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2,052 results for “tree species”
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a number of new lineages (L1–L13) identified in our study. The lineages are marked with grey bars which represent the criteria used to delimit species boundaries, where three gene bPTP (P3), genetic p-distance (GD), morphological separation (M) and geographic isolation (G) are used to predict the number of putative lineages. The nodes below 70% parametric bootstrap support are indicated with asterisk (*). "+" indicates that the status of A. nasuta cf. isabellina needs further work (see Deepak et al. 2019).
FIGURE 3 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 3. Outline of Meisterfeldia bitsevi: ventral (left) and lateral (right) views. 1–5—characters of the shell measurements. Scale bar: 15 μm.
FIGURE 2 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 2. Scanning electron microscopic image of Meisterfeldia bitsevi: a—ventral view, b—lateral view, c—dorsal view. Scale bar 10 µm. Magnification x 2,500.
FIGURE 1 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 1. Light micrographs of Meisterfeldia bitsevi: a—ventral view, b—dorsal view, c, d—lateral views. Scale bar—15 µm. Magnification x 400.
FIGURE 5 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 5. Outlines of the species from the genus Meisterfeldia: a, b—M. bitsevi, c, d—M. chibisovi, e, f—M. wegeneri, g, h—M. vanhoornei, i, j—M. polygonia, k—M. turfacea; a, d, f, h, j—ventral views; b, c, e, g, i, k—lateral views; c–f, i, j—from Bobrov, 2016; g, h—from Beyens et al., 1986; k—from Zacharias, 1903. Scale bar 15 µm.
FIGURE 2. Maximum likelihood tree using 28S D2 & D3–5, ITS2 in Read between the lineata: A revision of the tattooed wasps, Zagrammosoma Ashmead (Hymenoptera: Eulophidae), with descriptions of eleven new species
FIGURE 2. Maximum likelihood tree using 28S D2 & D3–5, ITS2, and COI NJ. Bootstrap values shown. The varying colors within Zagrammosoma indicate different species.
Variations in leaf economics spectrum traits for an evergreen coniferous species: Tree size dominates over environment factors
<ol> <li>Many leaf traits strongly vary with tree size and environmental factors, but the importance of these factors to intraspecific variations of leaf traits in forest trees have rarely been <a><span>simultaneously</span></a> evaluated.</li> <li>We measured needle longevity and specific leaf area (SLA) and nitrogen (N) content of every needle age (0 to 4 year old) for 65 individuals with 0.3-100 cm diameter at breast height (DBH) for an evergreen coniferous species, <i>Pinus koraiensis</i> Sieb. et Zucc., in Northeast China. We <a><span>simultaneously</span></a> evaluated effects of tree size (DBH or tree height) and environment factors (light intensity, soil N content and water availability) on the needle longevity, SLA, foliage N content as well as the slopes of regressions of SLA and foliage N content against needle age.</li> <li>All of the studied leaf traits and slopes of regressions of SLA and foliage N content against needle age were significantly related to tree size. Tree height had a greater impact on SLA and area-based leaf N content (N<sub>area</sub>), whereas DBH was more important for needle longevity and mass-based leaf N content (N<sub>mass</sub>). The environment variables, light intensity, soil N content and water availability, were rather minor factors for trait variations compared with tree size. Significant influences of light intensity were found only on needle longevity, and soil N and water availability had no effects on the leaf traits.</li> <li>Our study clearly showed that tree size is an important driver of intraspecific variations in the key leaf traits of <i>Pinus koraiensis</i> in a natural forest. We also emphasize the importance of DBH or tree height varies depending on leaf traits, suggesting various mechanisms of size effects on the intraspecific variations in leaf traits. We suggest that ecological significance of leaf trait variations needs reconsideration incorporating tree size effect.</li> </ol>
Data from: Tropical tree species diversity in a mountain system in southern Mexico: local and regional patterns and determinant factors
Mechanisms explaining patterns of biodiversity along elevation gradients in tropical mountain systems remain controversial. We use a set of climatic, topographic and soil variables encompassing regional, landscape and local-level spatial scales to explain the spatial variation of tree species diversity in the Sierra Madre of Chiapas, Mexico. We sampled 128 circular plots (0.1-ha each) in four elevational bands along four elevation gradients or transects encompassing 100-2200 m. A total of 12,533 trees belonging to 444 species were recorded. Diversity patterns along the elevation gradient and the explanatory power of independent variables were dependent on spatial scale (regional vs transect) and functional group (total vs late-successional or pioneer species). Diversity of all species and late-successional species (1 - proportion of pioneer species) showed a constant pattern at the regional and transect scales, with low predictive power of climatic variables and/or elevation. A linear decrease of either number or proportion of pioneer species diversity was observed with increasing elevation, which was correlated with temperature, rainfall, and human disturbance trends. Total species diversity showed an increase with rainfall of the warmest quarter, indicating a regional-level limiting effect of seasonality (drought duration). Yet the explanatory power of climatic and topographic variables was higher at the individual transect level than at the regional scale, suggesting the parallel but differential influence of evolutionary and geological history factors on diversification not so far studied to explain elevation patterns of species diversity in tropical mountain systems.
