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Data and scripts for Co-phylogeny, narrow host breadth and local conditions drive highly specialized bird-haemosporidian associations in West-Central African sky islands
<p>This document includes the raw datafiles, host and parasite phylogenies and r-code use to conduct analyses for "Co-phylogeny, narrow host breadth and local conditions drive highly specialized bird-haemosporidian associations in West-Central African sky islands". Please see the readme file to get more detailed information about each file.</p>
Fig. 6. Batrachocamallanus xenopodis, photomicrographs. A in Novel information on the morphology, phylogeny and distribution of camallanid nematodes from marine and freshwater hosts in South Africa, including the description of Camallanus sodwanaensis n. sp.
Fig. 6. Batrachocamallanus xenopodis, photomicrographs. A – male, general view; B – anterior part of body, male, apical view; C – optical section at base of buccal capsule level, male, apical view; D – buccal capsule, female, lateral view; E – female, general view; F – posterior part of body, male, lateral view; G – part of body at vulva region, lateral view; H – posterior part of body, female, lateral view. Scale bars: A, E, F–H – 100, B–D – 50.
Fig. 8 in Novel information on the morphology, phylogeny and distribution of camallanid nematodes from marine and freshwater hosts in South Africa, including the description of Camallanus sodwanaensis n. sp.
Fig. 8. Phylogenetic tree of Camallanidae nematodes based on 491 nucleotides long alignments of 28 rDNA gene. Nodal support presented for Bayesian Inference and Maximum Likelihood analyses (BI/ML).
Fig. 3. Paracamallanus cyathopgharynx, photomicrographs. A in Novel information on the morphology, phylogeny and distribution of camallanid nematodes from marine and freshwater hosts in South Africa, including the description of Camallanus sodwanaensis n. sp.
Fig. 3. Paracamallanus cyathopgharynx, photomicrographs. A – anterior part of body, male, lateral view; B – buccal capsule, male, lateral view; C – anterior part of body, male, apical view; D – female, general view; E - optical section at level of buccal capsule valves mid-length, male, dorsal view; F - part of body at vulva region, lateral view; G – posterior end of body, female, lateral view; H – posterior end of body, male, lateral view. Scale bars: A–C, E–H – 100; D – 1 mm.
Fig. 1. Camallanus sodwanaensis n in Novel information on the morphology, phylogeny and distribution of camallanid nematodes from marine and freshwater hosts in South Africa, including the description of Camallanus sodwanaensis n. sp.
Fig. 1. Camallanus sodwanaensis n. sp., line-drawings. A – anterior part of body, female, lateral view; B – buccal capsule, female, lateral view; C – anterior part of body, female, apical view; D – posterior part of body, male, ventral view; E – dorsal trident, male, lateral view; F – posterior part of body, female, lateral view; G – spicules, lateral view. Scale bars: A – 500; B–D, F–G – 100; E – 50.
Fig. 2. Camallanus sodwanaensis n in Novel information on the morphology, phylogeny and distribution of camallanid nematodes from marine and freshwater hosts in South Africa, including the description of Camallanus sodwanaensis n. sp.
Fig. 2. Camallanus sodwanaensis n. sp., photomicrographs. A – male, general view; B – anterior part of body, female, lateral view; C – buccal capsule, female, lateral view; D – optical section at level of buccal capsule valves mid-width, male, dorsal view; E – dorsal trident, male, dorsal view; F – anterior part of body, female, apical view; G - optical section at level of buccal capsule valves mid-length, male, apical view; H – right spicule, lateral view; I – posterior end of body, male, ventral view; J – part of body at vulva region, lateral view; K – posterior end of body, female, lateral view. Scale bars: A – 1 mm, B – 500, C–K – 100.
FIG. 6 in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 6. — Cladogram showing phylogenetic relationship of Characiformes based on morphologic data, after Buckup (1991). The cladogram represents only the families analyzed in the present work. *, Characoidea (sensu Buckup 1998); **, clade sensu Malabarba 1998.
FIG. 3 in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 3. — Sclerotized structures in Rhinoxenus; A-F, R. curimbatae n. sp.; A, male copulatory organ (MCO); B, vagina; C, ventral anchor; D, dorsal anchor; E, hook; F, ventral bar; G-M, R. guianensis n. sp.; G, male copulatory organ (MCO); H, vagina; I, hook from pair 2; J, hook from pairs 1, 3-7; K, ventral bar; L, ventral anchor; M, dorsal anchor. Scale bars: A, B, 20 μm; C, D, F, 30 μm; E, I, J, 15 μm; G, H, 10 μm; K-M, 50 μm.
FIG. 1 in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 1. — Sclerotized structures of selected Rhinoxenus species; A, R. piranhus Kritsky, Boeger & Thatcher, 1988, male copulatory organ (MCO); B, R. piranhus, vagina; C, R. nyttus Kritsky, Boeger & Thatcher, 1988, MCO; D, R. nyttus, detail of the base of the MCO (distal portion of MCO not shown); E, R. nyttus, ventral anchor; F, R. arietinus Kritsky, Boeger & Thatcher, 1988, MCO. Arrow indicates the circular tandem sclerotized brims. Scale bars: A-D, F, 20 μm; E, 50 μm.
