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727 results for “phylogenetic diversity”
The role of riparian functional and phylogenetic diversity on leaf litter processing in rivers
While taxonomic diversity mediates changes in ecosystem function is well-studied, how deeper dimensions of biodiversity, specifically phylogenetic and functional, independent of taxonomic diversity, drive important processes is understudied. The overarching goal of this work was to determine the role of these dimensions of biodiversity independently and/or interactively explain carbon processing in rivers. Here, we explicitly link community structure and subsequent traits of riparian forests to adjacent ecosystem processing of carbon (e.g., leaf litter). This was accomplished by examining how forests are actually structured in addition to experimental manipulations of phylogenetic and functional diversities of riparian forest community inputs of leaf litter to streams. Experimental field manipulations were carried out in three Piedmont headwater streams to answer the following questions: (1) Does existing variation in taxonomic, functional and phylogenetic diversity of riparian communities differentially drive decomposition in rivers? And (2) Independent of taxonomic diversity, how does functional and phylogenetic diversity of leaf litter assemblages influence rates of decomposition in rivers? We observed significant interspecific variation in breakdown among 30 riparian tree species, in addition to significant relationships between breakdown rate and important foliar tissue chemistries. Breakdown of mixtures that reflected the composition of the riparian species composition did not vary with functional nor phylogenetic diversity, but breakdown of litter mixtures was higher than that of single species. In a separate study, when manipulated independently, functional and phylogenetic diversity were positively related to breakdown, and explained similar degrees of variation. These results are important to understand in light of deepening knowledge of the role different dimensions of biodiversity take in explaining ecosystem function, as well as how these measures can b
Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria: phylogenetic data
<p>Alignments, trees and Biogeobears analyses related to the study: Leliaert F, Payo DA, Gurgel CFD, Schils T, Draisma SGA, Saunders GW, Kamiya M, Sherwood AR, Lin S-M, Huisman John M, Le Gall L, Anderson RJ, Bolton John J, Mattio L, Zubia M, Spokes T, Vieira C, Payri CE, Coppejans E, D'hondt S, Verbruggen H, De Clerck O. Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography. 2018;45(10):2299-313. doi:10.1111/jbi.13410</p> <p>Abstract: Biogeographical processes underlying Indo-Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals. Species diversity estimates were inferred using DNA-based species delimitation methods. Historical biogeographical patterns were inferred based on a six-gene time-calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographic range evolution. The importance of geographic isolation for speciation was further evaluated by population genetic analyses at the intraspecific level. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo-Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long-term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA. Our results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.</p>
Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"
<p>Supplementary phylogenetic data for Rouïl <em>et. al.</em> 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"</p> <p> </p> <p>The data set consists of the following sub-directories:</p> <p>1) "APSE_conserved_proteins_alns": Single-copy conserved genes codon sequences and alignments in FASTA format.</p> <p>2) "APSE_phylogeny": Files used for APSE phylogenetic and recombination analyses.</p> <p>3) "APSE_reannotations": GenBank-formatted files of the assemblies and re-annotations of APSE phages. Newly-sequenced phages deposited at the European nucleotide Archive are also included. ***New in this version***</p> <p>4) "APSE_toxin_lyzozyme": Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies.</p> <p>5) "Arsenophonus_PHASTER": PHASTER phage annotation output files organised by organisim and contig/scaffold.</p> <p>6) "Hamiltonella_drafts": Newly-sequenced low-coverage draft <em>Hamiltonella</em> genomes in FASTA format.</p> <p>7) "Hamiltonella_phylogeny": files used for <em>Hamiltonella</em> phylogenetic analysis.</p> <p> </p> <p>See enclosed README.txt file for more details.</p> <p> </p> <p>* ver. 1.1.1: Updated annotations for APSE genomes including inteins missing in previous annotation files.</p>
Fig. 6 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 6. Paratypes of Pristimantis boucephalus sp. nov. in dorsal (upper row) and ventral (lower row) views. From left to right: ♀ (MUSM 24479), ♂ (MUSM 24477), ♂ (MUSM 24478), juvenile (MUSM 24474). Photos by E. Lehr.
Fig. 7 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 7. Type locality of Pristimantis boucephalus sp. nov. in the Yanachaga-Chemillén National Park. Photo by E. Lehr.
Fig. 4 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 4. Preserved holotype (MUSM 31102, SVL 14.1 mm) of Pristimantis boucephalus sp. nov. A. Dorsal view. B. Ventral view. Photos by E. Lehr.
Fig. 5 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 5. Pristimantis boucephalus sp. nov., holotype (MUSM 31102). A. Dorsal view of head. B. Lateral view of head. C. Ventral view of hand. D. Ventral view of foot. Drawings by J. Moravec.
Fig. 3 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 3. Live holotype (MUSM 31102, SVL 14.1 mm) of Pristimantis boucephalus sp. nov. A. Dorsal view. B. Dorsolateral view. C. Ventral view. Photos by E. Lehr.