Data from: Neighbour species richness and local structural variability modulate aboveground allocation patterns and crown morphology of individual trees
<p>Local neighbourhood interactions are considered a main driver for biodiversity–productivity relationships in forests. Yet, the structural responses of individual trees in species mixtures and their relation to crown complementarity remain poorly understood. Using a large‐scale forest experiment, we studied the impact of local tree species richness and structural variability on above‐ground wood volume allocation patterns and crown morphology. We applied terrestrial laser scanning to capture the three‐dimensional structure of trees and their temporal dynamics. We found that crown complementarity and crown plasticity increased with species richness. Trees growing in species‐rich neighbourhoods showed enhanced aboveground wood volume both in trunks and branches. Over time, neighbourhood diversity induced shifts in wood volume allocation in favour of branches, in particular for morphologically flexible species. Our results demonstrate that diversity‐mediated shifts in allocation pattern and crown morphology are a fundamental mechanism for crown complementarity and may be an important driver of overyielding.</p> <p> </p>
Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's Rule could account for differences in timing estimates between mitochondrial and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
Data from: To include or not to include: the impact of gene filtering on species tree estimation methods
With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that co-estimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci. Due to concerns that poor quality loci will reduce the accuracy of estimated species trees, many recent phylogenomic studies have removed or filtered genes on the basis of phylogenetic signal and/or missing data prior to inferring species trees; little is known about the performance of species tree estimation methods when gene filtering is performed. We examine how incomplete lineage sorting, phylogenetic signal of individual loci, and missing data affect the absolute and the relative accuracy of species tree estimation methods and show how these properties affect methods' responses to gene filtering strategies. In particular, summary methods (ASTRAL-II, ASTRID, and MP-EST), a site-based coalescent method (SVDquartets within PAUP), and an unpartitioned concatenation analysis using maximum likelihood (RAxML) were evaluated on a heterogeneous collection of simulated multi-locus datasets, and the following trends were observed. Filtering genes based on gene tree estimation error improved the accuracy of the summary methods when levels of incomplete lineage sorting were low to moderate but did not benefit the summary methods under higher levels of incomplete lineage sorting, unless gene tree estimation error was also extremely high (a model condition with few replicates). Neither SVDquartets nor concatenation analysis using RAxML benefited from filtering genes on the basis of gene tree estimation error. Finally, filtering genes based on missing data was either neutral (i.e., did not impact accuracy) or else reduced the accuracy of all five methods. By providing insight into the consequences of gene filtering, we offer recommendations for estimating species tree in the presence of incomplete lineage sorting and reconcile seemingly conflicting observations made in prior studies regarding the impact of gene filtering.