FIG. 8 in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 8. — Summary of the proposed historical relationships of Rhinoxenus species and their hosts. The parasite cladogram (solid lines) is superimposed on that (broad grey lines) of their hosts taxa. Dotted lines indicate postulated extinction or sampling error of parasites; dashed-dotted lines indicate postulated dispersion of parasite clades; circles indicate cospeciation events; triangle indicates duplication event. *, clade sensu Malabarba 1998.
FIG. 4. — Rhinoxenus euryxenus n in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 4. — Rhinoxenus euryxenus n. sp.; A, holotype (ventral); B, vagina; C, male copulatory organ (MCO); D, hook from pairs 1, 3-7; E, hook from pair 2; F, ventral bar; G, ventral anchor; H, dorsal anchor. Scale bars: A, 100 μm; B-E, 10 μm; F-H, 50 μm.
FIG. 2. — Rhinoxenus anaclaudiae n in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 2. — Rhinoxenus anaclaudiae n. sp.; A, holotype (ventral); B, male copulatory organ (MCO); C, hook from pair 2; D, hook from pairs 1, 3-7; E, vagina; F, ventral bar; G, dorsal anchor; H, ventral anchor. Scale bars: A, 100 μm; B-E, 10 μm; F-H, 30 μm.
FIG. 7 in Neotropical Monogenoidea. 47. Phylogeny and coevolution of species of Rhinoxenus (Platyhelminthes, Monogenoidea, Dactylogyridae) and their Characiformes hosts (Teleostei, Ostariophysi) with description of four new species
FIG. 7. — Cladogram of hosts groups of Rhinoxenus species constructed from parasitological data and using Characiformes taxa analyzed in the present work. Dashed lines postulate dispersion. Each host group is labeled with its taxonomic epithet followed by the Rhinoxenus species parasitizing its members.
Figure 1 in Phylogeny-based species delimitations and the evolution of host associations in symbiotic zoanthids (Anthozoa, Zoanthidea) of the wider Caribbean region
Figure 1. Phylogeny of Caribbean symbiotic zoanthids based on the internal transcribed spacer (ITS) region of the rRNA nuclear gene. Support values are 100 pseudoreplicate maximum likelihood (ML) bootstrap values followed by three million iteration Bayesian posterior probabilities. The clades of symbiotic species are colour coded according to their host associations. The information presented in parentheses after the specimens collected for this study includes: the colour of the zoanthid, presence of Symbiodinium, host taxa, and individual identifier (which includes the collection location).
Resources from: Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers
<p>Understanding the factors that shape microbiomes can provide insight on the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary, and evolutionary influences on gut microbiome structure. We performed fecal metabarcoding to characterize both the gut microbiome and diet of fifteen wood-warbler species across a four-year period and from two geographic localities. We find host taxonomy generally explained ~10% of the variation between individuals, which is ~6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.</p>
Fig.3 in A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins
Fig.3 | Relativemeandispersalratesofbutterfliesbetweenbioregions. Numbersbesideeacharrowareaverageratesfrom 1,000 simulationsusing biogeographicstochasticmappingin BioGeoBEARS. Thesenumbersweredividedby 100 foreaseof comparison (rawvaluescanbefoundin Supplementary Data 5). E., Eastern;W., Western.
Fig. 1 in A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins
Fig. 1 | Evolutionaryrelationshipsanddiversificationpatternsofbutterflies. Time-calibratedtreeof 2,244 butterflyspeciesbasedon 391 loci and 150 amino acidpartitions.Branchesshowdistinctchangesindiversification (circles) asestimatedbyclade-specificmodels.Lettersatnodesrefertocladeswith significantrateshifts (seesection 6 of Supplementary Results).Colouredlines intheouterringbesidetipsindicateassociationwithoneof the 13 hostmodules (seesection 17 of Extended Online Methods).Blacklinesinthehostassociation ringindicatespecieswithoutdata,andasterisksdenotenon-monophyletic subfamilies.Supplementary Fig. 1 showsthistreewithvisiblespeciesnamesand agesforallnodes.
Fig. 2 in A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins
Fig. 2 | Distributionofbutterfliesovertime. Bioregionshadingindicatesthenumberofbutterflylineagesthatwereassociatedwiththatbioregionduringthattime period,asdeterminedby BioGeoBEARSancestralstatereconstruction.Eachmapcorrespondstoa 15-Maintervalofbutterfly evolution.Resultsarebasedon data fromthisstudy.
Resources from: Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers
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Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation
<p><span>The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of </span><em>Cornus</em> from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of <em>Cornus</em>. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in <em>Liriodendron</em> and <em>Cornus</em>, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in <em>Cornus</em>. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.</p>
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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.