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1,492 results for “species delimitation”
Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Data from: Upstream analyses create problems with DNA-based species delimitation
Genetic-based delimitation of species typically involves a multistep process in which DNA data are analyzed with a series of different programs. Although the performance of the programs associated with each step has been evaluated separately, no analysis has considered how errors in the upstream assignment of individuals to putative species impacts the accuracy of species delimited in downstream analyses, such as those associated with the coalescent-based Bayesian program bpp. Here we show that because the minimal data requirements for accurate performance in each of the separate steps involved in the delimitation process differ, the reliability of inferences about species delimited from DNA sequences can be compromised. Our results provide important insights into the practice of species delimitation. Specifically, even if users exercise the practices advocated for DNA-based delimitation, there may very well be errors in individual-species association, and consequently uncertainty in the guide tree (both derived from upstream analyses that are prerequisites for analyses with bpp), which can lead to under or overestimation of biodiversity, even though the Bayesian program bpp itself may perform very well. These results highlight the usefulness of complementary data (i.e., data in addition to genetic data), especially for the assignment of individuals to putative species, to improve the accuracy of species delimitation.
Data from: Delimiting species of marine gastropods (Turridae, Conoidea) using RAD-sequencing in an integrative taxonomy framework
Species delimitation in poorly-known and diverse taxa is usually performed based on monolocus, DNA barcoding-like approaches, while multilocus data are often used to test alternative species hypotheses in well-studied groups. We combined both approaches to delimit species in the Xenuroturris / Iotyrris complex, a group of venomous marine gastropods from the Indo-Pacific. First, COI sequences were analyzed using three methods of species delimitation, ABGD, PTP and GMYC to propose primary species hypotheses (PSH). Second, RAD-seq data were also obtained and an IQ-tree phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-seq data. Alternative species partitions revealed with the COI dataset were also tested using the RAD-seq data and the BFD method. The congruence between the species hypotheses proposed with the mitochondrial gene and the clades in the RAD-seq tree, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the PSH into secondary species hypotheses (SSH). Allopatric PSH defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.
FIGURE 8 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 8. The second syntype of Agrostis pleiophylla, also its lectotype, Clarke 26852 (B).
FIGURE 5 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 5. Holotype of Deyeuxia diffusa (NY, p.p., the left hand plant on the sheet).
FIGURE 9 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 9. Holotype of Agrostis zenkeri (LE in Hb. Trinius).
Figure 8. The species delimitation model retrieved a in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 8. The species delimitation model retrieved a maximum of eight species.
FIGURE 1 in Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa
FIGURE 1. TCS networks analyses results based on (A) ITS sequences and (B) trnS-G sequences.
FIGURE 1. Sporangia containing 64 in Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China
FIGURE 1. Sporangia containing 64 (A) and 32 spores (B).
FIGURE 5 in Sorting out the muddle: taxonomy and nomenclature of Thymus ×porcii (Lamiaceae) and related nothotaxa, with comments on parent species delimitation
FIGURE 5. Holotype of Thymus ×porcii nothovar. calvariensis (KW).
FIGURE 2 in Sorting out the muddle: taxonomy and nomenclature of Thymus ×porcii (Lamiaceae) and related nothotaxa, with comments on parent species delimitation
FIGURE 2. Lectotype of Thymus ×porcii (BP550310).
FIGURE 3 in Sorting out the muddle: taxonomy and nomenclature of Thymus ×porcii (Lamiaceae) and related nothotaxa, with comments on parent species delimitation
FIGURE 3. Lectotype of Thymus ×pilisiensis (BP352954).
Figure 3 in Phylogeny-based species delimitations and the evolution of host associations in symbiotic zoanthids (Anthozoa, Zoanthidea) of the wider Caribbean region
Figure 3. Map of the wider Caribbean region showing a compilation of observed symbiotic zoanthid species in each location. The following list defines the location abbreviations, and credits the source of observations. Species observations without citations are from the current study. Abbreviations: PR, La Parguera, Puerto Rico, West 1979; USVI, US Virgin Islands, Duchassaing & Michelotti, 1860, this study, and (P.t.) Pax, 1910; GUA, Guadeloupe, Pax & Müller, 1956; DOM, Dominica; BAR, Barbados, Crocker & Reiswig, 1981 and this study; TOB, Tobago; SUR, Suriname, USNM 50878; AMA, Amazon River outfall, Brazil, USNM 1084839; MSB, Maranhão State, Brazil, Campos et al., 2005; BUZ, Búzios, Brazil; CUR, Curaçao; COL, Colombia, (Santa Marta, P. pu.) Alvarez, Van Soest & Rützler, 1998, (Cartagena) J. Sanchez pers. comm.; PAN, Bocas del Toro, Panama; HON, Utila, Honduras, Sinniger et al., 2005; BEL, Carrie Bow Cay, Belize, (P.c.) USNM 32338, (P.pa.) Lewis, 1982, (P.pu) USNM 32345, (P.s.) J. Wulff pers. comm.; CUB, Havana, Cuba, Varela, Ortiz & Lalana, 2003; FGB, Flower Garden Banks, USA; FLG, Gulf coast of Florida, USA; FLK, Florida Keys, USA, (P.c.) USNM 41535; JAM, Jamaica, Duchassaing & Michelotti, 1860, (P.pu. and P.t.) West, 1979; NAV, Navassa Island, USA; BAH, Bahamas, Duchassaing & Michelotti 1860, (E.c.) Willenz & Hartman, 1994; DR, Dominican Republic, Williams et al., 1983; C&G, Carolinas and Georgia, USA, (P.a.) USNM 16870, (P.pa.) USNM 51535, (P.s.) this study; BUR, Bermuda, Ryland & Westphlen, 2004.
