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3,507 results for “Species identification”
Fig. 9 in A revision of the genus Rhinotorus Förster, 1869 (Hymenoptera, Ichneumonidae, Ctenopelmatinae), with descriptions of three new species and an illustrated identification key
Fig. 9. Rhinotorus mesocostanus (Thomson, 1894). A. Face. B. Metasoma. C. Habitus.
Fig. 14 in A revision of the genus Rhinotorus Förster, 1869 (Hymenoptera, Ichneumonidae, Ctenopelmatinae), with descriptions of three new species and an illustrated identification key
Fig. 14. Rhinotorus umbrarum (Holmgren, 1857). A. ♂, habitus. B. ♀, habitus.
Fig. 12 in A revision of the genus Rhinotorus Förster, 1869 (Hymenoptera, Ichneumonidae, Ctenopelmatinae), with descriptions of three new species and an illustrated identification key
Fig. 12. Rhinotorus similis (Brischke, 1892), ♂. A. Face. B. Propodeum. C. Habitus.
Data from: Modeling the mito-nuclear compatibility and its role in species identification
<p>Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation -- as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (<em>T. californicus</em>). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.</p>
Phylogenomic species delimitation, taxonomy, and "bird guide" identification for the Neotropical ant genus Rasopone (Hymenoptera: Formicidae)
<p><i>Rasopone</i> Schmidt & Shattuck is a poorly known lineage of ants that live in Neotropical forests. Informed by phylogenetic results from thousands of ultraconserved elements (UCEs) and mitochondrial DNA barcodes, we revise the genus, providing a new morphological diagnosis and a species-level treatment. Analysis of UCE data from many <i>Rasopone</i> samples and select outgroups revealed non-monophyly of the genus. Monophyly of <i>Rasopone</i> was restored by transferring several species to the unrelated genus <i>Mayaponera </i>Schmidt & Shattuck. Within <i>Rasopone</i>, species are morphologically very similar, and we provide a "bird guide" approach to identification rather than the traditional dichotomous key. Species are arranged by size in a table, along with geographic range and standard images. Additional diagnostic information is then provided in individual species accounts. We recognize a total of 15 named species, of which the following are described as <b>new species</b>: <i>R. costaricensis</i>, <i>R. cryptergates</i>,<i> R. cubitalis</i>,<i> R. guatemalensis</i>,<i> R. mesoamericana</i>,<i> R. pluviselva</i>,<i> R. politognatha</i>, <i>R. subcubitalis</i>, and <i>R. titanis</i>. An additional 12 morphospecies are described but not formally named due to insufficient material. <i>Rasopone panamensis</i> (Forel, 1899) is <b>removed from synonymy</b> and <b>elevated to species</b>. The following species are removed from <i>Rasopone</i> and made <b>new combinations</b> in <i>Mayaponera</i>: <i>M. arhuaca</i> (Forel, 1901), <i>M. becculata</i> (Mackay & Mackay, 2010), <i>M. cernua</i> (Mackay & Mackay, 2010), <i>M. conicula</i> (Mackay & Mackay, 2010), <i>M. longidentata</i> (Mackay & Mackay, 2010), and <i>M. pergandei</i> (Forel, 1909).</p>
Longer is not always better: optimizing barcode length for large-scale species discovery and identification
New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens (5,500 species) and six clade-specific datasets from GenBank covering ca. 98,000 specimens (>20,000 species). All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 – 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5' end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.
Figure 4 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 4. Response graphs of habitat suitability (ordinate axis) according to the explanatory variables that intervened in the adjustment of the model for brown brocket deer (A, B, C). The temperature is expressed in degrees Celsius.Source of bioclimatic variables (bio), site https://www.worldclim.org/data/bioclim.html.
Figure 8 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 8. Species richness maps obtained using three algorithms, (A) "fuzzy union″, (B) "species richness″ and (C) "total beta″.
Figure 7 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 7. Response graphs of habitat suitability (ordinate axis) according to the explanatory variables that intervened in theadjustment of themodel for collared peccary (A,B, C).Temperature is expressed in degrees Celsius and altitude in meters.Source of bioclimatic variables (bio), site https://www.worldclim.org/data/bioclim.html.
