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Sample records for multipurpose tree species

  1. Vegetative and reproductive phenology of some multipurpose tree species in the homegardens of Barak Valley, northeast India.

    PubMed

    Das, Tapasi; Das, Ashesh Kumar

    2013-01-01

    Traditional homegardens are an important component of the farming systems in many rural communities and have been highlighted considerably due to their sustainability and role in the conservation of biodiversity. However, the functional aspect of the homegardens, which includes the phenological behavior of the dominant tree species in such agroforestry systems, has been undermined till date, and there is a lack of adequate data on this aspect of the traditional homegardens. As a step in this direction the present study was carried out to determine the phenological behavior of important multipurpose trees in the homegardens of the village of Dargakona, Assam, northeast India. The study revealed the dominance of periodic growth deciduous species from a total of 25 tree species selected for phenological observation. The diversity of multipurpose trees in the homegardens is represented by different plant functional types with different phenological behavior which showed significant changes in their responses to inter-annual climatic variations. The diversity of tree species with different phenological behavior has implications for the temporal partitioning of resources, especially during periods of scarcity, thereby resulting in efficient utilization of resources such as water. Also the diverse phenological behavior plays an important role in regulating the food supply for the herbivore population and the year-round availability of products, and such information can be useful in the selection of species for integration into other agroforestry systems which can be sustainable in the long run. PMID:22555388

  2. Vegetative and reproductive phenology of some multipurpose tree species in the homegardens of Barak Valley, northeast India

    NASA Astrophysics Data System (ADS)

    Das, Tapasi; Das, Ashesh Kumar

    2013-01-01

    Traditional homegardens are an important component of the farming systems in many rural communities and have been highlighted considerably due to their sustainability and role in the conservation of biodiversity. However, the functional aspect of the homegardens, which includes the phenological behavior of the dominant tree species in such agroforestry systems, has been undermined till date, and there is a lack of adequate data on this aspect of the traditional homegardens. As a step in this direction the present study was carried out to determine the phenological behavior of important multipurpose trees in the homegardens of the village of Dargakona, Assam, northeast India. The study revealed the dominance of periodic growth deciduous species from a total of 25 tree species selected for phenological observation. The diversity of multipurpose trees in the homegardens is represented by different plant functional types with different phenological behavior which showed significant changes in their responses to inter-annual climatic variations. The diversity of tree species with different phenological behavior has implications for the temporal partitioning of resources, especially during periods of scarcity, thereby resulting in efficient utilization of resources such as water. Also the diverse phenological behavior plays an important role in regulating the food supply for the herbivore population and the year-round availability of products, and such information can be useful in the selection of species for integration into other agroforestry systems which can be sustainable in the long run.

  3. Village agroforestry systems and tree-use practices: A case study in Sri Lanka. Multipurpose tree species network research series

    SciTech Connect

    Wickramasinghe, A.

    1992-01-01

    Village agroforestry systems in Sri Lanka have evolved through farmers' efforts to meet their survival needs. The paper examines farmers' land-use systems and their perceptions of the role of trees in the villages of Bambarabedda and Madugalla in central Sri Lanka. The benefits of village agroforestry are diverse food, fuelwood, fodder, timber, and mulch, but food products are of outstanding importance. The ability of Artocarpus heterophyllus (the jackfruit tree) and Cocos nucifera (coconut) to ensure food security during the dry season and provide traditional foods throughout the year, as well as to grow in limited space, make them popular crops in the two study villages. The study recommends that further research precede the formulation of agricultural interventions and that efforts to promote improved tree varieties recognize farmers' practices and expressed needs.

  4. In vitro propagation, micromorphological studies and ex vitro rooting of cannon ball tree (Couroupita guianensis aubl.): a multipurpose threatened species.

    PubMed

    Shekhawat, Mahipal S; Manokari, M

    2016-01-01

    In vitro propagation methods using seeds and nodal segments of a 21-year old Couroupita guianensis - a medicinally important but threatened tree have been developed. Hundred percent of the seeds germinated on half strength Murashige and Skoog (MS) medium with 2.0 mg l(-1) indole-3 butyric acid (IBA). Nodal segments were found most suitable for the establishment of cultures. About 90 % explants responded and 4.1 ± 0.23 shoots per node were induced after five weeks of inoculation on MS medium +4.0 mg l(-1) 6-benzylaminopurine (BAP). Further shoot multiplication was achieved by repeated transfer of mother explants and subculturing of in vitro produced shoots on fresh medium. Maximum number (8.2 ± 0.17) of shoots were regenerated on MS medium with 1.0 mg l(-1) each of BAP and Kinetin (Kin) + 0.5 mg l(-1) α-naphthalene acetic acid (NAA) with additives (50 mg l(-1) of ascorbic acid and 25 mg l(-1) each of adenine sulphate, L-arginine and citric acid). The multiplied shoots rooted (4.3 ± 0.26 roots/shoot) on half strength MS medium with 2.5 mg l(-1) IBA. All the shoots were rooted ex vitro when pulse treated with 400 mg l(-1) of IBA for five min with an average of 7.3 ± 0.23 roots per shoot. Nearly 86 % of these plantlets were acclimatized within 7-8 weeks and successfully transferred in the field. Biologically significant developmental changes were observed during acclimation particularly in leaf micromorphology in terms of changes in stomata, veins and vein-islets, and trichomes. This study helps in understanding the response by the plants towards outer environmental conditions during acclimatization. This is the first report on micropropagation of C. guianensis, which could be used for the large-scale multiplication, restoration and conservation of germplasm of this threatened and medicinally important tree. PMID:27186027

  5. Assessing the extent of "conflict of use" in multipurpose tropical forest trees: a regional view.

    PubMed

    Herrero-Jáuregui, Cristina; Guariguata, Manuel R; Cárdenas, Dairon; Vilanova, Emilio; Robles, Marco; Licona, Juan Carlos; Nalvarte, Walter