Data from: Tree-growth is more sensitive than species distributions to recent changes in climate and acidic deposition in the northeastern United States
Tree-growth responses to environmental change could provide early detection of shifts in forest composition and help facilitate ecosystem management and conservation. We studied forest tree responses to recent trends in climate and acidic deposition using analyses of tree rings and long-term climate, deposition and forest plot data along an elevational climatic gradient in the northeastern United States. We analyzed how (a) individual growth of dominant species (Picea rubens, Abies balsamea), and (b) spatial distributions of all species, changed with elevation over time due to changing environment. We observed a mean 220 m upslope shift of temperature envelopes since the 1960s, consistent with regional climate warming, but found no evidence of synchronous upslope shifts in species abundance. Species' ranges were stable although some leaned upslope or downslope, suggesting species-specific migration lags or controls on species' ranges. Compared to species distributions, the growth of dominant species was more responsive to environmental change. Although the basal area of P. rubens declined within its range since the 1960s, its growth has increased recently with increasing precipitation pH and to a lesser extent with warming climate. Abies balsamea has gradually increased in both basal area and density since the 1960s, with its growth responding to precipitation pH but not climate. Historically, P. rubens grew better at lower and A. balsamea at higher elevations, but these elevation effects appeared to be mediated primarily by moisture, and have disappeared over time. Synthesis and applications. Mean tree-growth responses to changing climate (temperature, moisture) and precipitation chemistry were more consistent and more clearly detectable than shifts in tree species' ranges, suggesting that monitoring tree growth across climatically-controlled species' ranges (e.g. along elevational or latitudinal gradients) may provide a powerful tool for early detection of potential future changes in forest composition in a changing environment.
Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consist of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy decreased when using only one individual per species or 25% of the full sequence length. In addition, locus 'informativeness' was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed towards further assessment of other factors that can impact performance of species trees, including gene flow, data 'informativeness', tree shape, missing data, and uncertain species boundaries.
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The mole salamanders (family Ambystomatidae) are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny and which ones yield phylogenetically inaccurate reconstructions. To shed light on this conflict, we present the first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae. We utilized a range of analyses, including coalescent-based methods of species-tree estimation that account for incomplete lineage sorting within a locus and concordance-based methods that estimate the number of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Collectively, these results robustly resolved many deep and relatively shallow clades within Ambystoma, including the placement of A. gracile and A. talpoideum as the sister clade to a clade containing all remaining ambystomatids, and the placement of A. maculatum as the sister lineage to all remaining ambystomatids excluding A. gracile and A. talpoideum. Both Bayesian coalescent and concordance methods produced similar results, highlighting strongly supported branches in the species tree. Furthermore, coalescent-based analyses that excluded loci produced overlapping species-tree posterior distributions, suggesting that no particular locus – including mtDNA – disproportionately contributed to our species-tree estimates. Overall, our phylogenetic estimates have greater similarity with previous allozyme and mitochondrial sequence-based phylogenetic estimates. However, intermediate depths of divergence in the ambystomatid species tree remain unresolved, potentially highlighting a region of rapid species radiation or a hard polytomy, which limits our ability to comment on previous morphologically-based taxonomic groups.
Data from: Limitation of seedling growth by potassium and magnesium supply for two ectomycorrhizal tree species of a Central African rain forest and its implication for their recruitment
In the ectomycorrhizal caesalpiniaceous groves of southern Korup National Park, the dominant tree species, Microberlinia bisulcata, displays very poor in situ recruitment compared with its codominant, Tetraberlinia bifoliolata. The reported ex situ experiment tested whether availabilities of soil potassium and magnesium play a role. Seedlings of the two species received applications of K and Mg fertilizer in potted native soil in a local shade house, and their responses in terms of growth and nutrient concentrations were recorded over 2 years. Amended soil concentrations were also determined. Microberlinia responded strongly and positively in its growth to Mg, but less to K; Tetraberlinia responded weakly to both. Added Mg led to strongly increased Mg concentration for Microberlinia while added K changed that concentration only slightly; Tetraberlinia strongly increased its concentration of K with added K, but only somewhat its Mg concentration with added Mg. Additions of Mg and K had small but important antagonistic effects. Microberlinia is Mg-demanding and apparently Mg-limited in Korup soil; Tetraberlinia, whilst K-demanding, appeared not to be K-limited (for growth). Added K enhanced plant P concentrations of both species. Extra applied Mg may also be alleviating soil aluminum toxicity, and hence improving growth indirectly and especially to the benefit of Microberlinia. Mg appears to be essential for Microberlinia seedling growth and its low soil availability in grove soils at Korup may be an important contributing factor to its poor recruitment. Microberlinia is highly shade-intolerant and strongly light-responding, whilst Tetraberlinia is more shade-tolerant and moderately light-responding, which affords an interesting contrast with respect to their differing responses to Mg supply. The study revealed novel aspects of functional traits and likely niche-partitioning among ectomycorrhizal caesalps in African rain forests. Identifying the direct and interacting indirect effects of essential elements on tropical tree seedling growth presents a considerable challenge due the complex nexus of causes involved.