DNA barcoding is currently unreliable for species identification in Crayfish
<p>DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (<em>Decapoda</em>: <em>Astacidea</em>). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps, if present, met a previously suggested 10 × threshold.</p> <p>Using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database, we created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N<sub>H</sub>) per species, and another that focused on total number of sequences (N<sub>S</sub>; i.e., including redundant haplotypes) per species. Ultimately, a total of 81 species were included, with 58 species and five genera from family <em>Cambaridae</em> and 23 species from three genera from family <em>Parastacidae</em>.</p> <p>We found that local barcoding gaps were present in only 30 species (20 members of <em>Cambaridae </em>and 10 <em>Parastacidae</em>). Global barcoding gaps were detected in only four genera (<em>Cambarus, Cherax, Euastacus, and Tenuibranchiurus</em>), and they were all well below the previously suggested 10× threshold. We propose that a ~5x threshold could act as a more appropriate working hypothesis for species discovery. While the N<sub>H</sub> and N<sub>S</sub> datasets yielded largely similar results, there were some discrepant inferences.</p> <p>Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when molecular approaches are used in place of taxonomic expertise.</p> <p>Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.</p>
Data from: A universal tool for marine metazoan species identification – Towards best practices in proteomic fingerprinting
<p><span>Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1,246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.</span></p>
Figure 18 in Objective identification of Lepidocyclina (Foraminifera) species from the Eocene of Cuba based on growth-invariant morphometric characters
Figure 18. Mean growth functions of row measurements.
Figure 16 in Objective identification of Lepidocyclina (Foraminifera) species from the Eocene of Cuba based on growth-invariant morphometric characters
Figure 16. Mean growth functions of chamberlet measurements.
Figure 9 in Objective identification of Lepidocyclina (Foraminifera) species from the Eocene of Cuba based on growth-invariant morphometric characters
Figure 9. Cluster analysis based on Ward's method. Sample locations indicated by colours.
Fig. 2 in Identification of freshwater snail species and survey of their trematode infections in Ordos, China
Fig. 2. Trematodes larvae in freshwater snails A–G: Cercaria; H, I: sporocyst; J, K: metacercariae.
Figure 2 in DNA barcoding for the identification of Limonia crane flies (Diptera: Limoniidae) from China, including a new species and a newly recorded species
Figure 2. Barcoding gap of Limonia COI sequences.
Figures 1–2 in Review of the genus Lasioseius Berlese (Acari: Blattisociidae) in Iran, and a key for identification of the Iranian species of the genus
Figures 1–2. Lasioseius parberlesei (female) – 1. Idiosoma, dorsal view; 2. Idiosoma, ventral view.
Figures 3–4 in Review of the genus Lasioseius Berlese (Acari: Blattisociidae) in Iran, and a key for identification of the Iranian species of the genus
Figures 3–4. Lasioseius parberlesei (male) – 3. Idiosoma, dorsal view; 4. Idiosoma, ventral view.
Dataset: DNA barcodes and microsatellites: how they complement for species identification in the complex genus Tamarix (Tamaricaceae)
<p class="CuerpoA">DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions (barcodes) with a previously compiled database, and it can be useful for taxonomic identification of species in complex genera, such as <i>Tamarix</i>. Many species of this genus show convergent morphology, which leads to frequent errors in their identification. Highly variable genetic markers, such as microsatellites or short sequence repeats (SSR), could be used to differentiate species where DNA barcodes fail. Here, we tested the ability of both, five different marker regions (<i>rbcL</i>, <i>matK</i>, ITS, <i>trnH</i>-<i>psbA</i>, and <i>ycf1</i>), and 14 microsatellites, to properly identify <i>Tamarix</i> species, especially those from the Mediterranean Basin, and compared the pros and cons of the different analytical methods for species identification. DNA barcoding allows the genetic identification of certain species in <i>Tamarix</i>. The two-locus barcodes <i>matK</i>+ITS and ITS+<i>ycf1</i> were the best-performing combinations, allowing up to 69% and 70%, respectively, correct identification. However, DNA barcoding failed in phylogenetically close groups, such as many Mediterranean species. The use of SSR can aid the identification of species, and the combination of both types of data (DNA barcoding and SSR) improved the success. The combination of data was especially relevant in detecting the presence of hybridization processes, which are common in the genus. However, caution must be exercised when choosing the clustering methods for the SSR data, since different methods can lead to very different results.</p>
Fig. 9 in Diagnostic Criteria For Identification Of Microtus S. L. Species (Rodentia, Arvicolidae) Of The Ukrainian Carpathians
Fig. 9. Algorithm of diagnostics of Microtus s. l. voles according to dental characters.
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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)
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.