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54 results for “isolated trees”
Data from: Isolated trees support lower bird taxonomic richness than trees within habitat patches but similar functional diversity
<p><span>Large isolated trees are keystone structures that can help maintain biodiversity in fragmented landscapes, with evidence that open areas with isolated trees may support similar levels of taxonomic diversity to nearby patches of habitat. However, it is not clear if isolated trees can support the same diversity of ecological functions as trees in habitat patches. We compared species richness, community composition and functional diversity of birds in trees at forest edges and isolated trees. Twenty isolated trees and ten edge trees of American muskwood (<i>Guarea guidonia</i>) were selected, and sampled on 11 occasions, each of 20 minutes, over four months. All individual birds that landed at trees were recorded using a standardized protocol. Species richness was, on average, almost twice as high at edge trees than at isolated trees. Taxonomic composition differed between edge and isolated trees, with many forest-dependent birds restricted to edge trees, and some open-area birds restricted to isolated trees. Overall functional diversity was similar at edge and isolated trees, but some ecological functions (e.g. frugivory) were less frequent, while others (e.g. granivory) were more frequent at isolated compared to edge trees. Isolated trees are important for supporting many ecological functions in modified areas. However, the maintenance of forest patches is essential to complement the provision of such functions in modified landscapes. </span></p>
Data from: Learning to see the wood for the trees: machine learning, decision trees and the classification of isolated theropod teeth
Taxonomic identification of fossils based on morphometric data traditionally relies on the use of standard linear models to classify such data. Machine learning and decision trees offer powerful alternative approaches to this problem but are not widely used in palaeontology. Here, we apply these techniques to published morphometric data of isolated theropod teeth in order to explore their utility in tackling taxonomic problems. We chose two published datasets consisting of 886 teeth from 14 taxa and 3020 teeth from 17 taxa, respectively, each with five morphometric variables per tooth. We also explored the effects that missing data have on the final classification accuracy. Our results suggest that machine learning and decision trees yield superior classification results over a wide range of data permutations, with decision trees achieving accuracies of 96% in classifying test data in some cases. Missing data or attempts to generate synthetic data to overcome missing data seriously degrade all classifiers predictive accuracy. The results of our analyses also indicate that using ensemble classifiers combining different classification techniques and the examination of posterior probabilities is a useful aid in checking final class assignments. The application of such techniques to isolated theropod teeth demonstrate that simple morphometric data can be used to yield statistically robust taxonomic classifications and that lower classification accuracy is more likely to reflect preservational limitations of the data or poor application of the methods.
Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads
<p><b>Premise of the study</b></p> <p>Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such trees. To investigate this possibility, we studied the genetic structures of two such species on isolated pasture trees and surrounding forest, in relation to their local abundances in different habitat types and aspects of their reproductive biology including pollen and seed dispersal agents, and looked for evidence of increased or diminished gene flow.</p> <p><b>Methods</b></p> <p>We used microsatellite markers to assess geographic patterns of genetic diversity and differentiation in two epiphytic bromeliads, <i>Catopsis nitida</i> and <i>Werauhia tonduziana,</i> in the Monteverde region of Costa Rica.</p> <p><b>Key results</b></p> <p>About 85%<sup> </sup>of the <i>F</i><sub>ST</sub> value for <i>Catopsis nitida</i> was found among pastures within regions, while for <i>Weruahia tonduziana,</i> about 80% of the <i>F</i><sub>ST </sub>value was contributed by differences between regions, indicating much more gene flow within regions, relative to <i>C. nitida</i>.</p> <p><b>Conclusions</b></p> <p>Although there was substantial genetic differentiation among epiphyte populations, those on isolated pasture trees were not substantially less diverse than those in adjacent forests, suggesting that pasture trees may serve as "stepping stones" that help these species maintain their genetic connectedness and diversity at larger geographic scales.</p>
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.
RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees
<p>A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus <i>Diospyros</i> in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene <i>Diospyros</i> species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene <i>Diospyros</i> species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene <i>Diospyros,</i> and its relevance for conservation.</p>
Data from: Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat
Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population.
Data from: Landscape structure mediates zoochorous-dispersed seed rain under isolated pasture trees across distinct tropical regions
Context: Isolated pasture trees play an important role in forest recovery within fragmented tropical landscapes by attracting seed dispersers and facilitating seedling growth. However, studies with conflicting results have led to confusion about what drives variation in zoochorous-dispersed seed rain patterns under isolated tree canopies. Objectives: To assess the role of landscape and biological factors impacting zoochorous-dispersed seed rain under isolated pasture trees across three tropical regions of the world. Methods: We measured seed dispersal under 144 isolated pasture trees found in 12 fragmented tropical and sub-tropical landscapes in Australia, Colombia and Nigeria. Using linear mixed effect models, we modeled seed diversity, abundance, richness and evenness as functions of the biological features and landscape context of isolated trees. Results: Throughout all regions, the amount of woody vegetation surrounding trees in pastures was negatively related to rainforest seed diversity, evenness and abundance. Seed diversity and evenness increased significantly with the distance of isolated trees to forest fragments in the Australian sub-tropics, but elsewhere, seed diversity and evenness tended to decline with distance to forest, though not significantly. Conclusions: Our results suggest that the tree composition of landscapes surrounding isolated pasture trees is important for influencing zoochorous-dispersed seed rain, regardless of the region studied. Our study highlights the prominent role of landscape-scale, rather than local-scale factors on seed dispersal to isolated pasture trees, while providing strong evidence that early stage successional processes involving isolated pasture trees are similar throughout global tropical regions.
Data from: Edge-mediated compositional and functional decay of tree assemblages in Amazonian forest islands after 26 years of isolation
1.Islands formed upstream of mega hydroelectric dams are excellent experimental landscapes to assess the impacts of habitat fragmentation on biodiversity. We examined the effects of plot-, patch- and landscape-scale variables on the patterns of floristic diversity across 34 forest islands that had experienced 26 years of isolation since the creation of the 4,437 km2 Balbina Hydroelectric Reservoir of central Brazilian Amazonia. In addition, three undisturbed continuous forest sites in neighbouring mainland areas were also sampled across a comparable elevational gradient. 2.We identified all live trees ≥10 cm DBH at species level within a total of 87 quarter-hectare forest plots and conducted a comprehensive compilation of functional attributes of each tree species. We then examined species-area relationships (SARs) and the additional effects of patch and landscape scale metrics on patterns of tree assemblage heterogeneity, both in terms of taxonomic and functional diversity. 3.Despite a clearly positive SAR, edge-mediated forest disturbance was the single most important driver of species composition and abundance within islands. Our results suggest that non-random floristic transitions within island plots followed a predictable pattern, with different life-history traits either penalizing or rewarding local persistence of different functional groups. Distance to edges mediated the probability of tree mortality induced by windfalls and episodic surface fires, clearly resulting in faster species turnover and unidirectional changes in guild structure within small islands where light-wooded fast-growing pioneers largely replaced heavy-wooded species of the old-growth flora. 3.Synthesis ─ Following a simultaneous 26-year post-isolation history, we disentangle the effects of habitat loss and insularization on tree assemblages within a large set of Amazonian 'true' forest islands, of variable sizes, sharing a uniform open-water matrix. Area effects are expressed via a response to edge effects, with trees in smaller islands being more vulnerable to edge-related surface fires and windthrows. Additionally, forest edge effects can be a powerful driver of non-random floristic transitions across islands within the Balbina archipelago via a process of rapid pioneer proliferation, drastically affecting both the taxonomic and functional composition of insular tree communities. Finally, our results indicate that detrimental effects of forest fragmentation induced by hydroelectric dams are considerably stronger than those of forest patches embedded within a terrestrial vegetation matrix.