    2013-11-30

    In the context of multiple forest management, multipurpose tree species which provide both timber and non-timber forest products (NTFP), present particular challenges as the potential of conflicting use for either product may be high. One key aspect is that the magnitude of conflict of use can be location specific, thus adding complexity to policy development. This paper focuses on the extent to which the potential for conflict of use in multipurpose tree species varies across the Amazonian lowland forests shared by Peru, Bolivia, Colombia, Ecuador and Venezuela, emphasizing the economic dimension of conflict. Based on a review of the current normative and regulatory aspects of timber and NTFP extraction in the five countries, the paper also briefly discusses the opportunities and constraints for harmonization of timber and NTFP management of multipurpose species across the region. It was found that about half of the 336 timber species reviewed across the five countries also have non-timber uses. Eleven timber species are multipurpose in all five countries: Calophyllum brasiliense, Cedrela odorata, Ceiba pentandra, Clarisia racemosa, Ficus insipida, Jacaranda copaia, Schefflera morototoni, Simarouba amara and Terminalia amazonia. Seven other multipurpose species occurred only in either Venezuela (Tabebuia impetiginosa, Spondias mombin, Pentaclethra macroloba, Copaifera officinalis, Chlorophora tinctoria, Carapa guianensis) or Ecuador (Tabebuia chrysantha). Four multipurpose tree species presented the highest potential of conflict of use across the region: Dipteryx odorata, Tabebuia serratifolia, Hymenaea courbaril and Myroxylon balsamum yet these were not evenly distributed across all five countries. None of the five studied countries have specific legislation to promote sustainable use of any of the multipurpose species reported here and thus mitigate potential conflict of use; nor documented management options for integration or else segregation of both their

  6. De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba

    PubMed Central

    2013-01-01

    Background Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus. Results Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads. Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic. Conclusions This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data. The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will

  7. Species integrity in trees.

    PubMed

    Ortiz-Barrientos, Daniel; Baack, Eric J

    2014-09-01

    From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space. PMID:25155715

  8. Reproductive traits affect the rescue of valuable and endangered multipurpose tropical trees

    PubMed Central

    Sinébou, Viviane; Quinet, Muriel; Ahohuendo, Bonaventure C.; Jacquemart, Anne-Laure

    2016-01-01

    Conservation strategies are urgently needed in Tropical areas for widely used tree species. Increasing numbers of species are threatened by overexploitation and their recovery might be poor due to low reproductive success and poor regeneration rates. One of the first steps in developing any conservation policy should be an assessment of the reproductive biology of species that are threatened by overexploitation. This work aimed to study the flowering biology, pollination and breeding system of V. doniana, a multipurpose threatened African tree, as one step in assessing the development of successful conservation strategies. To this end, we studied (1) traits directly involved in pollinator attraction like flowering phenology, flower numbers and morphology, and floral rewards; (2) abundance, diversity and efficiency of flower visitors; (3) breeding system, through controlled hand-pollination experiments involving exclusion of pollinators and pollen from different sources; and (4) optimal conditions for seed germination. The flowering phenology was asynchronous among inflorescences, trees and sites. The flowers produced a large quantity of pollen and nectar with high sugar content. Flowers attracted diverse and abundant visitors, counting both insects and birds, and efficient pollinators included several Hymenoptera species. We detected no spontaneous self-pollination, indicating a total dependence on pollen vectors. Vitex doniana is self-compatible and no inbreeding depression occurred in the first developmental stages. After extraction of the seed from the fruit, seed germination did not require any particular conditions or pre-treatments and the seeds showed high germination rates. These pollination and breeding characteristics as well as germination potential offer the required conditions to develop successful conservation strategies. Protection, cultivation and integration in agroforestry systems are required to improve the regeneration of the tree. PMID:27354660

  9. Reproductive traits affect the rescue of valuable and endangered multipurpose tropical trees.

    PubMed

    Sinébou, Viviane; Quinet, Muriel; Ahohuendo, Bonaventure C; Jacquemart, Anne-Laure

    2016-01-01

    Conservation strategies are urgently needed in Tropical areas for widely used tree species. Increasing numbers of species are threatened by overexploitation and their recovery might be poor due to low reproductive success and poor regeneration rates. One of the first steps in developing any conservation policy should be an assessment of the reproductive biology of species that are threatened by overexploitation. This work aimed to study the flowering biology, pollination and breeding system of V. doniana, a multipurpose threatened African tree, as one step in assessing the development of successful conservation strategies. To this end, we studied (1) traits directly involved in pollinator attraction like flowering phenology, flower numbers and morphology, and floral rewards; (2) abundance, diversity and efficiency of flower visitors; (3) breeding system, through controlled hand-pollination experiments involving exclusion of pollinators and pollen from different sources; and (4) optimal conditions for seed germination. The flowering phenology was asynchronous among inflorescences, trees and sites. The flowers produced a large quantity of pollen and nectar with high sugar content. Flowers attracted diverse and abundant visitors, counting both insects and birds, and efficient pollinators included several Hymenoptera species. We detected no spontaneous self-pollination, indicating a total dependence on pollen vectors. Vitex doniana is self-compatible and no inbreeding depression occurred in the first developmental stages. After extraction of the seed from the fruit, seed germination did not require any particular conditions or pre-treatments and the seeds showed high germination rates. These pollination and breeding characteristics as well as germination potential offer the required conditions to develop successful conservation strategies. Protection, cultivation and integration in agroforestry systems are required to improve the regeneration of the tree. PMID:27354660

  10. Breeding status of tung tree (Vernicia sp.) in China, a multipurpose oilseed crop with industrial uses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As a developing country with the world’s largest population, China faces a serious challenge in satisfying its continuously increasing energy demands. Tung trees (Vernicia sp., especially V. fordii and V. montana), are multipurpose, perennial plants belonging to the Euphorbiaceae family. The unique ...

  11. Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq.

