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356 results for “Species concepts”
Data for: An AAV-CRISPR/Cas9-strategy for gene editing across divergent rodent species: Targeting neural oxytocin receptors as a proof of concept
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Random forests for predicting species identity of forensically important blow flies (Diptera: Calliphoridae) and flesh flies (Sarcophagidae) using geometric morphometric data: proof of concept
<p>Wing shape variation has been shown to be useful for delineating forensically important fly species in two Diptera families: Calliphoridae and Sarcophagidae. Compared to DNA-based identification, the cost of geometric morphometric data acquisition and analysis is relatively much lower because the tools required are basic, and stable softwares are available. However, to date, an explicit demonstration of using wing geometric morphometric data for species identity prediction in these two families remains lacking. Here, geometric morphometric data from 19 homologous landmarks on the left wing of males from seven species of Calliphoridae (<em>n</em>=55), and eight species of Sarcophagidae (<em>n</em>=40) were obtained and processed using Generalized Procrustes Analysis. Allometric effect was removed by regressing centroid size (in log10) against the Procrustes coordinates. Subsequently, principal component analysis of the allometry-adjusted Procrustes variables was done, with the first 15 principal components used to train a random forests model for species prediction. Using a real test sample consisting of 33 male fly specimens collected around a human corpse at a crime scene, the estimated percentage of concordance between species identities predicted using the random forests model and those inferred using DNA-based identification was about 80.6% (approximate 95% confidence interval = [68.9%, 92.2%]). In contrast, baseline concordance using naive majority class prediction was 36.4%. The results provide proof of concept that geometric morphometric data has good potential to complement morphological and DNA-based identification of blow flies and flesh flies in forensic work. </p>
Molecular systematics, species concepts and myrmecophytism in Cecropia (Cecropieae: Urticaceae): Insights from restriction-site associated DNA
<p><em>Cecropia</em> is a group of fast-growing pioneer trees that are important in forest regeneration and a common ant-plant mutualism in the Neotropics. To investigate the evolution of mutualism between <em>Cecropia</em> and associated ants a phylogenetic framework is necessary. <em>Cecropia</em> species are difficult to distinguish morphologically and conventional genetic markers are insufficiently variable to resolve phylogeny. Our study aimed to infer relationships in approximately half of the species in the genus using restriction site associated DNA (RAD) sequencing. RAD sequence data resolved and supported species level relationships, despite potential introgression based on D-statistic tests. Our results support a deeply divergent non-myrmecophytic clade including <em>C. sciadophylla </em>and African <em>Musanga</em>. Results from geographically widespread and morphologically heterogenous <em>C. obtusifolia</em> and <em>C. angustifolia</em> suggests that current synonymy lumps together genetically dissimilar lineages. Reconstruction of ant associations on the highly supported <em>Cecropia</em> phylogeny inferred equal probability of the ancestor of <em>Cecropia </em>being myrmecophytic or not. More intensive genetic study is needed to refine species concepts in <em>Cecropia</em>.</p>
The soundscape of swarming: Proof of concept for a non-invasive acoustic species identification of swarming Myotis bats
<p>Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species-specific calls can facilitate species identification, especially when mist-netting is not feasible. However, some taxa, such as Myotis bats are hard to distinguish acoustically. In crowded situations where calls of many individuals overlap the subtle differences between species are additionally attenuated. Here we sought to non-invasively study the phenology of <em>Myotis</em> bats during autumn swarming at a prominent hibernaculum. To do so we recorded sequences of overlapping echolocation calls (N=564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and Linear Frequency Cepstral Coefficients (LFCCs) which additionally encompass the timbre (vocal 'colour') of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying <em>Myotis</em> <em>daubentonii</em> and <em>Myotis</em> <em>nattereri</em>, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either <em>M</em>. <em>daubentonii</em> or <em>M</em>. <em>nattereri</em>, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying a second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide the basis for a new non-invasive acoustic monitoring technique that analyses "swarming soundscapes" by combining classical acoustic parameters and LFCCs, instead of analysing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.</p>
figure of habitus (Palma, 1863) fits the concept of Merodon aberrans. in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species
figure of habitus (Palma, 1863) fits the concept of Merodon aberrans.
Data from: How do lianas and vines influence competitive differences and niche differences among tree species? Concepts and a case study in a tropical forest
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Random forests for predicting species identity of forensically important blow flies (Diptera: Calliphoridae) and flesh flies (Sarcophagidae) using geometric morphometric data: proof of concept
Open the record for dataset details and reuse information.