Data from: Current climate, isolation and history drive global patterns of tree phylogenetic endemism
Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions, and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants, and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g. mean annual temperature), geographical characteristics (e.g. isolation) and historical conditions (e.g. tree cover at the last glacial maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the last glacial maximum was a positive predictor of PE in the Paleotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographic, historical, and current factors. Some geographic variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographic drivers and regional climatic histories.
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322). in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322).
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T in Chryseoglobus indicus sp. nov., isolated from deep sea water
Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T and closely related species. The phylogenetic relationship of the related genomes was determined using UBCG pipeline3 tool with GTR + CAT model based on concatenated alignment of 92 core genes. Genome sequences for each of the type strains are available from the NCBI databases, with the GenBank accession numbers shown in parentheses. Tropheryma whipplei Neuro14T (CAUR000000000) was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) over 70% are shown at branching nodes. Bar, 0.05 substitutions per nucleotide position.
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S in Lysobacter humi sp. nov., isolated from soil
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S rRNA gene sequences of strains FJY8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained as percentages of 1000 replicates. Filled circles indicate the corresponding nodes recovered by using the maximum-parsimony algorithm. Bar, 0.02 substitutions per nucleotide position.
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 in Trichoderma changiae (Hypocreales), a new species isolated from a native orchid in Taiwan
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 sequences using Maximum-likelihood analysis. The new species Trichoderma changiae is highlighted in bold blue. Bootstrap values above 50% from RAxML-HPC2 on XSEDE (left) and posterior probabilities above 0.95 from Bayesian analysis (right) are displayed at the nodes. The scale bar represents 0.05 substitutions per nucleotide position. Trichoderma vulgatum was used as the outgroup. "T" denotes type strains.
Facilitation by isolated trees triggers woody encroachment and a biome shift at the savanna-forest transition
<p>1. Woody encroachment into grassy biomes is a global phenomenon, often resulting in a nearly complete turnover of species, with savanna specialists being replaced by forest-adapted species. Understanding the mechanisms involved in this change is important for devising strategies for managing savannas.</p> <p>2. We examined how isolated trees favor woody encroachment and species turnover by overcoming dispersal limitation and environmental filtering. In a savanna released from fire in southeastern Brazil (Cerrado) we sampled woody plants establishing under 40 tree canopies and in paired treeless plots. These trees comprised eight species selected for habitat preference (savanna or forest) and dispersal syndrome (bird-dispersed or not). We recorded dimensions of each tree, dispersal syndrome and habitat preference of recruits, and quantified the physical environment within each plot, aiming at a mechanistic understanding of woody encroachment.</p> <p>3. We found clear evidence that isolated trees cause nucleation and drive changes in functional composition of savanna. Effectiveness as nucleator differed among species, but was unrelated to their functional guilds (habitat preference or dispersal syndrome). Density of saplings in nuclei was partially explained by soil moisture (+), daily temperature amplitude (-), and sum of bases (-).</p> <p>4. Our results indicate that isolated trees act first as perches, strongly favoring bird-dispersed species. They then act as nurse trees, considerably changing the environment in favor of forest-adapted recruits. In the long term, as the nuclei expand and merge, savanna specialists tend to disappear and the savanna turns into a low-diversity forest.</p> <p>5. Synthesis and applications: Fire suppression has allowed the nucleation process and consequently the woody encroachment and fast replacement of savanna specialists by forest species in the Cerrado. By elucidating the mechanisms behind woody encroachment, we recommend using prescribed fires to burn forest seedlings and to reduce tree canopy size wherever the management goal is to maintain the typical savanna structure and composition.</p>
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees
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Facilitation by isolated trees triggers woody encroachment and a biome shift at the savanna-forest transition
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Data from: Learning to see the wood for the trees: machine learning, decision trees and the classification of isolated theropod teeth
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