    PubMed

    Ouyang, Kunxi; Li, Juncheng; Zhao, Xianhai; Que, Qingmin; Li, Pei; Huang, Hao; Deng, Xiaomei; Singh, Sunil Kumar; Wu, Ai-Min; Chen, Xiaoyang

    2016-01-01

    Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees. PMID:27438485

  12. Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq

    PubMed Central

    Zhao, Xianhai; Que, Qingmin; Li, Pei; Huang, Hao; Deng, Xiaomei; Singh, Sunil Kumar; Wu, Ai-Min; Chen, Xiaoyang

    2016-01-01

    Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees. PMID:27438485

  13. STRAW: Species TRee Analysis Web server

    PubMed Central

    Shaw, Timothy I.; Ruan, Zheng; Glenn, Travis C.; Liu, Liang

    2013-01-01

    The coalescent methods for species tree reconstruction are increasingly popular because they can accommodate coalescence and multilocus data sets. Herein, we present STRAW, a web server that offers workflows for reconstruction of phylogenies of species using three species tree methods—MP-EST, STAR and NJst. The input data are a collection of rooted gene trees (for STAR and MP-EST methods) or unrooted gene trees (for NJst). The output includes the estimated species tree, modified Robinson-Foulds distances between gene trees and the estimated species tree and visualization of trees to compare gene trees with the estimated species tree. The web sever is available at http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/. PMID:23661681

  14. The Inference of Gene Trees with Species Trees

    PubMed Central

    Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

    2015-01-01

    This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

  15. Coalescent Histories for Lodgepole Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2015-10-01

    Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the lodgepole species trees (λn)n ≥ 0, in which tree λn has m = 2n+1 taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with m!! in the number of taxa m. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with m taxa, increasing a previous bound of [Formula: see text] to [Formula: see text]. We discuss the implications of our enumerative results for phylogenetic computations. PMID:25973633

  16. Exact solutions for species tree inference from discordant gene trees.

    PubMed

    Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

    2013-10-01

    Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions. PMID:24131054

  17. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

    PubMed Central

    Rose, Christopher M.; Russell, Jason D.; Ledvina, Aaron R.; McAlister, Graeme C.; Westphall, Michael S.; Griep-Raming, Jens; Schwartz, Jae C.; Coon, Joshua J.; Syka, John E.P.

    2013-01-01

    We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section RF ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately two-fold higher quadrupole field frequency of this cell relative to that of the A-QLT, enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell’s longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation. PMID:23609185

  18. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

    NASA Astrophysics Data System (ADS)

    Rose, Christopher M.; Russell, Jason D.; Ledvina, Aaron R.; McAlister, Graeme C.; Westphall, Michael S.; Griep-Raming, Jens; Schwartz, Jae C.; Coon, Joshua J.; Syka, John E. P.

    2013-06-01

    We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately 2-fold higher quadrupole field frequency of this cell relative to that of the A-QLT enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell's longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation.

  19. Multipurpose dissociation cell for enhanced ETD of intact protein species.

    PubMed

    Rose, Christopher M; Russell, Jason D; Ledvina, Aaron R; McAlister, Graeme C; Westphall, Michael S; Griep-Raming, Jens; Schwartz, Jae C; Coon, Joshua J; Syka, John E P

    2013-06-01

    We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately 2-fold higher quadrupole field frequency of this cell relative to that of the A-QLT enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell's longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation. PMID:23609185

  20. Reconciliation with Non-Binary Species Trees

    PubMed Central

    Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton

    2008-01-01

    Abstract Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|VG| · (kS + hS)) time, where |VG| is the number of nodes in the gene tree, hS is the height of the species tree and kS is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in Notung, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets. PMID:18808330

  1. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

    Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic

  2. Reconciliation of Gene and Species Trees

    PubMed Central

    Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

    2014-01-01

    The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

  3. Pushing the pace of tree species migration.

    PubMed

    Lazarus, Eli D; McGill, Brian J

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  4. Pushing the Pace of Tree Species Migration

    PubMed Central

    Lazarus, Eli D.; McGill, Brian J.

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  5. Region effects influence local tree species diversity

    PubMed Central

    Ricklefs, Robert E.; He, Fangliang

    2016-01-01

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  6. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  7. Profiling glucosinolates and phenolics in vegetative and reproductive tissues of the multi-purpose trees Moringa oleifera L. (horseradish tree) and Moringa stenopetala L.

    PubMed

    Bennett, Richard N; Mellon, Fred A; Foidl, Nikolaus; Pratt, John H; Dupont, M Susan; Perkins, Lionel; Kroon, Paul A

    2003-06-01

    Moringa species are important multi-purpose tropical crops, as human foods and for medicine and oil production. There has been no previous comprehensive analysis of the secondary metabolites in Moringa species. Tissues of M. oleifera from a wide variety of sources and M. stenopetala from a single source were analyzed for glucosinolates and phenolics (flavonoids, anthocyanins, proanthocyanidins, and cinnamates). M. oleifera and M. stenopetala seeds only contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate at high concentrations. Roots of M. oleifera and M. stenopetala had high concentrations of both 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and benzyl glucosinolate. Leaves from both species contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and three monoacetyl isomers of this glucosinolate. Only 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate was detected in M. oleifera bark tissue. M. oleifera leaves contained quercetin-3-O-glucoside and quercetin-3-O-(6' '-malonyl-glucoside), and lower amounts of kaempferol-3-O-glucoside and kaempferol-3-O-(6' '-malonyl-glucoside). M. oleifera leaves also contained 3-caffeoylquinic acid and 5-caffeoylquinic acid. Leaves of M. stenopetala contained quercetin 3-O-rhamnoglucoside (rutin) and 5-caffeoylquinic acid. Neither proanthocyanidins nor anthocyanins were detected in any of the tissues of either species. PMID:12769522

  8. A tree species inventory over Europe

    NASA Astrophysics Data System (ADS)

    Ambelas Skjøth, C.; Geels, C.; Hvidberg, M.; Hertel, O.; Brandt, J.; Frohn, L. M.; Hansen, K. M.; Hedegaard, G. B.; Christensen, J. H.; Moseholm, L.

    2009-04-01

    Atmospheric transport models are used in studies of atmospheric chemistry as well as aerobiology. Atmospheric transport models in general needs accurate emissions inventories, which includes biogenic emissions such as Volatile Organic Compounds (VOCs) and pollen. Trees are important VOC and pollen sources and a needed requirement is specie distribution which takes into account important species such as Betula and Alnus. We present here a detailed tree species inventory covering Europe, parts of Africa and parts of Asia. Forest inventories have been obtained for each European country, parts of Asia and parts of Africa. The national inventories vary with respect to number of species as well as the number of sub-regions each nation is divided into. The inventories are therefore harmonised within a GIS system and afterwards gridded to the model grid defined by the EMEP model: 50 km x 50 km. The inventory is designed to be used with existing land-use data, which separates forest cover into broad leaved, mixed and conifer forests. This will be exemplified by using two different remote sensing products with different grid resolution such as GLC2000 and CLC2000 in selected areas. The final inventory includes 16 conifer species and 23 broadleaved species that are important for biogenic VOCs or pollen emission calculations. For example: Oak (Quercus), poplar (Populus), pines (Pinus), spruce (Picea), birch (Betula) and alder (Alnus). 774 regions with forest inventories are included, mainly on sub-national level. The coverage of each specie ranges from national to European scale, where the latter includes VOC and allergy relevant species such as Quercus, Alnus and Betula. The inventory is gridded to the model grid defined by the EMEP model, which is also the basis for many emissions inventories throughout Europe. The inventory is therefore prepared for easy implementation into atmospheric transport models by providing an extension to already applied land use data such as the