Molecular systematics, species concepts and myrmecophytism in Cecropia (Cecropieae: Urticaceae): Insights from restriction-site associated DNA
Open the record for dataset details and reuse information.
The soundscape of swarming: Proof of concept for a non-invasive acoustic species identification of swarming Myotis bats
Open the record for dataset details and reuse information.
FIGURE 32 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURE 32. Neighbor joining tree showing the clustering of similar COI sequences in Cyclocephala taxa. Parentheses after the taxon name indicate the number of sequences represented in that cluster. Parentheses are followed by a three-letter country code. CRI = Costa Rica, GLP = Guadeloupe, GTM = Guatemala, HND = Honduras, KNA = St. Kitts and Nevis, MEX = Mexico, NIC = Nicaragua, PAN = Panama, SLV = El Salvador, VEN = Venezuela. Colored branches highlight taxa of the C. mafaffa species complex (green = C. deceptor; red = C. mafaffa mafaffa; blue = C. mafaffa grandis).
FIGURES 25–30 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 25–30. Stigmalia deficiens Casey, lectotype male and paralectotype female. 25, Stigmalia deficiens Casey lectotype male, dorsal habitus. 26, Stigmalia deficiens Casey paralectotype female, dorsal habitus. 27, Parameres of lectotype male, caudal view. 28, Aedeagus of lectotype male, lateral view. 29, Lectotype male specimen labels. 30, paralectotype female specimen labels.
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17, Stigmalia cuernavacana Casey holotype female, dorsal habitus. 18, Elytral epipleural flange of holotype female, dorsal view. 19, Elytral epipleural flange of holotype female, lateral view. 20, Holotype female specimen labels.
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21, Stigmalia fallaciosa Casey holotype male, dorsal habitus. 22, Parameres of holotype male, caudal view. 23, Aedeagus of holotype male, lateral view. 24, Holotype male specimen labels.
FIGURES 11–16 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 11–16. Stigmalia deceptor Casey, lectotype male and paralectotype female. 11, Stigmalia deceptor Casey lectotype male, dorsal habitus. 12, Stigmalia deceptor Casey paralectotype female, dorsal habitus. 13, Parameres of lectotype male, caudal view. 14, Aedeagus of lectotype male, lateral view. 15, Lectotype male specimen labels. 16, Paralectotype female specimen labels.
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7, Stigmalia mafaffa histrionica Casey holotype female, dorsal habitus. 8, Holotype female, elytral epipleural flange in dorsal view. 9, Holotype female, elytral epipleural flange in lateral view. 10, Holotype female specimen labels.
FIGURES 1–2. Cyclocephala deceptor and C in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 1–2. Cyclocephala deceptor and C. mafaffa, basal margin of the pronotum. 1, Cyclocephala deceptor with pronotal basal bead medially complete. 2, Cyclocephala mafaffa with pronotal basal bead medially incomplete.
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3, Lectotype male, dorsal habitus. 4, Lectotype male, ventral habitus. 5, Lectotype male, lateral habitus. 6, Lectotype male specimen labels and aedeagus. Photographs courtesy of Matthias Seidel (Department of Entomology, National Museum, Prague, Czech Republic).
FIGURE 1 in Additional DNA barcodes confirm recent morphological species concepts and synonymies in Callomyia Meigen (Diptera: Platypezidae)
FIGURE 1. Neighbour-Joining tree of 30 Callomyia specimens and two outgroup specimens with COI sequences ≥550 bp, including sex, unique voucher number, sequence length, geographic locality and GenBank number. Bracketed species names are the current species concepts used in Cumming & Wheeler (2016) and include Nearctic synonyms and misidentifications (shown on branch terminals) that are found in Kessel & Buegler (1972).
Data from: Visualizing connectivity of ecological and evolutionary concepts – an exploration of research on plant species rarity
<p>Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.</p>
FIGURES 37–43 in Two new species of Zetzellia Oudemans (Acari: Stigmaeidae) that threaten the concept of genera: disgeneric marriage?
FIGURES 37–43: Zetzellia quasagistemas sp. n. (immatures) 37–38. Larva. 37. dorsum, 38. anogenital region. 39–40. Protonymph. 39. dorsum, 40. anogenital region. 41–42. Deutonymph female. 41. dorsum, 42. anogenital region. 42. Anogenital region of deutonymph male.
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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.