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2,052 results for “tree species”
Data from: Variability in potential to exploit different soil organic phosphorus compounds among tropical montane tree species
We hypothesized that tropical plant species with different mycorrhizal associations reduce competition for soil phosphorus (P) by specializing to exploit different soil organic P compounds. We assayed the activity of root/mycorrhizal phosphatase enzymes of four tree species with contrasting root symbiotic relationships–arbuscular mycorrhizal (angiosperm and conifer), ectomycorrhizal and non-mycorrhizal–collected from one of three soil sites within a montane tropical forest. We also measured growth and foliar P of these seedlings in an experiment with P provided exclusively as inorganic orthophosphate, a simple phosphomonoester (glucose phosphate), a phosphodiester (RNA), phytate (the sodium salt of myo-inositol hexakisphosphate), or a no-P control. The ectomycorrhizal tree species expressed twice the phosphomonoesterase activity as the arbuscular mycorrhizal tree species, but had similar phosphodiesterase activity. The non-mycorrhizal Proteaceae tree had markedly greater activity of both enzymes than the mycorrhizal tree species, with root clusters expressing greater phosphomonoesterase activity than fine roots. Both the mycorrhizal and non-mycorrhizal tree species contained significantly greater foliar P than in no-P controls when limited to inorganic phosphate, glucose phosphate, and RNA. The ectomycorrhizal species did not perform better than the arbuscular mycorrhizal tree species when limited to organic P in any form. In contrast, the non-mycorrhizal Proteaceae tree was the only species capable of exploiting phytate, with nearly three times the leaf area and more than twice the foliar P of the no-P control. Our results suggest that arbuscular and ectomycorrhizal tree species exploit similar forms of P, despite differences in phosphomonoesterase activity. In contrast, the mycorrhizal tree species and non-mycorrhizal Proteaceae appear to differ in their ability to exploit phytate. We conclude that resource partitioning of soil P plays a coarse but potentially ecologically important role in fostering the coexistence of tree species in tropical montane forests.
Data from: Assessing approaches for inferring species trees from multi-copy genes
With the availability of genomic sequence data, there is increasing interest in using genes with a possible history of duplication and loss for species tree inference. Here we assess the performance of both non-probabilistic and probabilistic species tree inference approaches using gene duplication and loss and coalescence simulations. We evaluated the performance of gene tree parsimony (GTP) based on duplication (Only-dup), duplication and loss (Dup-loss), and deep coalescence (Deep-c) costs, the NJst distance method, the MulRF supertree method, and PHYLDOG, which jointly estimates gene trees and species tree using a hierarchical probabilistic model. We examined the effects of gene tree and species sampling, gene tree error, and duplication and loss rates on the accuracy of phylogenetic estimates. In the 10-taxon duplication and loss simulation experiments, MulRF is more accurate than the other methods when the duplication and loss rates are low, and Dup-loss is generally the most accurate when the duplication and loss rates are high. PHYLDOG performs well in 10-taxon duplication and loss simulations, but its run time is prohibitively long on larger data sets. In the larger duplication and loss simulation experiments, MulRF outperforms all other methods in experiments with at most 100 taxa; however, in the larger simulation, Dup-loss generally performs best. In all duplication and loss simulation experiments with more than 10 taxa, all methods perform better with more gene trees and fewer missing sequences, and they are all affected by gene tree error. Our results also highlight high levels of error in estimates of duplications and losses from GTP methods and demonstrate the usefulness of methods based on generic tree distances for large analyses.
Data from: Assignment of homoeologues to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae)
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have been carried out in the context of dichotomous species trees, these processes operate also in more complex evolutionary histories involving multiple hybridizations and polyploidy. Recently, methods have been developed that accurately handle incomplete lineage sorting in allopolyploids, but they are thus far restricted to networks of diploids and tetraploids. We propose a procedure that improves on this limitation by designing a workflow that assigns homoeologues to hypothetical diploid ancestral genomes prior to genome tree construction. Conflicting assignment hypotheses are evaluated against substitution model error and coalescent stochasticity. Incongruence that cannot be explained by stochastic mechanisms needs to be explained by other processes (e.g., homoploid hybridization or paralogy). The data can then be filtered to build multilabeled genome phylogenies using inference methods that can recover species trees, either in the face of substitution model error and coalescent stochasticity alone, or while simultaneously accounting for hybridization. Methods are already available for folding the resulting multilabeled genome phylogeny into a network. We apply the workflow to the reconstruction of the reticulate phylogeny of the plant genus Fumaria (Papaveraceae) with ploidal levels ranging from 2x to 14x. We describe the challenges in recovering nuclear NRPB2 homoeologues in high ploidy species while combining in vivo cloning and direct sequencing techniques. Using parametric bootstrapping simulations we assign nuclear homoeologues and chloroplast sequences (four concatenated loci) to their common hypothetical diploid ancestral genomes. As these assignments hinge on effective population size assumptions, we investigate how varying these assumptions impacts the recovered multilabeled genome phylogeny.