  9. Liana competition with tropical trees varies seasonally but not with tree species identity.

    PubMed

    Leonor, Alvarez-Cansino; Schnitzer, Stefan A; Reid, Joseph P; Powers, Jennifer S

    2015-01-01

    Lianas in tropical forests compete intensely with trees for above- and belowground resources and limit tree growth and regeneration. Liana competition with adult canopy trees may be particularly strong, and, if lianas compete more intensely with some tree species than others, they may influence tree species composition. We performed the first systematic, large-scale liana removal experiment to assess the competitive effects of lianas on multiple tropical tree species by measuring sap velocity and growth in a lowland tropical forest in Panama. Tree sap velocity increased 60% soon after liana removal compared to control trees, and tree diameter growth increased 25% after one year. Although tree species varied in their response to lianas, this variation was not significant, suggesting that lianas competed similarly with all tree species examined. The effect of lianas on tree sap velocity was particularly strong during the dry season, when soil moisture was low, suggesting that lianas compete intensely with trees for water. Under the predicted global change scenario of increased temperature and drought intensity, competition from lianas may become more prevalent in seasonal tropical forests, which, according to our data, should have a negative effect on most tropical tree species. PMID:26236888

  10. The probability of topological concordance of gene trees and species trees.

    PubMed

    Rosenberg, Noah A

    2002-03-01

    The concordance of gene trees and species trees is reconsidered in detail, allowing for samples of arbitrary size to be taken from the species. A sense of concordance for gene tree and species tree topologies is clarified, such that if the "collapsed gene tree" produced by a gene tree has the same topology as the species tree, the gene tree is said to be topologically concordant with the species tree. The term speciodendric is introduced to refer to genes whose trees are topologically concordant with species trees. For a given three-species topology, probabilities of each of the three possible collapsed gene tree topologies are given, as are probabilities of monophyletic concordance and concordance in the sense of N. Takahata (1989), Genetics 122, 957-966. Increasing the sample size is found to increase the probability of topological concordance, but a limit exists on how much the topological concordance probability can be increased. Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation. PMID:11969392

  11. Exploring tree species signature using waveform LiDAR data

    NASA Astrophysics Data System (ADS)

    Zhou, T.; Popescu, S. C.; Krause, K.

    2015-12-01

    Successful classification of tree species with waveform LiDAR data would be of considerable value to estimate the biomass stocks and changes in forests. Current approaches emphasize converting the full waveform data into discrete points to get larger amount of parameters and identify tree species using several discrete-points variables. However, ignores intensity values and waveform shapes which convey important structural characteristics. The overall goal of this study was to employ the intensity and waveform shape of individual tree as the waveform signature to detect tree species. The data was acquired by the National Ecological Observatory Network (NEON) within 250*250 m study area located in San Joaquin Experimental Range. Specific objectives were to: (1) segment individual trees using the smoothed canopy height model (CHM) derived from discrete LiDAR points; (2) link waveform LiDAR with above individual tree boundaries to derive sample signatures of three tree species and use these signatures to discriminate tree species in a large area; and (3) compare tree species detection results from discrete LiDAR data and waveform LiDAR data. An overall accuracy of the segmented individual tree of more than 80% was obtained. The preliminary results show that compared with the discrete LiDAR data, the waveform LiDAR signature has a higher potential for accurate tree species classification.

  12. An estimate of the number of tropical tree species

    PubMed Central

    Slik, J. W. Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F.; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L.; Bellingham, Peter J.; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q.; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L. M.; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K.; Chazdon, Robin L.; Clark, Connie; Clark, David B.; Clark, Deborah A.; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S.; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J.; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A. O.; Eisenlohr, Pedro V.; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J.; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T.; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M.; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A.; Joly, Carlos A.; de Jong, Bernardus H. J.; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L.; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F.; Lawes, Michael J.; do Amaral, Ieda Leao; Letcher, Susan G.; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H.; Meilby, Henrik; Melo, Felipe P. L.; Metcalfe, Daniel J.; Medjibe, Vincent P.; Metzger, Jean Paul; Millet, Jerome; Mohandass, D.; Montero, Juan C.; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T. F.; Pitman, Nigel C. A.; Poorter, Lourens; Poulsen, Axel D.; Poulsen, John; Powers, Jennifer; Prasad, Rama C.; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A.; Santos, Fernanda; Sarker, Swapan K.; Satdichanh, Manichanh; Schmitt, Christine B.; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S.; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I.-Fang; Sunderland, Terry; Suresh, H. S.; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W.; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L. C. H.; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A.; Webb, Campbell O.; Whitfeld, Timothy; Wich, Serge A.; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C. Yves; Yap, Sandra L.; Yoneda, Tsuyoshi; Zahawi, Rakan A.; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L.; Garcia Luize, Bruno; Venticinque, Eduardo M.