Fig. 25 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 25. Habitat of Tachydromia ebejeri Gonçalves, Grootaert & Andrade sp. nov. in a forest of Quercus pyrenaica Willd. in Portugal, Arganil, Benfeita (Mata da Margaraça), a region under submediterranean influence.
Fig. 24 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 24. Forest of Fagus sylvatica L. in the Apennine Mountains, where Tachydromia apterygon Plant & Deeming, 2006 can be found.
Fig. 21 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 21. Drawings of the tip of stenopterous wings and images obtained by scanning electron microscope (SEM) of the micropterous wings. Males are pictured in the left column, females in the right. A, C. T. pandellei (Séguy, 1941). B–C. T. pieltaini (Gil Collado, 1936). D–E. T. semiaptera (Gil Collado, 1923). F–G. T. stenoptera Gonçalves, Grootaert & Andrade sp. nov. Scale bars: A–D, F = 50 µm; E, G = 10 µm.
Fig. 19 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 19. Images obtained by scanning electron microscopy of the spur-like structures present on the apical portion of the male mid tibia. A. T. lusitanica (Grootaert, Shamshev & Andrade, 2009). B. T. pandellei (Séguy, 1941). C. T. pieltaini (Gil Collado, 1936). D. T. ebejeri Gonçalves, Grootaert & Andrade sp. nov. E–F. T. semiaptera (Gil Collado, 1923). G. T. stenoptera Gonçalves, Grootaert & Andrade sp. nov. H. T. cantabrica Gonçalves, Grootaert & Andrade sp. nov. I. T. nigrohirta Gonçalves, Grootaert & Andrade sp. nov. J. T. apterygon Plant & Deeming, 2006. Scale bars: 10 µm.
Fig. 17 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 17. Mounted specimens of the Iberian ant-like Tachydromia Meigen, 1803. Males are pictured in the left column, females in the right. A–B. T. lusitanica (Grootaert, Shamshev & Andrade, 2009). C–D. T. nigrohirta Gonçalves, Grootaert & Andrade sp. nov. E–F. T. ebejeri Gonçalves, Grootaert & Andrade sp. nov. G–H. T. stenoptera Gonçalves, Grootaert & Andrade sp. nov. Scale bars: 1 mm.
Fig. 23 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 23. Distribution of Tachydromia apterygon Plant & Deeming, 2006 in Italy. Nine localities are currently known.
Fig. 15 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 15. Habitus of live specimens of the Iberian ant-like Tachydromia Meigen, 1803. Males are pictured in the left column, females in the right. A–B. T. lusitanica (Grootaert, Shamshev & Andrade, 2009). C–D. T. nigrohirta Gonçalves, Grootaert & Andrade sp. nov. E–F. T. ebejeri Gonçalves, Grootaert & Andrade sp. nov. G–H. T. stenoptera Gonçalves, Grootaert & Andrade sp. nov. I–J. T. cantabrica Gonçalves, Grootaert & Andrade sp. nov.
Fig. 18 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 18. Mounted specimens of the Iberian ant-like Tachydromia Meigen, 1803. Males are pictured in the left column, females in the right. A–B. T. cantabrica Gonçalves, Grootaert & Andrade sp. nov. C–D. T. iberica (Arias, 1919). E–F. T. semiaptera (Gil Collado, 1923). G–H. T. pieltaini (Gil Collado, 1936). I–J. T. pandellei (Séguy, 1941). Scale bars: 1 mm.
Fig. 16 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 16. Habitus of live specimens of the Iberian ant-like Tachydromia Meigen, 1803 and the Italian flightless Tachydromia. Males are pictured in the left column, females in the right. A–B. T. iberica (Arias, 1919). C–D. T. semiaptera (Gil Collado, 1923). E–F. T. pieltaini (Gil Collado, 1936). G–H. T. pandellei (Séguy, 1941). I–J. T. apterygon Plant & Deeming, 2006 (Italy).
Fig. 11 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 11. Terminalia of the topotype ofTachydromia pandellei (Séguy, 1941) from France, Hautes-Pyrénées, Arrens-Marsous, lectotype (RBINS). A. Right surstylus and right epandrial lamella. B. Epandrium with cerci. C. Left epandrial lamella and left surstylus. D. Right surstylus. Scale bar: 0.1 mm.
Fig. 14 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 14. Terminalia of Tachydromia stenoptera Gonçalves, Grootaert & Andrade sp. nov., holotype (RBINS). A. Right surstylus and right epandrial lamella. B. Epandrium with cerci. C. Left epandrial lamella and left surstylus. D–E. Right surstylus. Scale bar: 0.1 mm.
Fig. 13 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 13. Terminalia of Tachydromia semiaptera (Gil Collado, 1923) (RBINS). A. Right surstylus and right epandrial lamella. B. Epandrium with cerci. C. Left epandrial lamella and left surstylus. D. Right surstylus. Scale bar: 0.1 mm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.