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727 results for “phylogenetic diversity”
Data from: Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related, and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale whereas those assemblages in regions with rainy summers have a stronger signature of coarser-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water-related conditions is the key cause behind this difference. Differences in climatological regimes within the tropics may affect processes mediating species coexistence. The role of broad-scale gradients (e.g. temperature, precipitation) in structuring tropical ectothermic assemblages is greater in regions with rainy summers where climatic niche partitioning is more likely. Our findings highlight the potential stronger role of biotic interactions and neutral processes in structuring ectothermic assemblages facing changes towards warmer and dryer climates.
Data from: A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world
There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled eighteen lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within a small geographical area. The results showed highly diverse communities non-randomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity approach shared similar patterns and were primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies for microorganisms.
Data from: A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135–130 million yr ago (Ma); Pentapetalae is 126–121 Ma; and Rosidae (123–115 Ma) preceded Asteridae (119–110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.
FIGURE 6 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 6. Five species of Micropeplinae from China and Vietnam. A–F: three Micropeplus species most closely related to M. jason sp. n., forming the sculptus species-group and inhabiting the Chang Shan Mountain Range (A–B), Mount Gongga (C–D) and the Tam Dao Mountain Range (E–F); G–H: Cerapeplus spp., C. sinensis from the Qin Ling Mountain Range (G) and Cerapeplus sp. from the Tam Dao Mountain Range (H). Phylogenetic position of respective specimens can be found by tracing unique specimen numbers in Fig. 2, except for Micropeplus #0882 from the Cang Shan Mountain Range (A–B), which did not amplify and was not represented in the DNA analysis.
FIGURE 3 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 3. Micropeplus jason sp. n. from Mount Emei, Sichuan. A–D: holotype, female, #0907, habitus; E–H: paratype, female, #0906, tergite and sternite 8 with enclosed hemisternites (E), hemisternites (F), tergite (G) and ventrite (H) 8; I–M: paratype, male, #0911, tergite and sternite 8 with enclosed aedeagus (I), aedeagus (J, K), tergite (L) and sternite (M) 8.
FIGURE 7 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 7. Adult habitus of representatives of three consecutive sister groups of Micropeplinae, as hypothesised by Newton & Thayer (1995). Body length of Empelus 2.7 mm, Proteinus 2.0 mm and Microsilpha 2.9 mm.
FIGURE 2 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 2. Maximum Likelihood inference phylogram of 85 Micropeplinae ingroup specimens from Southwest China and two neighbouring localities using the 658 nt of the mtDNA barcoding CO1 gene fragment. The outgroup clades and terminals are in grey. The nine red terminal clades are those from hyperdiverse Mount Emei. Clades A–G are discussed in the text. The digits at branches separated by a slash (/) are ML and MP bootstrap values, respectively; a dash (-) after a slash denotes five ML clades not recovered in MP analysis. BIN, GDTC and OUT are interim taxonomic clusters explained in Methods. Seven grey boxes indicate mismatches between GDTC and BINs. Insert in the upper left corner shows different backbone tree arrangement recovered in alternative MP analysis.
FIGURE 1 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 1. Geographical origin of the ingroup Micropeplinae specimens. Eight sampled localities in Southwest China are in the oval. The red frame denotes hyperdiverse mount Emei with at least ten species of Micropeplinae, including Micropeplus jason sp. n. The number in brackets after the regional names indicates the amount of sifted litter in kilograms, followed by Micropeplinae species diversity of Micropeplus (M) and Cerapeplus (C). We failed to amplify DNA of the single Micropeplus specimen #0882 detected from the Cang Mountain Range and, therefore, the entire locality is not included in the DNA analysis.
FIGURE 5 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 5. Ten species of Micropeplinae detected on Mount Emei, Sichuan. A–H: Micropeplus spp.; I: Micropeplus jason sp. n., J: Cerapeplus sp. Phylogenetic position of respective specimens can be found by tracing unique specimen numbers in Fig. 2, except for Cerapeplus #2874, which did not amplify and was not represented in the DNA analysis.