    2015-01-01

    The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa. PMID:26034279

  13. An estimate of the number of tropical tree species.

    PubMed

    Slik, J W Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L; Bellingham, Peter J; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L M; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K; Chazdon, Robin L; Robin, Chazdon L; Clark, Connie; Clark, David B; Clark, Deborah A; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A O; Eisenlohr, Pedro V; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A; Joly, Carlos A; de Jong, Bernardus H J; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F; Lawes, Michael J; Amaral, Ieda Leao do; Letcher, Susan G; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H; Meilby, Henrik; Melo, Felipe P L; Metcalfe, Daniel J; Medjibe, Vincent P; Metzger, Jean Paul; Millet, Jerome; Mohandass, D; Montero, Juan C; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T F; Pitman, Nigel C A; Poorter, Lourens; Poulsen, Axel D; Poulsen, John; Powers, Jennifer; Prasad, Rama C; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; Dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A; Santos, Fernanda; Sarker, Swapan K; Satdichanh, Manichanh; Schmitt, Christine B; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I-Fang; Sunderland, Terry; Sunderand, Terry; Suresh, H S; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L C H; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A; Webb, Campbell O; Whitfeld, Timothy; Wich, Serge A; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C Yves; Yap, Sandra L; Yoneda, Tsuyoshi; Zahawi, Rakan A; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L; Garcia Luize, Bruno; Venticinque, Eduardo M

    2015-06-16

    The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa. PMID:26034279

  14. Tree species richness affecting fine root biomass in European forests

    NASA Astrophysics Data System (ADS)

    Finér, Leena; Domisch, Timo; Vesterdal, Lars; Dawud, Seid M.; Raulund-Rasmussen, Karsten

    2016-04-01

    Fine roots are an important factor in the forest carbon cycle, contributing significantly to below-ground biomass and soil carbon storage. Therefore it is essential to understand the role of the forest structure, indicated by tree species diversity in controlling below-ground biomass and managing the carbon pools of forest soils. We studied how tree species richness would affect fine root biomass and its distribution in the soil profile and biomass above- and below-ground allocation patterns of different tree species. Our main hypothesis was that increasing tree species richness would lead to below-ground niche differentiation and more efficient soil exploitation by the roots, resulting in a higher fine root biomass in the soil. We sampled fine roots of trees and understorey vegetation in six European forest types in Finland, Poland, Germany, Romania, Italy and Spain, representing boreal, temperate and Mediterranean forests, established within the FunDivEUROPE project for studying the effects of tree species diversity on forest functioning. After determining fine root biomasses, we identified the percentages of different tree species in the fine root samples using the near infrared reflectance spectroscopy (NIRS) method. Opposite to our hypothesis we did not find any general positive relationship between tree species richness and fine root biomass. A weak positive response found in Italy and Spain seemed to be related to dry environmental conditions during Mediterranean summers. At the Polish site where we could sample deeper soil layers (down to 40 cm), we found more tree fine roots in the deeper layers under species-rich forests, as compared to the monocultures, indicating the ability of trees to explore more resources and to increase soil carbon stocks. Tree species richness did not affect biomass allocation patterns between above- and below-ground parts of the trees.

  15. Inferring optimal species trees under gene duplication and loss.

    PubMed

    Bayzid, M S; Mirarab, S; Warnow, T

    2013-01-01

    Species tree estimation from multiple markers is complicated by the fact that gene trees can differ from each other (and from the true species tree) due to several biological processes, one of which is gene duplication and loss. Local search heuristics for two NP-hard optimization problems - minimize gene duplications (MGD) and minimize gene duplications and losses (MGDL) - are popular techniques for estimating species trees in the presence of gene duplication and loss. In this paper, we present an alternative approach to solving MGD and MGDL from rooted gene trees. First, we characterize each tree in terms of its "subtree-bipartitions" (a concept we introduce). Then we show that the MGD species tree is defined by a maximum weight clique in a vertex-weighted graph that can be computed from the subtree-bipartitions of the input gene trees, and the MGDL species tree is defined by a minimum weight clique in a similarly constructed graph. We also show that these optimal cliques can be found in polynomial time in the number of vertices of the graph using a dynamic programming algorithm (similar to that of Hallett and Lagergren(1)), because of the special structure of the graphs. Finally, we show that a constrained version of these problems, where the subtree-bipartitions of the species tree are drawn from the subtree-bipartitions of the input gene trees, can be solved in time that is polynomial in the number of gene trees and taxa. We have implemented our dynamic programming algorithm in a publicly available software tool, available at http://www.cs.utexas.edu/users/phylo/software/dynadup/. PMID:23424130

  16. Inconsistency of Species Tree Methods under Gene Flow.

    PubMed

    Solís-Lemus, Claudia; Yang, Mengyao; Ané, Cécile

    2016-09-01

    Coalescent-based methods are now broadly used to infer evolutionary relationships between groups of organisms under the assumption that incomplete lineage sorting (ILS) is the only source of gene tree discordance. Many of these methods are known to consistently estimate the species tree when all their assumptions are met. Nonetheless, little work has been done to test the robustness of such methods to violations of their assumptions. Here, we study the performance of two of the most efficient coalescent-based methods, ASTRAL and NJst, in the presence of gene flow. Gene flow violates the assumption that ILS is the sole source of gene tree conflict. We find anomalous gene trees on three-taxon rooted trees and on four-taxon unrooted trees. These anomalous trees do not exist under ILS only, but appear because of gene flow. Our simulations show that species tree methods (and concatenation) may reconstruct the wrong evolutionary history, even from a very large number of well-reconstructed gene trees. In other words, species tree methods can be inconsistent under gene flow. Our results underline the need for methods like PhyloNet, to account simultaneously for ILS and gene flow in a unified framework. Although much slower, PhyloNet had better accuracy and remained consistent at high levels of gene flow. PMID:27151419

  17. Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence.

    PubMed

    Garzon-Lopez, Carol X; Ballesteros-Mejia, Liliana; Ordoñez, Alejandro; Bohlman, Stephanie A; Olff, Han; Jansen, Patrick A

    2015-08-01

    The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings ('Janzen-Connell' effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest. PMID:25939379

  18. Exploring the Taxonomy of Oaks and Related Tree Species

    ERIC Educational Resources Information Center

    McMaster, Robert T.

    2004-01-01

    A lab in Eastern North America conducted a study to determine the taxonomic relationship between deciduous trees and several species of oaks by calculating the similarity index of all species to be studied. The study enabled students to classify the different species of oaks according to their distinct characteristics.

