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18,140 results for “Phylogenetic”
Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents
<p>Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective surrogate for among-host variation in habitat and resource quality, host–parasite relationships should evince phylogenetic signals (i.e. be contingent on host phylogeny). Because the strength of ecological relationships between parasites and their hosts may affect the likelihood of phylogenetic signals occurring in host–parasite relationships, we hypothesized that (1) host specificity would be positively correlated with the strength of phylogenetic signals and (2) the strength of phylogenetic signals will be greater for parasites that rely more on their host throughout their life cycle. Analyses were conducted for ectoparasites from tropical bats and for ectoparasites, helminths, and coccidians from desert rodents. Phylogenetic signals were evaluated for parasite presence and for parasite prevalence. The frequency of phylogenetic signal occurrence was similar for parasite presence and prevalence, with a signal detected in 24–27% of cases at the species level and in 67% and 15% of cases at the genus level for parasites of bats and rodents, respectively. No differences in signal strength or the likelihood of detecting a signal existed between groups of parasites. Phylogenetic signal strength was correlated with host specificity, suggesting that mechanisms increasing host specificity also increase the likelihood of a phylogenetic signal in host use by parasites. Differences in the transmission mode did not affect signal strength or the likelihood of detecting a signal, indicating that variation in host switching opportunities associated with the transmission mode does not affect signal strength.</p>
Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
1. Anthropogenic environmental changes are known to affect the Earth's ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.
Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of "legacy" phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
Anthropoid morphometric and phylogenetic data, with R replication code.
<p>This repository contains four files: 1) a NEXUS phylogeny of 100 anthropoid primates; 2) a CSV text file of anthropoid primate lower molar areas, body mass, and primary dietary category; 3) a CSV text file of modern human lower molar area proportions; and, 4) an R script containing replication code for fitting Bayesian phylogenetic generalized linear mixed models to the morphometric data. These files are associated with the paper "The Evolution of Anthropoid Molar Proportions" in BMC Evolutionary Biology (2016).</p>
FIGURES 28 30 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURES 28 30. Mouthparts of first instar Crozetia seguyi larvae. 28. Labral fan. Scale bar = 0.02 mm. 29. Larval hypostoma. Scale bar = 0.02 mm. 30. Larval mandibles. Scale bar = 0.02 mm. Abbreviations: lb labral fan; hyps hypostoma; mnd mandible.
FIGURE 3 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURE 3. Rivière du Camp, Possession Island, Crozet Islands, 1979. A typical habitat of Crozetia larvae. Pic du Mascarin (alt. 934 m) is in the background. (Courtesy, L. Davies).
FIGURE 2 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURE 2. Islands of the Crozet Archipelago. Bathymetric contours in meters. (Adapted from Boudon and Nougier 1982).
FIGURES 15 - 19. Crozetia. 15 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURES 15 - 19. Crozetia. 15. Cr. crozetensis, male paratype wing. Scale bar = 0.5 mm. 16. Cr. seguyi, higher magnification of male wing base. Scale bar = 0.5 mm. 17. Cr. seguyi, SEM of last instar larval head, frontal view. Scale bar = 0.1 mm. 18. Cr. crozetensis, LM of last instar larval head, dorsal view. Scale bar = 0.1 mm. 19. Cr. seguyi, LM of last instar larval head, dorsal view. Scale bar = 0.1 mm. Abbreviations: ant - antenna; ca - cephalic apotome; lf - labral fan; hyps - hypostoma; mnd - mandible; mx - maxilla; mxp - maxillary palpus.
FIGURES 13 - 14. Crozetia pupae. Left lateral views. 13 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURES 13 - 14. Crozetia pupae. Left lateral views. 13. Cr. crozetensis. 14. Cr. seguyi. Note rudimentary cocoon on posterior. Scale bar = 1.0 mm.
FIGURES 68 73 in Systematic revision of Anopinella Powell (Lepidoptera: Tortricidae: Euliini) and phylogenetic analysis of the Apolychrosis group of genera
FIGURES 68 73. Adults of Anopinella. 68, A. mariana; 69, A. carabayana; 70, A. cafrosana; 71, A. porrasa; 72, A. styraxivora, 73, A. fana.