FIGURE 8 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 8. Habitus of Micropeplus spp. A–D: M. tesserula ("Ünökö, Ost-Karpat" [= Rodna mountains, Romania], collector and date unknown, CNC); E–H: M. dokuchaevi (#3996, Russia, Magadan region, 26.vi.1990, A.S. Rjabukhin, CNC); I–L: M. porcatus (#2396, "Feistr. Styr." [= unknown locality], Diener, 9.viii.1904, CNC). Numbers indicate elytral striae. Scale bars: 1 mm.
FIGURE 4 in DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei
FIGURE 4. Micropeplus jason sp. n. from Mount Emei, Sichuan. Unsexed paratypes #0572 (H) and #0573 (A–G, I–J). Habitus (A-D), head fronto-ventral (E), lateral (F) and ventro-lateral (G), anterior body latero-ventral (H), posterior body ventro-terminal (I) and latero-terminal (J). Numbers on elytra indicate elytral costae starting with the weakly developed median (=sutural or adsutural) costa.
FIGURE 22 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 22. Male genital structures of S. totonacum sp.n. holotype (A–C), S. adelinae sp.n. holotype (D–F); and S. miztecum sp.n. holotype (G–I). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 21 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 21. Male genital structures of S. histrio: morphotype 3 (A–C), morphotype 4 (D–F), and morphotype 5 (G–I); and S. occidentalis sp.n. holotype (J–l). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 20 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 20. External morphology of S. histrio: morphotype 2 m (A and C) and f (B and D), morphotype 3 m (E) and f (F), morphotype 4 m (G) and f (H), and morphotype 5 m (I) and f (J); S. occidentalis sp.n. holotype m (K) and paratypes m #2 (M), f #3 (L) and f #4 (N); S. totonacum sp.n. holotype m (O) and paratype f #1 (P); S. adelinae sp.n. holotype m (Q) and paratype f #1 (R); S. miztecum sp.n. holotype m (S) and paratype f #1 (T) (Scale bars = 1cm).
FIGURE 19 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 19. Male genital structures of S. mexicanum: morphotype 1 (A–C) and morphotype 2 (D–F); S. histrio: morphotype 1 (G–I) and morphotype 2 (J–l). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 18 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 18. Type specimens of S. bolivari: lectotype m (A) and paralectotype m (B); S. histrio holotype m (C) and S. carinatum holotype m (D) (Scale bars = 1cm).
FIGURE 17 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 17. Type specimens of S. variabile: allotype f (A); S. mexicanum lectotype f (B) and paralectotype m (C); O. crassipes holotype m (D); S. ictericum: lectotype m (E) and paralectotype f (F); S. marginatum lectotype m (G) and paralectotype f (H) (Scale bars = 1cm).
FIGURE 16 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 16. Male genital structures of S. crypticum sp.n. holotype (A–C); S. borrei (D–F); S. variabile: morphotype 1 paratype #234 (G–I) and morphotype 2 (J–l). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 15 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 15. External morphology of S. rugosum: morphotype 2 m (A) and f (B), morphotype 3 m (C) and f (D); S. crypticum sp.n. holotype m (E) and paratype f #45 (F); S. borrei m (G) and f (H); S. variabile: morphotype 1 paratype m #134 (I) and f (J), and morphotype 2 m (K) and f (L); S. mexicanum: morphotype 1 m (M) and f (N), and morphotype 2 m (O) and f (P); S. histrio: morphotype 1 m (Q and S) and f (R and T) (Scale bars = 1cm).
FIGURE 13 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 13. Male genital structures of S. infernalis sp.n. holotype (A–C); S. rugosum: morphotype 1 (D–F), morphotype 2 (G–I) and morphotype 3 (J–l). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
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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.