  19. Mapping urban forest tree species using IKONOS imagery: preliminary results.

    PubMed

    Pu, Ruiliang

    2011-01-01

    A stepwise masking system with high-resolution IKONOS imagery was developed to identify and map urban forest tree species/groups in the City of Tampa, Florida, USA. The eight species/groups consist of sand live oak (Quercus geminata), laurel oak (Quercus laurifolia), live oak (Quercus virginiana), magnolia (Magnolia grandiflora), pine (species group), palm (species group), camphor (Cinnamomum camphora), and red maple (Acer rubrum). The system was implemented with soil-adjusted vegetation index (SAVI) threshold, textural information after running a low-pass filter, and brightness threshold of NIR band to separate tree canopies from non-vegetated areas from other vegetation types (e.g., grass/lawn) and to separate the tree canopies into sunlit and shadow areas. A maximum likelihood classifier was used to identify and map forest type and species. After IKONOS imagery was preprocessed, a total of nine spectral features were generated, including four spectral bands, three hue-intensity-saturation indices, one SAVI, and one texture image. The identified and mapped results were examined with independent ground survey data. The experimental results indicate that when classifying all the eight tree species/ groups with the high-resolution IKONOS image data, the identifying accuracy was very low and could not satisfy a practical application level, and when merging the eight species/groups into four major species/groups, the average accuracy is still low (average accuracy = 73%, overall accuracy = 86%, and κ = 0.76 with sunlit test samples). Such a low accuracy of identifying and mapping the urban tree species/groups is attributable to low spatial resolution IKONOS image data relative to tree crown size, to complex and variable background spectrum impact on crown spectra, and to shadow/shaded impact. The preliminary results imply that to improve the tree species identification accuracy and achieve a practical application level in urban area, multi-temporal (multi

  20. Soil nutrients influence spatial distributions of tropical tree species

    PubMed Central

    John, Robert; Dalling, James W.; Harms, Kyle E.; Yavitt, Joseph B.; Stallard, Robert F.; Mirabello, Matthew; Hubbell, Stephen P.; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B.

    2007-01-01

    The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757–1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<104 km2) and regional scales. At local scales (<1 km2), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant–soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36–51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant–soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. PMID:17215353

  1. Soil nutrients influence spatial distributions of tropical trees species

    USGS Publications Warehouse

    John, R.; Dalling, J.W.; Harms, K.E.; Yavitt, J.B.; Stallard, R.F.; Mirabello, M.; Hubbell, S.P.; Valencia, R.; Navarrete, H.; Vallejo, M.; Foster, R.B.

    2007-01-01

    The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. ?? 2007 by The National Academy of Sciences of the USA.

  2. Tree Species Classification By Multiseasonal High Resolution Satellite Data

    NASA Astrophysics Data System (ADS)

    Elatawneh, Alata; Wallner, Adelheid; Straub, Christoph; Schneider, Thomas; Knoke, Thomas

    2013-12-01

    Accurate forest tree species mapping is a fundamental issue for sustainable forest management and planning. Forest tree species mapping with the means of remote sensing data is still a topic to be investigated. The Bavaria state institute of forestry is investigating the potential of using digital aerial images for forest management purposes. However, using aerial images is still cost- and time-consuming, in addition to their acquisition restrictions. The new space-born sensor generations such as, RapidEye, with a very high temporal resolution, offering multiseasonal data have the potential to improve the forest tree species mapping. In this study, we investigated the potential of multiseasonal RapidEye data for mapping tree species in a Mid European forest in Southern Germany. The RapidEye data of level A3 were collected on ten different dates in the years 2009, 2010 and 2011. For data analysis, a model was developed, which combines the Spectral Angle Mapper technique with a 10-fold- cross-validation. The analysis succeeded to differentiate four tree species; Norway spruce (Picea abies L.), Silver Fir (Abies alba Mill.), European beech (Fagus sylvatica) and Maple (Acer pseudoplatanus). The model success was evaluated using digital aerial images acquired in the year 2009 and inventory point records from 2008/09 inventory. Model results of the multiseasonal RapidEye data analysis achieved an overall accuracy of 76%. However, the success of the model was evaluated only for all the identified species and not for the individual.

  3. Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

    PubMed Central

    Pollard, Daniel A; Eisen, Michael B

    2006-01-01

    The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this

  4. Multipurpose Spaces

    ERIC Educational Resources Information Center

    Gordon, Douglas

    2010-01-01

    The concept of multipurpose spaces in schools is certainly not new. Especially in elementary schools, the combination of cafeteria and auditorium (and sometimes indoor physical activity space as well) is a well-established approach to maximizing the use of school space and a school district's budget. Nonetheless, there continue to be refinements…

  5. Geographical Range and Local Abundance of Tree Species in China

    PubMed Central

    Ren, Haibao; Condit, Richard; Chen, Bin; Mi, Xiangcheng; Cao, Min; Ye, Wanhui; Hao, Zhanqing; Ma, Keping

    2013-01-01

    Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km2, and >90% of 651 species had ranges >105 km2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges. PMID:24130772

  6. Why abundant tropical tree species are phylogenetically old.

    PubMed

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W

    2013-10-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community. PMID:24043767

  7. Is tree species diversity or tree species identity the most important driver of European forest soil carbon stocks?

    NASA Astrophysics Data System (ADS)

    Vesterdal, Lars; Muhie Dawud, Seid; Raulund-Rasmussen, Karsten; Finér, Leena; Domisch, Timo

    2016-04-01

    Land management includes the selection of specific tree species and tree species mixtures for European forests. Studies of functional species diversity effects have reported positive effects for aboveground carbon (C) sequestration, but the question remains whether higher soil C stocks could also result from belowground niche differentiation including more efficient root exploitation of soils. We studied topsoil C stocks in tree species diversity gradients established within the FunDivEurope project to explore biodiversity-ecosystem functioning relationships in six European forest types in Finland, Poland, Germany, Romania, Spain and Italy. In the Polish forest type we extended the sampling to also include subsoils. We found consistent but modest effects of species diversity on total soil C stocks (forest floor and 0-20 cm) across the six European forest types. Carbon stocks in the forest floor alone and in the combined forest floor and mineral soil layers increased with increasing tree species diversity. In contrast, there was a strong effect of species identity (broadleaf vs. conifer) and its interaction with site-related factors. Within the Polish forest type we sampled soils down to 40 cm and found that species identity was again the main factor explaining total soil C stock. However, species diversity increased soil C stocks in deeper soil layers (20-40 cm), while species identity influenced C stocks significantly within forest floors and the 0-10 cm layer. Root biomass increased with diversity in 30-40 cm depth, and a positive relationship between C stocks and root biomass in the 30-40 cm layer suggested that belowground niche complementarity could be a driving mechanism for higher root carbon input and in turn a deeper distribution of C in diverse forests. We conclude that total C stocks are mainly driven by tree species identity. However, modest positive diversity effects were detected at the European scale, and stronger positive effects on subsoil C stocks

  8. Multilocus inference of species trees and DNA barcoding.

    PubMed

    Mallo, Diego; Posada, David

    2016-09-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481787

  9. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    PubMed Central

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  10. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    PubMed

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  11. Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation.