Figure 1 in Intraspecific or interspecific variation: delimitation of species boundaries within the genus Gammarus (Crustacea, Amphipoda, Gammaridae), with description of four new species
Figure 1. Sample sites for the species of Gammarus from China.
Figure 2 in Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves: Megaluridae)
Figure 2. Principal components analysis of morphometric data for the members of the Bradypterus thoracicus complex. See Table 4 for summary statistics.
Data from: Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species
<p><span>Since the last revision in 2015, the taxonomy of section <i>Flavipedes</i> evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section <i>Flavipedes </i>members using modern delimitation methods applied to an extended set of strains (n=90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (<i>benA</i>, <i>CaM</i>, <i>RPB2</i>) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. <i>A. alboluteus</i>, <i>A. alboviridis</i>, <i>A. inusitatus</i> and <i>A. lanuginosus</i>, and <i>A. capensis</i> is synonymized with <i>A. iizukae</i>. Phenotypic analyses were performed for the new species and their relatives and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, common species from the section are ecologically diverse, occurring in indoor environment (6 species), clinical samples (5 species), food and feed (4 species), droppings (4 species) and other less common substrates/environments. Due to the occurrence of section <i>Flavipedes</i> species in the clinical material/hospital environment, we also evaluated the susceptibility of 66 strains to six antifungals (Amphotericin B, Itraconazole, Posaconazole, Voriconazole, Isavuconazole, Terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for wild-type <i>A. fumigatus</i> were found for both triazoles and amphotericin B for <i>A. ardalensis, A. iizukae, </i>and<i> A. spelaeus</i> whereas <i>A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, </i>and<i> A. olivimuriae</i> were comparable to or more susceptible as <i>A. fumigatus</i>. Finally, terbinafine was <i>in vitro</i> active against all species except <i>A. alboviridis</i>.</span></p>
FIGURE 3 in Eriocaenus (Acari: Trombidiformes: Eriophyoidea), a new genus from Equisetum spp. (Equisetaceae): morphological and molecular delimitation of two morphologically similar species
FIGURE 3. Semi-schematic drawings of Eriocaenus ramosissimi n. sp.: N. Nymph; L. Larva.
Figure S1 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure S1 - The only parsimonious tree obtained from the maximum parsimony (MP) analysis. Topology of species groupings is similar to that of the Bayesian tree (see Figure 3). Node supports are reported on the branches; the first value is bootstrap support from MP analysis; the second value in bracket indicates the posterior probability obtained from Bayesian analysis; only moderate to high node support values are indicated; Jujubinus exasperatus is used as outgroup; A-E indicates different possible species-units in the dataset: A (Oxystele tabularis), B (Oxystele variegata), C (Oxystele impervia), D (Oxystele sinensis), E (Oxystele tigrina), as in Figure 3.
Figure S2 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure S2 - Bayesian tree assembled using MrBayes indicating the groupings of specimens and the posterior probability of the nodes.
Figure 4 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure 4 - Patterns of shell colour within the genus Oxystele. A–C Oxystele variegata from Namibia, 5 km north of Swakopmund, diameter 22.2 mm (NMSA E6038) D–F Oxystele impervia from the Western Cape, Groen Rivier, diameter 22.3 mm (NMSA E7353) G–I Oxystele sp. from theEastern Cape, Tsitsikamma National Park, diameter 16.5 mm (HVDBM058-10, NMSA W7371); the colour pattern of these specimens suggests Oxystele variegata, but these specimens group within the unit of Oxystele impervia J–L Oxystele sp. from the Northern Cape, Noup, diameter 18.0 mm (HVDBM185-10, NMSA W7608); the colour pattern suggests Oxystele impervia, but they group with Oxystele variegata (see Figure 4 and Appendix 2 for the phylogenetic groupings of these specimens and node supports; these groupings contradict their morphological identification).
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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
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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.