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248 results for “tree of life”
Data from: Fine-scale spatial genetic dynamics over the life-cycle of the tropical tree Prunus africana
Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.
Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results: Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
Data from: Evolution of diet across the animal Tree of Life
What an animal eats is a fundamental aspect of its biology, but the evolution of diet has not been studied across animal phylogeny. Here, we performed a large-scale phylogenetic analysis to address three unresolved questions about the evolution of animal diets. (i) Are diets conserved across animal phylogeny? (ii) Does diet influence rates of species proliferation (diversification) among animal phyla? (iii) What was the ancestral diet of animals and major animal clades? We analyzed diet data for 1,087 taxa, proportionally sampled among animal phyla based on the relative species richness of phyla. Our survey suggests that across animals, carnivory is most common (~63%), herbivory less common (~32%), and omnivory relatively rare (~3%). Despite considerable controversy over whether ecological traits are conserved or labile, we found strong conservatism in diet over extraordinarily deep timescales. We found that diet is unrelated to rates of species diversification across animal phyla, contrasting with previous studies showing that herbivory increased diversification within some important groups (e.g. crustaceans, insects, mammals). Finally, we estimated that the ancestor of all animals was most likely carnivorous, as were many major phyla (e.g. arthropods, mollusks, chordates). Remarkably, our results suggest that many carnivorous species living today may have maintained this diet through a continuous series of carnivorous ancestors for >800 million years.
Data from: Demography and growth of subadult savanna trees: interactions of life history, size, fire season, and grassy understory
Tree populations in mesic (>650 mm precipitation/yr) savannas of the world have strong demographic bottlenecks to the transition of subadult trees to the canopy layer. Although such bottlenecks are a major determinant of savanna physiognomy, the factors that allow subadults to traverse the bottleneck are little studied. In a landscape-scale field experiment in a northern Australia savanna, we determined the survival and growth of 1506 permanently marked juveniles (<150 cm tall) and saplings (150–599 cm tall) of canopy species in response to season of fire (early dry season, late dry season, wet season, and unburned), and understory type (herbaceous forbs vs. sorghum [native annual grass]) that differ in seasonal growth patterns and competitive regimes. Trees were assessed before fires and at the end of the following growing season, without repeat fires. We used Akaike-information-criterion-based model selection and multi-model inference for data analyses. Initial height was an important explanatory variable for all responses except genet mortality wherein fire season was important for juveniles and understory type for saplings. Fire season was important to height growth of large juveniles and small saplings (enhanced the year following dry-season fires). Fire season × understory interactions were important for height growth of small juveniles and for the proportion of juveniles transitioning to saplings. Changes in stem numbers were affected by all explanatory variables. All fires topkilled most juveniles (fewer in early dry-season fires in herbaceous understory), but genet death was rare. Late dry-season fires topkilled most saplings; they failed to regain previous height and some died the following year. Given no further fires, persistent large juveniles can grow to sapling size within a year; whereas sapling success is severely hampered by late-dry-season fires, especially in grassy understory. Differences in seasonal phenological patterns of both understory vegetation and trees that vary with size and life history stage are among suggested explanatory mechanisms. Weighted averaged model coefficients for all responses to the explanatory variables are provided for use in population dynamics models. A conceptual framework links landscape-scale variables to tree attributes and responses, with implications for population ecology and community assembly.
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Phaeoptyx.
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Astrapogon.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus.
Data from: Using ultraconserved elements to reconstruct the termite tree of life
<p><span>The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting </span><span>50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of <em>Cryptocercus</em>, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted <em>in silico</em> between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: </span><span><a href="https://github.com/oist/TER-UCE-DB/"><span>https://github.com/oist/TER-UCE-DB/</span></a></span><span>.</span></p>
Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.
Figure 1 in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 1. Maximum-likelihood (ML) tree showing the phylogenetic relationships among 41 newly sequenced specimens of pilidiophorans (indicated with solid blue circles). Numbers near nodes are support values, ML bootstrap/Bayesian inference (BI) posterior probability. Nodes with yellow triangles are fully supported, with 100% ML bootstrap and 1.00 BI posterior probability. New species names are indicated in bold. Some nodes were polytomous in the BI tree (indicated by hyphens in place of posterior probability values).
