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111 results for “tree species diversity”
R code and data for "Intraspecific and intraindividual trait variability decrease with tree species richness in a subtropical tree diversity experiment"
<p>R codes and dataset for tha statistical analyses and production of figures in "Intraspecific and intraindividual trait variability decrease with tree species richness in a subtropical tree diversity experiment" by Castro Sánchez-Bermejo et al.</p>
Figure 2. Coalescent species trees with 13 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Figure 2. Coalescent species trees with 13 (A) and 14 (B) assumed species based on 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene sequences. Posterior probabilities of clades are provided along internal branches and posterior probabilities for the presence of individual species are provided behind the terminal branches. Scale bars denote the fraction of substitutions per site.
Tree mixtures increase bird taxonomic and functional diversity over pure stands of tree species planted outside their natural range—but not over pure native stands
<p><span>Recent biodiversity loss has emphasized the necessity to critically evaluate the consequences of human alterations of forest ecosystems. Stand diversification via tree species mixtures and the use of non-native tree species are two such alterations currently gaining importance as climate change adaptations. However, the effects of local versus regional tree mixing on associated bio</span><span>diversity and notably the modifying role of tree species growing outside their natural range remain poorly understood. </span></p> <p><span>We assessed how monocultures and mixtures of native and introduced tree species influence the taxonomic and functional diversity of northwest German bird communities at stand and landscape scales. We focused on the dominant natural tree species (<em>Fagus sylvatica</em>) and economically important conifer species planted outside their natural range (the native <em>Picea abies</em> and non-native <em>Pseudotsuga menziesii</em>). </span></p> <p><span>We found that bird species richness and functional diversity were generally higher in pure and mixed stands of native <em>F. sylvatica</em> than in pure conifer stands, especially in comparison to non-native <em>P. menziesii</em>. These differences were particularly strong at the landscape scale. Pure conifer stands harbored only a reduced set of functionally similar bird species. Structural diversity based on tree microhabitat availability emerged as a key predictor of bird diversity. </span></p> <p><span>Synthesis and applications: Our study suggests that tree species mixtures do not necessarily increase bird diversity compared to pure stands of native trees, but can promote bird diversity relative to pure stands of species planted outside their natural range. Moreover, local mixtures, rather than a mosaic of pure stands, may promote bird diversity also at the landscape scale. By contrast, pure stands of tree species planted outside their natural range can increase the biotic homogenization of forest birds. Promoting structural diversity of microhabitats via tree retention and ensuring that non-native trees are planted in mixtures with native trees may alleviate potential limitations of climate change-oriented management for biodiversity. </span></p>
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C. ashi complex based on Bayesian analysis (BEAST) of concatenated mitochondrial and nuclear loci (5,285 bp). Posterior probabilities (PPs) are indicated at the nodes, with an asterisk indicating a PP of 1.00. Clades that are discussed in the text are labelled I–VIII and with the name of the taxon that has priority in the respective clade. The names of C. africana s.l. are in black font; the other species are in other colours (the six outgroup species are all in pale blue). The three taxa that are not present in any other analyses are indicated by a red '§'. Topological incongruence compared with other phylogenetic trees is indicated by a red '#'. The blue lines indicate the divergence times of two of the outgroup species pairs.
FIGURE 4. Bayesian trees constructed using 16S in Species diversity and phylogeny of fleas of small terrestrial mammals in the forests of the Central Highlands of Madagascar
FIGURE 4. Bayesian trees constructed using 16S (A) and 12S (B) sequences. Values at nodes correspond to the posterior probability values (P) obtained after 100 replicates. P values under 0.7 are not shown. Trees were rooted using sequences of the species Tunga trimamillata, T. penetrans, Hectopsylla cypha and H. pulex. The number of sequences we obtained for each species was given in brackets. Sequences of exotic species (available in our data) such as Xenopsylla brasiliensis and X. cheopis were added.
Fig. 4 Bayesian tree for fragment 1 in The world's economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus)
Fig. 4 Bayesian tree for fragment 1 haplotypes (mtDNA: 12S rRNA) of Pelodiscus. For GenBank haplotypes, accession numbers shown. Dash indicates this branch not found by MP analysis. Sequences labelled as P. axenaria or P. sinensis by Chen et al. (2005) and by
Fig. 8 Bayesian tree for fragment 3 in The world's economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus)
Fig. 8 Bayesian tree for fragment 3 haplotypes (mtDNA: cyt b + tRNA-Thr) of Pelodiscus. For GenBank haplotypes, accession numbers shown. Sequences labelled as P. axenaria or P. sinensis by
FIG. 2. Species tree for P in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 2. Species tree for P. brachyphona as estimated in ASTRAL. Numbers on the branches are local posterior probabilities/boostrap support values from RAxML (A). The identifiers are field numbers, followed by the ''I'' number (DNA sample identifier, see Table 1). State abbreviation and county where the sample was collected are also shown. The tree shows two well-supported clades, corresponding to P. brachyphona from the Northern and Southern distribution ranges, respectively. Pseudacris brimleyi and P. feriarum were included as outgroups. Branch lengths (B) are shown in the inset tree generated with RAxML.
