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1,344 results for “: phylogenomics”
Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy
<p>The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between <em>Serrasalmus</em> and <em>Pristobrycon</em>, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae.</p>
Quality Control, Assembly and Phylogenomics results using UCEasy from the UCEs
<p>UCEasy was used to reproduce the results of the analysis of UCEs of 115 individuals representing 53 species of birds of the genus Turdus, present in the work of Batista et al. (2020), available at https://doi.org/10.1098/rspb.2019.2400. The methodology adopted by UCEasy can be seen at https://github.com/uceasy/uceasy, and we obtained results for different constructions of phylogenetic matrices. Based on the amount of UCE loci, these matrices vary in the degree of missing data allowed, where 75% represents a matrix that allows a greater amount of missing data compared to the 85% matrix, since these percentages represent how complete the matrices of data are.</p>
Revisiting the evolution of Ostrinia moths with phylogenomics (Pyraloidea: Crambidae: Pyraustinae)
<p>Reconstructing a robust phylogenetic framework is key to understanding the ecology and evolution of many economically important taxa. The crambid moth genus <i>Ostrinia</i> contains multiple agricultural pests, and its classification and phylogeny has remained controversial due to the paucity of characters and the lack of clear morphological boundaries for its species. To address these issues, we inferred a molecular phylogeny of <i>Ostrinia</i> using a phylogenomic dataset containing 498 loci and 115,197 nucleotide sites and examined whether traditional morphological characters corroborate our molecular results. Our results strongly support the monophyly of one of the <i>Ostrinia</i> species groups but surprisingly do not support the monophyly of the other two. Based on the extensive morphological examination and broadly representative taxon sampling of the phylogenomic analyses, we propose a revised classification of the genus, defined by three species groups (<i>Ostrinia nubilalis</i> species group,<i> Ostrinia obumbratalis</i> species group, and<i> Ostrinia penitalis</i> species group), which differs from the traditional classification of Mutuura & Munroe (1970). Morphological and molecular evidence reveal the presence of a new North American species, <i>O. multispinosa </i>Yang, <b>sp.n.</b>, closely related to <i>O. obumbratalis</i>. Our analyses indicate that the <i>Ostrinia</i> ancestral larval host preference was for dicots, and that <i>O. nubilalis</i> (European corn borer) and <i>O. furnacalis </i>(Asian corn borer) independently evolved a preference for feeding on monocots (i.e., maize). Males of a few <i>Ostrinia </i>species have enlarged, grooved midtibiae with brush organs that are known to attract females during courtship. Males of the ancestral <i>Ostrinia </i>had relatively small midtibiae without brush organs, suggesting that the ancestral mate-finding behavior instead involved pheromones emitted by females. Our study provides a strong evolutionary framework for this agriculturally important insect lineage.</p>
Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene
<p>Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of <i>Oreocharis </i>(Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in <i>Oreocharis</i> and applied explicit birth-death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that <i>Oreocharis</i> underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of <i>Oreocharis</i>, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of <i>Oreocharis</i> is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in <i>Oreocharis</i>, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.</p>
Fig. 11 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 11. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia madrensis (holotype worker), S. JTL066 (worker, CASENT0610648), S. benevidesae (holotype worker), S. chiapaneca (holotype worker), S. parietalis (holotype worker), S. setosa (holotype worker), S. JTL073 (worker, MCZ-ENT00511569), S. JTL075 (worker, CASENT0601445), S. disjuncta (holotype worker), and S. augustae (worker, CASENT0644275). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 10 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 10. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia jennierussae (holotype worker), S. persimilis (holotype worker), S. JTL018 (worker, JTLC000013995), S. machaquila (holotype worker), S. murillocruzae (holotype worker), S. truncata (holotype worker), S. JTL084 (worker, FMNHINS0000095760), S. JTL050 (worker, CASENT0249320), S. JTL082 (worker, CASENT0617700), and S. honduriana (lectotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 7 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 7. Phylogenetic relationships among COI barcode sequences for Syscia. Red samples were sequenced for UCEs. Black samples were downloaded from the BOLD database.The tree was inferred using IQ-TREE with the data partitioned by codon position. Black circles on nodes indicate high support, which we define as ≥95% ultrafast bootstrap support and ≥95% SH-like branch support. Clades of named species are shaded as a visual aid, with gray outlines indicating non-monophyly of species.
Fig. 1 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 1. Variation in Syscia occipital carina. (A) Flange weakly developed, less visible in face view. (B) Flange strongly developed, easily visible in face view.
Fig. 6 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 6. Phylogeny of New World Syscia, inferred using the program IQ-TREE and 1,388 UCE loci.Two outgroup taxa (two species of Ooceraea) are not shown. Node support values (ultrafast bootstrap/SH-like) <100/100 are depicted with red dots.The imaged specimen is S. ticomontana (CASENT0644376).
