; g: cerci and paraprocts, lateral view. Abbreviations: FL = fore leg; ML = mid leg; HL = hind leg
FIGURE 2 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 2. Female of Inaequalium maranguapense sp. n. a: part of head, frontal view; b: detail of frontoocular area; c: cibarium; d: detail of teeth of cibarium; e: palpus; f: mandible and maxillary lacinia. Abbreviations: FOA = frontoocular area; MD = mandible; ML = maxillary lacinia.
FIGURE 6 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 6. Larva of Inaequalium maranguapense sp. n. a: coloration pattern, lateral view; b: cephalic apotome, arrow points to cervical sclerite; c: antenna and stem of cephalic fan; d: hypostomium; e: postgenal cleft, hypostomal bridge, and hypostomium.
FIGURE 9 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 9. Cibarium of Ectemnaspis perflava, arrow points to magnified area showing depression with teeth.
FIGURE 5 in First survey of Simuliidae (Diptera) from the North of Ceará State, Brazil, with description of a new species and identification keys for the immature stages
FIGURE 5. Abdomen of pupa of Inaequalium maranguapense sp. n. a: detail of abdominal tergite I; b: detail of tergites III and IV; c: detail of sternites IV and V; arrow points to fivebranched hook; d: detail of tergite IX; arrow points to 1+1 terminal spur.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.