Data from: Congruent phylogeographic patterns of eight tree species in Atlantic Central Africa provide insights on the past dynamics of forest cover
Cycles of Quaternary climate change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographic study of rainforest species represents a complementary approach because Pleistocene climate fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri, Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and north-eastern Gabon would have been more affected by past climate change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures.
Assisted migration across fixed seed zones detects adaptation lags in two major North American tree species
<p>Boreal forests are experiencing dramatic climate change, having warmed 1-1.9°C over the last century. Yet forest regeneration practices are often still dictated by a fixed seed zone framework, in which seeds are both harvested from and planted into predefined areas. Our goal was to determine whether seedlings sourced from southern seed zones in Minnesota USA are already better adapted to northerly seed zones because of climate change. Bur oak (Quercus macrocarpa) and northern red oak (Quercus rubra) seedlings from two seed zones (i.e. tree ecotypes) were planted into 16 sites in two northern seed zones and measured for three years. Our hypotheses were threefold: 1) tree species with more southern geographic distributions would thrive in northern forests where climate has already warmed substantially, 2) southern ecotypes of these species would have higher survival and growth than the northern ecotype in northern environments, and 3) natural selection would favor seedlings that expressed phenotypic and phenological traits characteristic of trees sourced from the more southern seed zone. For both species, survival was high (>93%), and southern ecotypes expressed traits consistent with our climate adaptation hypotheses. Ecotypic differences were especially evident for red oak; the southern ecotype had had higher survival, lower SLA, faster height and diameter growth, and extended leaf phenology relative to the northern ecotype. Bur oak results were weaker, but the southern ecotype also had earlier budburst and lower SLA than the northern ecotype. Models based on the fixed seed zones failed to explain seedling performance as well as those with continuous predictors (e.g. climate and geographical position), suggesting that plant adaptations within current seed zone delineations do align with changing climate conditions. Adding support for this conclusion, natural selection favored traits expressed by the more southern tree ecotypes. Collectively, these results suggest that state seed sourcing guidelines should be reexamined to permit plantings across seed zones, a form of assisted migration. More extensive experiments (i.e. provenance trails) are necessary to make species-specific seed transfer guidelines that account for climate trends while also considering the precise geographic origin of seed sources.</p>
Data from: Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species
Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the 'health' and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growth tree species, which could exacerbate the loss of timber value and carbon storage already associated to logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) are more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of "extinction debt".
Data from: Interactions among trees: a key element in the stabilising effect of species diversity on forest growth
1.There is mounting evidence that species diversity increases the temporal stability of forest growth. This stabilising effect of diversity has mainly been attributed to species differences in their response to fluctuating environmental conditions. Interactions among individuals could also contribute to the stabilising effect of diversity by increasing the mean and reducing the variance of tree growth, however, this has never been directly demonstrated. 2.We used tree‐ring width chronologies from temperate and boreal mixed stands of Eastern Canada to identify the role of interactions among individuals in the stabilising effect of diversity on forest growth. Using neighbourhood competition index and a mixed model we compared the effect of interspecific and intraspecific interactions on the mean and the variance of tree growth. 3.We found that interspecific interactions are less detrimental to tree growth than intraspecific interactions. We also found that interspecific interactions buffer tree response to drought and thereby reduce the variance of tree growth. 4.Our results indicate diversity may increase the mean and reduce the variance of tree growth through interactions among individuals. Thus, we demonstrate interactions among individuals play a role in the stabilising effect of diversity on forest growth, and in doing so, we bring to light other mechanisms of the insurance hypothesis.
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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.
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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.
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