    PubMed

    Waters, Jonathan M; Rowe, Diane L; Burridge, Christopher P; Wallis, Graham P

    2010-10-01

    Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA. PMID:20603441

  12. Nitrogen Addition Enhances Drought Sensitivity of Young Deciduous Tree Species.

    PubMed

    Dziedek, Christoph; Härdtle, Werner; von Oheimb, Goddert; Fichtner, Andreas

    2016-01-01

    Understanding how trees respond to global change drivers is central to predict changes in forest structure and functions. Although there is evidence on the mode of nitrogen (N) and drought (D) effects on tree growth, our understanding of the interplay of these factors is still limited. Simultaneously, as mixtures are expected to be less sensitive to global change as compared to monocultures, we aimed to investigate the combined effects of N addition and D on the productivity of three tree species (Fagus sylvatica, Quercus petraea, Pseudotsuga menziesii) in relation to functional diverse species mixtures using data from a 4-year field experiment in Northwest Germany. Here we show that species mixing can mitigate the negative effects of combined N fertilization and D events, but the community response is mainly driven by the combination of certain traits rather than the tree species richness of a community. For beech, we found that negative effects of D on growth rates were amplified by N fertilization (i.e., combined treatment effects were non-additive), while for oak and fir, the simultaneous effects of N and D were additive. Beech and oak were identified as most sensitive to combined N+D effects with a strong size-dependency observed for beech, suggesting that the negative impact of N+D becomes stronger with time as beech grows larger. As a consequence, the net biodiversity effect declined at the community level, which can be mainly assigned to a distinct loss of complementarity in beech-oak mixtures. This pattern, however, was not evident in the other species-mixtures, indicating that neighborhood composition (i.e., trait combination), but not tree species richness mediated the relationship between tree diversity and treatment effects on tree growth. Our findings point to the importance of the qualitative role ('trait portfolio') that biodiversity play in determining resistance of diverse tree communities to environmental changes. As such, they provide further

  13. Nitrogen Addition Enhances Drought Sensitivity of Young Deciduous Tree Species

    PubMed Central

    Dziedek, Christoph; Härdtle, Werner; von Oheimb, Goddert; Fichtner, Andreas

    2016-01-01

    Understanding how trees respond to global change drivers is central to predict changes in forest structure and functions. Although there is evidence on the mode of nitrogen (N) and drought (D) effects on tree growth, our understanding of the interplay of these factors is still limited. Simultaneously, as mixtures are expected to be less sensitive to global change as compared to monocultures, we aimed to investigate the combined effects of N addition and D on the productivity of three tree species (Fagus sylvatica, Quercus petraea, Pseudotsuga menziesii) in relation to functional diverse species mixtures using data from a 4-year field experiment in Northwest Germany. Here we show that species mixing can mitigate the negative effects of combined N fertilization and D events, but the community response is mainly driven by the combination of certain traits rather than the tree species richness of a community. For beech, we found that negative effects of D on growth rates were amplified by N fertilization (i.e., combined treatment effects were non-additive), while for oak and fir, the simultaneous effects of N and D were additive. Beech and oak were identified as most sensitive to combined N+D effects with a strong size-dependency observed for beech, suggesting that the negative impact of N+D becomes stronger with time as beech grows larger. As a consequence, the net biodiversity effect declined at the community level, which can be mainly assigned to a distinct loss of complementarity in beech-oak mixtures. This pattern, however, was not evident in the other species-mixtures, indicating that neighborhood composition (i.e., trait combination), but not tree species richness mediated the relationship between tree diversity and treatment effects on tree growth. Our findings point to the importance of the qualitative role (‘trait portfolio’) that biodiversity play in determining resistance of diverse tree communities to environmental changes. As such, they provide

  14. Early positive effects of tree species richness on herbivory in a large-scale forest biodiversity experiment influence tree growth

    PubMed Central

    Schuldt, Andreas; Bruelheide, Helge; Härdtle, Werner; Assmann, Thorsten; Li, Ying; Ma, Keping; von Oheimb, Goddert; Zhang, Jiayong

    2015-01-01

    Despite the importance of herbivory for the structure and functioning of species-rich forests, little is known about how herbivory is affected by tree species richness, and more specifically by random vs. non-random species loss. We assessed herbivore damage and its effects on tree growth in the early stage of a large-scale forest biodiversity experiment in subtropical China that features random and non-random extinction scenarios of tree mixtures numbering between one and 24 species. In contrast to random species loss, the non-random extinction scenarios were based on the tree species’ local rarity and specific leaf area – traits that may strongly influence the way herbivory is affected by plant species richness. Herbivory increased with tree species richness across all scenarios and was unaffected by the different species compositions in the random and non-random extinction scenarios. Whereas tree growth rates were positively related to herbivory on plots with smaller trees, growth rates significantly declined with increasing herbivory on plots with larger trees. Our results suggest that the effects of herbivory on growth rates increase from monocultures to the most species-rich plant communities and that negative effects with increasing tree species richness become more pronounced with time as trees grow larger. Synthesis. Our results indicate that key trophic interactions can be quick to become established in forest plantations (i.e. already 2.5 years after tree planting). Stronger herbivory effects on tree growth with increasing tree species richness suggest a potentially important role of herbivory in regulating ecosystem functions and the structural development of species-rich forests from the very start of secondary forest succession. The lack of significant differences between the extinction scenarios, however, contrasts with findings from natural forests of higher successional age, where rarity had negative effects on herbivory. This indicates that

  15. Multilocus inference of species trees and DNA barcoding

    PubMed Central

    2016-01-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481787

  16. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony.

