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1,492 results for “species delimitation”
FIGURE 9 in The damselfly genus Megaloprepus (Odonata: Pseudostigmatidae): Revalidation and delimitation of species-level taxa including the description of one new species
FIGURE 9. Megaloprepus caerulatus in copulation wheel on Barro Colorado Island (Panama) highlighting the sexual dimorphism.
FIGURE 5 in The damselfly genus Megaloprepus (Odonata: Pseudostigmatidae): Revalidation and delimitation of species-level taxa including the description of one new species
FIGURE 5. Megaloprepus caerulatus color patterns: (a) lateral view of prothorax, pterothorax including mesostigmal plates, wing base and coxa; (b) dorsal view of prothorax. al: prothorax anterior lobe. pl: prothorax posterior lobe. mp: mesostigmal plates. cx1–3: coxae.
FIGURE 4 in The damselfly genus Megaloprepus (Odonata: Pseudostigmatidae): Revalidation and delimitation of species-level taxa including the description of one new species
FIGURE 4. Megaloprepus brevistigma color patterns: (a) lateral view of prothorax, pterothorax including mesostigmal plates, wing base and coxa; (b) dorsal view of prothorax. al: prothorax anterior lobe. pl: prothorax posterior lobe. mp: mesostigmal plates. cx1–3: coxae.
Figure 2. Coalescent species trees with 13 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Figure 2. Coalescent species trees with 13 (A) and 14 (B) assumed species based on 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene sequences. Posterior probabilities of clades are provided along internal branches and posterior probabilities for the presence of individual species are provided behind the terminal branches. Scale bars denote the fraction of substitutions per site.
Figure 6 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 6. Summary of heuristic BPP delimitation based on the gdi under three topological scenarios (1, 2 and 3). Four BPP runs were combined in every step of a multiple analysis of progressive hierarchical lumping of sister taxa. Boxplots in the left (A) refer to the gdi of each well-supported phylogenetic subclade while those on the right (B) correspond to the three distinct evolutionary entities: Clade 1 (I), Clade 2 (II) and cypriaca (III).
Figure 5 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 5. Multilocus calibrated species-tree produced by StarBEAST2. Numbers above branches represent mean divergence times (Myr), while numbers below represent posterior probabilities. Asterisks represent posterior probabilities equal to 1. (Agama spp. contains Agama agama, A. boensis, A. bottega, A. boueti, A. boulengeri, A. impalearis, A. planices, A. sankaranica and A. spinosa).
Figure 4 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 4. Phylogenetic tree based on the concatenated dataset (mtDNA & nuDNA). Bayesian posterior probabilities (PP) and maximum likelihood bootstrap support (bs) values are represented in the form PP/bs above or beside nodes. (Agama spp. contains Agama agama, A. boensis, A. bottega, A. boueti, A. boulengeri, A. impalearis, A. planices, A. sankaranica and A. spinosa).
Figure 3 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 3. Map showing the sampling localities of specimens used in the present study. Different colours represent the phylogenetic subclades indicated in Figures 2 and 4.
Figure 2 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 2. Phylogenetic tree based on mtDNA (ND4-tRNAs and 16S rRNA). Bayesian posterior probabilities (PP) and maximum likelihood bootstrap support (bs) values are represented in the form PP/bs above or beside nodes. (Agama spp. contains Agama agama, A. boensis, A. bottega, A. boueti, A. boulengeri, A. impalearis, A. planices, A. sankaranica and A. spinosa).
Figure 1 in The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)
Figure 1. Map showing the distribution of all known morphological subspecies of Laudakia stellio in the East Mediterranean.
Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays
<p class="MsoNormal"><span>Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus <em>Aphelocoma</em> provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (<em>A. w. sumichrasti</em>), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage <em>A. w. texana</em>, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (<em>A. californica</em>) and Woodhouse's Scrub-Jay (<em>A. woodhouseii</em>), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.</span></p>
FIGURE 4 in Delimiting species within the Lysmata vittata (Stimpson, 1860) (Decapoda: Lysmatidae) species complex in a world full of invaders
FIGURE 4. Phylogenetic tree obtained from Maximum Likelihood (ML) analysis of the partial 16S rRNA gene for shrimps from the Lysmata vittata species complex, selected lysmatids, and Merguia. Numbers above or below the branches represent bootstrap values obtained from ML in the webserver W-IQ-TREE (Trifinopoulos et al. 2016; http://iqtree.cibiv.univie.ac.at/). Low node values (<50) were removed from the final topology. Asterisk indicates the neotype of L. vittata. Vertical bars represent dissimilar taxonomic units suggested by ASAP. Numbers below vertical bars indicate the number of species identified by ASAP (27) and ASAP-score (2.0) in the corresponding partition.