Fig. 3 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 3. Variation in Syscia profiles and pilosity. (A) AIII in dorsal view trapezoidal, with convex sides. (B) AIII in dorsal view weakly trapezoidal, with convex sides. (C) AIII in dorsal view trapezoidal, with flat sides. (D) AIV in dorsal view, with convex sides, anterior margin not truncate. (E) AIV in dorsal view, with convex sides, anterior margin moderately truncate. (F) AIV in dorsal view, with nearly flat sides, anterior margin strongly truncate. (G) AIII dorsal profile strongly convex. (H) AIII dorsal profile weakly convex. (I) AIII dorsal profile flat. (J) AIV dorsal profile convex. (K) AIV dorsal profile weakly convex. (L) AIV dorsal profile flat. (A, B, G, J) Standing pilosity long, coarse. (C, H, K) Standing pilosity of medium length and thickness. (I, L) Standing pilosity short, fine.
Fig. 12 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 12. Present-day distributional records of Biastes projected on a global map with reconstructed continental boundaries of the mid Miocene. Shown is a polar projection centered on the Geographic North Pole. During this time peri od, large parts of the present-day Bering and Chukchi seas were likely above sea level, forming a continuous land bridge between the Nearctic and the Palearctic. Locality records are taken from the Discover Life database (Ascher and Pickering 2020) and own databasing efforts. Selected entries were further taken from GBIF (2019). Note that certain Far Eastern records are regional centroids and do not represent exact collection localities.
Fig. 11 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 11. Morphological differences between species of Schwarzia. (A) Mesosoma of S. gretae in lateral view (♀, paratype). Left arrow points to the produced, lamellate axilla. Right arrow points to the produced, dorsally protruding metanotum. (B) Posterior dorsolateral view of S. icipensis (♀, paratype).The axillae are not produced or lamellate. Scale bars show 1 mm.
Fig. 13 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 13. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia latepunctata (holotype worker), S. borowieci (holotype worker), S. volucris (holotype worker), S. JTL076 (queen, CASENT0614221),S. JTL064 (worker, CASENT0631661), S. JTL033 (worker, CASENT0611831),S. grandis (holotype worker), and S. JTL003 (worker, INB0003213589). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 9 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 9. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia pervagata (holotype worker), S. peten (holotype worker), S. JTL074 (worker, MCZ-ENT00511564), S. brachyptera (holotype worker), S. valenzuelai (holotype worker), S. JTL071 (worker, FMNHINS0000095759), S. quisquillis (holotype worker), S. sumnichti (holotype worker), S. JTL060 (worker, CASENT0644220), and S. JTL085 (worker, CASENT0602939). Scale bars 0.2 mm. Species are in order of mean HW, which is shown in the lower left of the distribution map. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 8 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 8. Male paratype of Schwarzia icipensis sp. nov. (A) Habitus, dorsal view. (B) Habitus, frontal view. (C) Habitus, lateral view. (D) Label information as deposited with the paratype. (E) Details ofT7. Scale bars show 1 mm.
Fig. 10 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 10. Characteristic morphological features of different species of Schwarzia. (A) Head of female S. emmae, anterior dorsolateral view.The upper two arrows point to granulose protrusions on the supra-antennal area, the lower arrow points to the indented inner margin of the compound eye. (B) Female paratype of S. gretae in same view.The supra-antennal area is evenly punctate and the inner margin of the compound eye is not indented. (C) Details ofT1–T2 of S. icipensis (♀, paratype). (D) Details ofT1–T2 of S. gretae (♀, paratype). Scale bars show 1 mm.
Fig. 7 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 7. Female holotype of Schwarzia icipensis sp. nov. (A) Habitus, dorsal view. (B) Habitus, frontal view. Arrow points to region of supra-antennal area with slightly less dense punctation than surroundings. (C) Habitus, lateral view. (D) Details ofT4–T5. (E) Label information as deposited with the holotype. Scale bars show 1 mm.
Fig. 9 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 9. Male holotype of Schwarzia lualenyiensis sp. nov. (A) Habitus, lateral view. (B) Habitus, frontal view. (C) Habitus, dorsal view. (D) Details of T7. (E) Label information as deposited with the holotype. Scale bars show 1 mm.
Fig. 2 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 2. Variation in Syscia subpetiolar process. (A) Subtriangular with flat to concave posterior margin. (B) Subtriangular with convex posterior margin. (C) Subtriangular with small tooth on posterior margin. (D) Subquadrate. (E) Subtriangular with large acute tooth on posterior margin. F. With fenestra and notch on posterior margin.
Fig. 6 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia
Fig. 6. Male paratype of Schwarzia gretae sp. nov. (A) Habitus, lateral view. Left arrow points to the lamellate axilla. Right arrow points to the produced, dorsally protruding metanotum. (B) Habitus, frontal view. Arrows point to produced ridges along the mesoscutellar line. (C) Habitus, dorsal view. (D) Details ofT6–T7. (E) Label information as deposited with the paratype. Scale bars show 1 mm.
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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.