Figure 7. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 7. A, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, entire body, showing characteristic lateral edges; B, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132, entire body; C, Baseodiscus aff. marmoratus (Bürger, 1890), anterior end of body, ventral view, head to the left; D, E, Baseodiscus ohtsukai sp. nov., holotype, ICHUM, 6327, drawings of anterior end of body viewed dorsally (D) and ventrally (E); F, G, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, anterior end of body viewed dorsally (F) and ventrolaterally (G). Photos by T. Naruse (A), A. V. Chernyshev (B, C), and G. Giribet (F, G).
Figure 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. A, anterior fragment in contracted state, lateral view; B, anterior end of body, ventral view; C, transverse section showing proboscis; D, magnification of anterior proboscis musculature (arrowhead, radial muscle fibre); E, transverse section showing rhynchocoel musculature. Photos by H. Kajihara.
Figure 3. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 3. A, Baseodiscus aff. marmoratus (Bürger, 1890) (voucher DNA, ICHUM 6322); B, Baseodiscus aff. maculosus (Bürger, 1895a) (voucher DNA, ICHUM 6324); C–E, Baseodiscus delineatus (Delle Chiaje, 1822-1829), ICHUM 6326; F, Baseodiscus cf. curtus (Hubrecht, 1879), ICHUM 6328; G, H, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, entire body (G) and protruding proboscis (indicated by an arrowhead, H); I, Baseodiscus punnetti (Coe, 1904), specimen different from any voucher specimens in this study; J, K, Baseodiscus kakuii sp. nov., holotype, ICHUM 6334, anterior body (J) and
Figure 4. A–C in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 4. A–C, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, anterior end of body, ventral view, head to the right (A), frontal view (B), squeezed-slide preparation (C); D, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior end of body, ventral view. Photos by H. Kajihara.
Figure 6. A–E in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 6. A–E, Baseodiscus takakurai Gibson, 1995, ICHUM 6308, A, anterior end of body, ventral view; B, middle body region, showing appearance of body markings in differently contracted states; C, juvenile, showing dorsal mottling; D, juvenile, with head viewed ventrolaterally, showing two ocelli; E, transverse section of proboscis; F, Baseodiscus komatsui sp. nov., holotype, NSNM NMNS-Ne 1, entire body. Photos by H. Kajihara (A–E) and H. Komatsu (F).
Figure 2. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 2. A, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, lateral view, head to the right; B, Oxypolella hiebertae sp. nov., holotype, MIMB 42256; C, Cephalomastax brevis Iwata, 1957, ICHUM 6304; D, E, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior body fragment (D) and enlargement of intestinal region (E) showing yellowish proboscis (indicated by arrowheads); F, Baseodiscus takakurai Gibson, 1995, ICHUM 6306; G, Baseodiscus profundus sp. nov., holotype, MIMB 42257; H, I, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, anterior end of body, dorsal (H) and ventral (I) views; J, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132; K, Baseodiscus komatsui sp. nov., holotype, NMNS-Ne 1; L, Baseodiscus unicolor Stiasny-Wijnhoff, 1925; M, Baseodiscus giribeti sp. nov., holotype, MCZ IZ-135324; N, Baseodiscus cf. amboinensis (Staub, 1900); O, Baseodiscus hemprichii (Ehrenberg, 1828-1831), specimen from Okinawa, different from any voucher specimens in this study; P, Baseodiscus zebra sp. nov., holotype, RUMF-ZN-00001; Q, Baseodiscus quinquelineatus (Quoy & Gaimard, 1833), ICHUM 6319. Photographs by H. Kajihara (A, C, D, E, F, O), A. V. Chernyshev (B, G, J), T. Naruse (H, I), H. Komatsu (K), G. Giribet (L, M), D. Uyeno (P), and R. Yoshida (Q).
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 (ECP1) sequences of five nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Description of a new Kempnyia Klapálek from Brazil (Plecoptera: Perlidae) with life stages associated using DNA barcodes
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (450 bp) from Kempnyia KlapÁlek and related stoneflies from Rio de Janeiro, Brazil modeled by Kimura-2-parameter (K2P).
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (433 bp) from Anacroneuria flintorum Froehlich and related stoneflies from Espírito Santo and São Paulo States, Brazil, modeled by Kimura-2-parameter (K2P).
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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)
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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.