FIGURE 5. Maximum-likelihood tree obtained from a in Unravelling the diversity behind the Ophiocordyceps unilateralis (Ophiocordycipitaceae) complex: Three new species of zombie-ant fungi from the Brazilian Amazon
FIGURE 5. Maximum-likelihood tree obtained from a concatenated dataset of three genes (nu-SSU, nu-LSU, ITS) showing the placement of O.camponoti-atricipis, O. camponoti-bispinosi and O. camponoti-indiani within Ophiocordyceps unilateralis complex and relative to other Ophiocordycipitaceae species. Numbers above branches indicate bootstrap scores>70 (ML/MP).
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I in Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat-forming sibling species
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I (left; log likelihood: -399.5730) and nuclear adenine nucleotide transporter intron (right; log likelihood: -12170.8682) sequences of Pyura praeputialis and Pyura doppelgangera sp. nov. Nodal support from 1000 bootstrap replications (> 75%) is indicated next to some branches. Circles indicate regions in which a particular allele was present. For simplicity, allele frequencies are not indicated.
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I (COI) gene sequences. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I (COI) gene sequences using MEGA 5. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 2. Phylogenetic tree resulting from a in Host specialization and species diversity in the genus Stylops (Strepsiptera: Stylopidae), revealed by molecular phylogenetic analysis
Figure 2. Phylogenetic tree resulting from a Bayesian analysis of the partial sequence from the mitochondrial NADH gene. The names of the host Andrena bees are indicated with every Stylops voucher number. The posterior probabilities are given before the slash; the bootstrap values from the maximum-likelihood (ML) analysis are given after the slash. Posterior probability values lower than 0.9, and bootstrap values lower than 50, are considered as unsupported and are thus replaced by an asterisk (*); incongruent nodes between the two analyses are indicated by a dash (-). Branch support is omitted at the nodes that were unsupported in both the Bayesian and the ML analyses.
Figure 3. Phylogenetic tree resulting from a in Host specialization and species diversity in the genus Stylops (Strepsiptera: Stylopidae), revealed by molecular phylogenetic analysis
Figure 3. Phylogenetic tree resulting from a Bayesian analysis of the partial sequence from the nuclear EF1 gene. Names of host Andrena bees are indicated at every Stylops voucher number. The names of the host Andrena bees are indicated with every Stylops voucher number. The posterior probabilities are given before the slash; the bootstrap values from the maximum-likelihood (ML) analysis are given after the slash. Posterior probability values lower than 0.9, and bootstrap values lower than 50, are considered as unsupported and thus replaced by an asterisk (*); incongruent nodes between the two analyses are indicated by a dash (-). Branch support is omitted at the nodes that were unsupported in both the Bayesian and the ML analyses.
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I in Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae)
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I data set under the general time reversible model with gamma distribution, displaying all compatible groupings and with average branch lengths proportional to numbers of substitutions per site, indicated by the scale bar. Bootstrap support values above 80% are shown below each branch; posterior probabilities above 0.8 from 36 000 sampled trees from the Bayesian analysis are shown above each branch. Support values for within-species relationships are not shown. Filled circles indicate clades (and singlets) identified by the 4¥ rule; open diamonds indicate clades (and singlets) identified by the generalized mixed yule coalescent model. Names refer to the species and the clonal populations.
Data from: Changes in beta diversity and species functional traits differ between saplings and mature trees in an old growth forest
<p class="MsoCommentText">1. Invasion by generalist tree species can cause biotic homogenization and such community impoverishment is likely more important in rare forest types. We quantified changes in tree diversity within Carolinian (range in Central Hardwoods), northern (range reached Northern hardwood-conifer/Boreal-spruce-fir) and central species (range in Central Hardwood region and Northern hardwood-conifer) in an old forest in southern Canada at points surveyed 24 years apart.</p> <p class="MsoCommentText">2. We asked: How did mature tree and sapling composition and abundance change for the 3 species' groups? Did those changes lead to biotic homogenization? Can species' changes be explained by community traits? We tested for differences in temporal and spatial tree <span>β</span>-diversity, as well as forest composition and structure, using univariate/multivariate analyses and a community trait-based approach to identify drivers-of-change.</p> <p class="MsoCommentText">3. Major increases occurred in abundance for mature <i>Acer rubrum</i> (northern), while others decreased (<i>Fraxinus americana</i>, <i>Populus grandidentata</i>); declines were found in <i>A. saccharinum </i>(central) and <i>Cornus florida</i> (Carolinian). Species composition of saplings, but not mature trees, changed due to replacement; no evidence for biotic homogenization existed in either cohort. As a group, northern mature tree species increased significantly, while central species declined; saplings of Carolinian species declined. </p> <p class="MsoCommentText">4. Shade-tolerance in mature trees increased, reflecting successional changes, while drought-tolerance decreased perhaps due to changing temperatures, altered precipitation or ground water levels. Saplings showed declines in all traits, probably because of compositional change. </p> <p class="MsoCommentText">5. Our results demonstrated that saplings can more closely reflect change in forest dynamics than mature trees, especially over short time periods. Based on sapling trends, this remnant could ultimately transition to a mesophytic hardwood stand dominated by <i>A. rubrum</i> and other shade-tolerant species, creating a more homogeneous forest. </p> <p class="MsoCommentText">6. While encouraging regeneration for Carolinian and central tree species could ensure high levels of diversity are conserved in the future, it is important that this is balanced with the primary management goal of maintaining the older-growth characteristics of the forest.</p>
Data from: Changes in beta diversity and species functional traits differ between saplings and mature trees in an old growth forest
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Data from: AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua’s critically endangered seasonally dry forest
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Data from: Are tree species diversity and genotypic diversity effects on insect herbivores mediated by ants?
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Data from: Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance
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