FIGURE 5 in Delimiting species within the Lysmata vittata (Stimpson, 1860) (Decapoda: Lysmatidae) species complex in a world full of invaders
FIGURE 5. Distribution map showing confirmed records for each of the species within the Lysmata vittata species complex (Stimpson, 1860). Stars represent type locality of each species.
FIGURE 2 in Delimiting species within the Lysmata vittata (Stimpson, 1860) (Decapoda: Lysmatidae) species complex in a world full of invaders
FIGURE 2. Color pattern variation of Lysmata vittata sensu lato from various localities. A, Lysmata vittata sensu stricto from Chesapeake Bay, USA (Aguilar et al. 2022; photograph by Robert Aguilar); B, L. rauli sensu stricto from Bocas del Toro, Panama (Pachelle et al. 2018; photograph by Robert Lasley); C, L. cf. rauli from Lazarus Island, Singapore (Anker & De Grave 2016; photograph by Arthur Anker); D, L. cf. vittata from Posyet Bay, Russia (Marin et al. 2012); E, type specimen of L. rauli collected in Salvador, Brazil (Laubenheimer & Rhyne 2010); F, L. vittata sensu stricto from Hong Kong (photograph by Gustav Paulay). Arrows indicate the presence of red transverse band on pleonal segments.
FIGURE 3. Multivariate analysis. A in Delimiting species within the Lysmata vittata (Stimpson, 1860) (Decapoda: Lysmatidae) species complex in a world full of invaders
FIGURE 3. Multivariate analysis. A, resultant biplot of Principal Component Analysis computed between Brazil (red) and USA (green) populations representing Lysmata vittata species complex based on 11 morphological characters showing the two first principal components, which represent 44.08% of total variation. B, resultant histogram of Discriminant Function Analysis values computed between Brazil (red) and USA (green) populations representing Lysmata vittata species complex based on 10 morphological characters.
Figure 2 in Discovery of the male of Loxaulus hyalinus, and implications for the sympatric species Loxaulus laeta (Hymenoptera: Cynipidae: Cynipini): an integrative taxonomical case of species delimitation
Figure 2. Overview of molecular results. Left: best maximum likelihood (ML) tree based on three genes (COI, cytb and 28SD2). Black squares at nodes indicate both ≥95% posterior probability (Bayesian inference) and ≥80% bootstrap (ML) node support. White squares at nodes indicate both <95% posterior probability (Bayesian inference) and ≥80% bootstrap (ML) node support. Right: Sexual generation for each terminal indicated; grey bars indicate the assignations of individuals to candidate species for the ABGD, bPTP, BPP, and BFD approaches. Striped grey bars indicate the omission of the signalled taxa in some of the analyses.
Figure 1 in Discovery of the male of Loxaulus hyalinus, and implications for the sympatric species Loxaulus laeta (Hymenoptera: Cynipidae: Cynipini): an integrative taxonomical case of species delimitation
Figure 1. SEM pictures of Loxaulus hyalinus male: (a) head in frontal view, (b) head in dorsal view, (c) head in posterior view, (d) antenna, (e) mesosoma in dorsal view, (f) head and mesosoma in lateral view, (g) radial cell, (h) metasoma.
Figure 3 in Discovery of the male of Loxaulus hyalinus, and implications for the sympatric species Loxaulus laeta (Hymenoptera: Cynipidae: Cynipini): an integrative taxonomical case of species delimitation
Figure 3. Summarised tree of the terminals (A–D) and nodes (I–III) recovered from the BPP analyses. Results of the BPP analyses for the three subsets used (1–3). For each subset, the four models of priors (M1–M4) are given, with varying values of population size (θ) and divergence time (τ). Each model was iterated by changing between two algorithms, A0 and A1. The first rows correspond to the best trees recovered for each analysis. The last rows for each subset show the posterior probability support for every node (I–III) in the given subset.
Fig. 2 in Molecular Phylogenetic Analysis and Species Delimitation in the Pine Needle-feeding Aphid Genus Essigella (Hemiptera, Sternorrhyncha, Aphididae)
Fig. 2. Phylogenetic tree (ML and BI) of Essigella species using concatenate ATP6, COI, EF-1α and Gnd. Pinus species of the subgenus Strobus appear either in orange or in red, those of the subgenus Pinus either in green or in blue. Color nuances represent infragroup within each subgenus. Nonidentified Pinus and other Pinaceae are in black.Values indicate ML bootstrap % values followed by Bayesian posterior probabilities % values.
Fig. 1 in Molecular Phylogenetic Analysis and Species Delimitation in the Pine Needle-feeding Aphid Genus Essigella (Hemiptera, Sternorrhyncha, Aphididae)
Fig. 1. Essigella hoerneri on Pinus monophylla (left) and Essigella sp. on Pinus ponderosa (right) (pictures from C. Favret).
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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.