Fig. 4 in From a lost world: an integrative phylogenetic analysis of Ansonia Stoliczka, 1870 (Lissamphibia: Anura: Bufonidae), with the description of a new species
Fig. 4 First and second-best morphometric ratio for the separation of a Ansonia sp. Usun Apau and Ansonia platysoma, b Ansonia sp. Usun Apau and Ansonia minuta, and c Ansonia platysoma and Ansonia minuta
CLDF dataset derived from Kitchen et al.'s "Bayesian phylogenetic analysis of Semitic languages" from 2009
<p>Cite the source of the dataset as:</p> <blockquote> <p>Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Andrew Kitchen, Christopher Ehret, Shiferaw Assefa, Connie J. Mulligan. Proc. R. Soc. B 2009 -; DOI: 10.1098/rspb.2009.0408. Published 29 April 2009</p> </blockquote>
Figure 9 in Phylogenetic analysis of the subgenus Lampetis (Spinthoptera) (Coleoptera: Buprestidae) of North and Central America, and the West Indies
Figure 9. One of the two equally parsimonious cladograms of Lampetis (Spinthoptera) of North and Central America and the West Indies, and 11 species of different generic groups of the subtribe Dicercina (outgroups). Synapomorphies and homoplastic changes of nodes are listed in Table II. Asterisks indicate the nodes collapsed in the strict consensus cladogram.
Figure 10 in Phylogenetic analysis of the subgenus Lampetis (Spinthoptera) (Coleoptera: Buprestidae) of North and Central America, and the West Indies
Figure 10. Cladogram resulting from the bootstrap analysis of Lampetis (Spinthoptera) of North and Central America and the West Indies, and 11 species of different generic groups of the subtribe Dicercina (outgroups). Numbers are the percentages obtained.
Figures 1–8 in Phylogenetic analysis of the subgenus Lampetis (Spinthoptera) (Coleoptera: Buprestidae) of North and Central America, and the West Indies
Figures 1–8. Illustration of some characters and character states. (1, 2) Punctures on frons: (1) Lampetis (Spinthoptera) simplex (scarce); (2) L. tigrina (abundant). (3, 4) Punctures on base of mandibles: (3) L. aurata (scarce); (4) Lampetis (Lampetis) amaurotica (abundant). (5, 6) Prosternum with punctures confluent laterally: (5) Oedisterna bisulcata (scarce); (6) Perotis unicolor (abundant). (7, 8) Elytra with transversal depressions on basal surface: (7) L. auropunctata (scarce); (8) L. drummondi (abundant).
FIG. 21 in The anatomy and phylogenetic affinities of Cynthiacetus peruvianus, a large Dorudon-like basilosaurid (Cetacea, Mammalia) from the late Eocene of Peru
FIG. 21. — Ventral view of the right periotic of MNHN.F.PRU10, holotype of Cynthiacetus peruvianus. Abbreviations: aes, ventral edge of the anteroexternal sulcus; apd, anterior pedicle for the tympanic; app, anterior process of the periotic; fc, cochlear window; fo, foramen pseudovale; fpb, falcate process of the basioccipital; fps, falciform process of the squamosal; fs, facial sulcus; fv, vestibular window; gtt, groove for the tensor tempani; inc, incudal fossa; jn, jugular notch; Ma, malleus; mce, medial crest of the exoccipital; men, groove for the meningeal arteries; mf, mallear fossa; nc, nuchal crest; plc, posterolateral crest; ppd, posterior inner pedicle of the tympanic; ppe, paroccipital process of the exoccipital; ppp, posterior process of the periotic; ppt, posterior process of the tympanic bulla; pr, promontorium; V3, path of the mandibular nerve; VII, foramen for the facia nerve; vlt, ventrolateral tuberosity. Dark grey-shaded regions and hatched regions represent the sediment and broken portions of bone, respectively. Not to scale.
Fig. 2 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 2. The neighbour-joining (A) and Bayesian (B) trees for Suncus inferred from 1140 base-pairs of cytochrome b gene sequence. Bootstrap and posterior probability values are given above branches.
Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.
Fig. 3 in A New Species Of The Unicornfish Genus Naso (Teleostei: Acanthuridae) From Taiwan, With Comments On Its Phylogenetic Relationship
Fig. 3. Scanning microscopy image of the mesial face of right sagittal otolith taken from Naso tergus, NMMB-P10816, adult male, 342 mm SL. Scale bar = 1 mm.
Fig. 1 in A New Species Of The Unicornfish Genus Naso (Teleostei: Acanthuridae) From Taiwan, With Comments On Its Phylogenetic Relationship
Fig. 1. Naso tergus, new species: a, Holotype, NMMB-P10808, adult male, 335 mm SL; b, Paratype, NMMB-P10813, adult female, 320 mm SL.
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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.