Data from: The influence sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile)
In this study, we explore the long-standing issue of how many loci are needed to infer accurate phylogenetic relationships, and whether loci with particular attributes (i.e., parsimony informativeness, variability, gene tree resolution) outperform others. To do so, we use an empirical dataset consisting of the seven species of chickadees (Aves: Paridae), an analytically tractable, recently diverged group, and well studied ecologically but lacking a nuclear phylogeny. We estimate relationships using 40 nuclear loci and mitochondrial DNA using four coalescent-based species tree inference methods (BEST, *BEAST, STEM, STELLS). Collectively, our analyses contrast with previous studies and support a sister relationship between the Black-capped and Carolina Chickadee, two superficially similar species that hybridize along a long zone of contact. Gene flow is a potential source of conflict between nuclear and mitochondrial gene trees, yet, we find a significant, albeit low, signal of gene flow. Our results suggest that relatively few loci with high information content may be sufficient for estimating an accurate species tree, but that substantially more loci are necessary for accurate parameter estimation. We provide an empirical reference point for researchers designing sampling protocols with the purpose of inferring phylogenies and population parameters of closely related taxa.
Data from: Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)
Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them.
Data from: The negative effect of lianas on tree growth varies with tree species and season
<p>Lianas reduce tree growth, reproduction, and survival in tropical forests. Liana competition can be particularly intense in isolated forest fragments, where liana densities are high, and thus host tree infestation is common. Furthermore, lianas appear to grow particularly well during seasonal drought, when they may compete particularly intensely with trees. Few studies, however, have experimentally quantified the seasonal effects of liana competition on multiple tree species in tropical forests. We used a liana-removal experiment in a forest fragment in southeastern Brazil to test whether the effects of lianas on tree growth varies with season and tree species identity. We conducted monthly diameter measurements using dendrometer bands on 88 individuals of five tree species for 24 months. We found that lianas had a stronger negative effect on some tree species during the wet season compared to the dry season. Furthermore, lianas significantly reduced the diameter growth of two tree species but had no effect on the other three tree species. The strong negative effect of lianas on some trees, particularly during the wet season, indicates that the effect of lianas on trees varies both seasonally and with tree species identity.</p>
FIGURE 3 in A new species of tree frog, genus Dendropsophus (Anura: Hylidae), from the Amazon of northern Bolivia
FIGURE 3. Adult male paratype of Dendropsophus juliani sp. nov. (NMP6V 72799/1) in life.
FIGURE 2 in A new species of tree frog, genus Dendropsophus (Anura: Hylidae), from the Amazon of northern Bolivia
FIGURE 2. Ventral view of adult male holotype of Dendropsophus juliani sp. nov. (CBF 5923) in life.
FIGURE 1 in A new species of tree frog, genus Dendropsophus (Anura: Hylidae), from the Amazon of northern Bolivia
FIGURE 1. Adult male holotype of Dendropsophus juliani sp. nov. (CBF 5923) in life.
FIGURE 10. 100 in A new tree-frog genus and species from Ivory Coast, West Africa (Amphibia: Anura: Hyperoliidae)
FIGURE 10. 100% consensus topology of NJ, ML, MP and Bayes trees (see Fig. 9).
FIGURE 5. Neighbour Joining tree obtained from the 505 in On the identity of Isoperla curtata (Plecoptera: Perlodidae): behavioural and molecular approaches show the existence of two separate species
FIGURE 5. Neighbour Joining tree obtained from the 505 bp COI fragment for studied populations.
FIGURES 9 in A new genus and species of Cheyletidae (Acariformes: Prostigmata) from citrus trees in Florida
FIGURES 9. Lanceacheyla whartoni gen. nov., sp. nov., male. 9, Dorsal view.
FIGURE 14 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 14. Pterygosoma chilensis sp. nov., female; A, ventral view; B, mid-dorsal seta.
FIGURE 13 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 13. Pterygosoma chilensis sp. nov., female; A, dorsal view; B, antero-dorsal seta.
FIGURE 11 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 11. Pterygosoma levissima sp. nov., female; A, ventral view; B, peripheral seta.
FIGURE 8 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 8. Pterygosoma ovata sp. nov., female; A, ventral view; B, mid-dorsal seta.
FIGURE 4 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 4. Pterygosoma formosus sp. nov., female. A, dorsal view; B, antero-dorsal seta.
FIGURE 16 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 16. Pterygosoma cyanogasteri sp. nov., female; A, dorsal view; B, antero-dorsal seta.
FIGURE 17 in Pterygosomatid mites of a new species group ligare (Acariformes: Pterygosomatidae: Pterygosoma) parasitizing tree iguanas (Squamata: Liolaemidae: Liolaemus)
FIGURE 17. Pterygosoma cyanogasteri sp. nov., female; A, ventral view.
FIGURE 21 in Eriophyes species (Acari: Eriophyoidea) inhabiting lime trees (Tilia spp.: Tiliaceae) — supplementary description and morphological variability related to host plants and female forms
FIGURE 21. Nail galls on leaf of Tilia platyphyllos inhabited by Eriophyes tiliae Nalepa 1890.
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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.