    PubMed

    Shi, Tao

    2016-03-01

    Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. However, phylogenomic approaches, such as gene tree parsimony (GTP), show advantage over some other approaches in its ability to use gene families with duplications. GTP searches the 'optimal' species tree by minimizing the total cost of biological events such as duplications, but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of different gene families can impact on species tree inference, 3900 gene families from seven angiosperms encompassing a wide range of gene content, lineage-specific expansions and contractions were analyzed. It was found that the gene content and total duplication number in a gene family strongly influence species tree inference accuracy, with the highest accuracy achieved at either very low or very high gene content (or duplication number) and lowest accuracy centered in intermediate gene content (or duplication number), as the relationship can fit a binomial regression. Besides, for gene families of similar level of average gene content, those with relatively higher lineage-specific expansion or duplication rates tend to show lower accuracy. Additional correlation tests support that high accuracy for those gene families with large gene content may rely on abundant ancestral copies to provide many subtrees to resolve conflicts, whereas high accuracy for single or low copy gene families are just subject to sequence substitution per se. Very low accuracy reached by gene families of intermediate gene content or duplication number can be due to insufficient subtrees to resolve the conflicts from loss of alternative copies. As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by

  17. Widespread Discordance of Gene Trees with Species Tree inDrosophila: Evidence for Incomplete Lineage Sorting

    SciTech Connect

    Pollard, Daniel A.; Iyer, Venky N.; Moses, Alan M.; Eisen,Michael B.

    2006-08-28

    The phylogenetic relationship of the now fully sequencedspecies Drosophila erecta and D. yakuba with respect to the D.melanogaster species complex has been a subject of controversy. All threepossible groupings of the species have been reported in the past, thoughrecent multi-gene studies suggest that D. erecta and D. yakuba are sisterspecies. Using the whole genomes of each of these species as well as thefour other fully sequenced species in the subgenus Sophophora, we set outto investigate the placement of D. erecta and D. yakuba in the D.melanogaster species group and to understand the cause of the pastincongruence. Though we find that the phylogeny grouping D. erecta and D.yakuba together is the best supported, we also find widespreadincongruence in nucleotide and amino acid substitutions, insertions anddeletions, and gene trees. The time inferred to span the two keyspeciation events is short enough that under the coalescent model, theincongruence could be the result of incomplete lineage sorting.Consistent with the lineage-sorting hypothesis, substitutions supportingthe same tree were spatially clustered. Support for the different treeswas found to be linked to recombination such that adjacent genes supportthe same tree most often in regions of low recombination andsubstitutions supporting the same tree are most enriched roughly on thesame scale as linkage disequilibrium, also consistent with lineagesorting. The incongruence was found to be statistically significant androbust to model and species choice. No systematic biases were found. Weconclude that phylogenetic incongruence in the D. melanogaster speciescomplex is the result, at least in part, of incomplete lineage sorting.Incomplete lineage sorting will likely cause phylogenetic incongruence inmany comparative genomics datasets. Methods to infer the correct speciestree, the history of every base in the genome, and comparative methodsthat control for and/or utilize this information will be

  18. Diversification rates and species richness across the Tree of Life.

    PubMed

    Scholl, Joshua P; Wiens, John J

    2016-09-14

    Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. PMID:27605507

  19. A multigene species tree for Western Mediterranean painted frogs (Discoglossus).

    PubMed

    Pabijan, Maciej; Crottini, Angelica; Reckwell, Dennis; Irisarri, Iker; Hauswaldt, J Susanne; Vences, Miguel

    2012-09-01

    Painted frogs (Discoglossus) are an anuran clade that originated in the Upper Miocene. Extant species are morphologically similar and have a circum-Mediterranean distribution. We assembled a multilocus dataset from seven nuclear and four mitochondrial genes for several individuals of all but one of the extant species and reconstructed a robust phylogeny by applying a coalescent-based species-tree method and a concatenation approach, both of which gave congruent results. The earliest phylogenetic split within Discoglossus separates D. montalentii from a clade comprising all other species. Discoglossus montalentii is monophyletic for haplotype variation at all loci and has distinct morphological, bioacoustic and karyotypic characters. We find moderate support for a sister-group relationship between the Iberian taxa and the Moroccan D. scovazzi, and high support for a D. pictus -D. sardus clade distributed around the Tyrrhenian basin. Topological discordance among gene trees during the speciation of D. galganoi, D. scovazzi, D. pictus and D. sardus is interpreted as the consequence of nearly simultaneous, vicariant diversification. The timing of these events is unclear, but possibly coincided with the final geotectonic rearrangement of the Western Mediterranean in the Middle Miocene or later during the Messinian salinity crisis. The Iberian taxa D. galganoi galganoi and D. g. jeanneae are reciprocally monophyletic in mitochondrial DNA but not in nuclear gene trees, and are therefore treated as subspecies of D. galganoi. PMID:22641173

  20. Climatic extremes improve predictions of spatial patterns of tree species

    USGS Publications Warehouse

    Zimmermann, N.E.; Yoccoz, N.G.; Edwards, T.C., Jr.; Meier, E.S.; Thuiller, W.; Guisan, A.; Schmatz, D.R.; Pearman, P.B.

    2009-01-01

    Understanding niche evolution, dynamics, and the response of species to climate change requires knowledge of the determinants of the environmental niche and species range limits. Mean values of climatic variables are often used in such analyses. In contrast, the increasing frequency of climate extremes suggests the importance of understanding their additional influence on range limits. Here, we assess how measures representing climate extremes (i.e., interannual variability in climate parameters) explain and predict spatial patterns of 11 tree species in Switzerland. We find clear, although comparably small, improvement (+20% in adjusted D2, +8% and +3% in cross-validated True Skill Statistic and area under the receiver operating characteristics curve values) in models that use measures of extremes in addition to means. The primary effect of including information on climate extremes is a correction of local overprediction and underprediction. Our results demonstrate that measures of climate extremes are important for understanding the climatic limits of tree species and assessing species niche characteristics. The inclusion of climate variability likely will improve models of species range limits under future conditions, where changes in mean climate and increased variability are expected.

  1. Semi-supervised SVM for individual tree crown species classification

    NASA Astrophysics Data System (ADS)

    Dalponte, Michele; Ene, Liviu Theodor; Marconcini, Mattia; Gobakken, Terje; Næsset, Erik

    2015-12-01

    In this paper a novel semi-supervised SVM classifier is presented, specifically developed for tree species classification at individual tree crown (ITC) level. In ITC tree species classification, all the pixels belonging to an ITC should have the same label. This assumption is used in the learning of the proposed semi-supervised SVM classifier (ITC-S3VM). This method exploits the information contained in the unlabeled ITC samples in order to improve the classification accuracy of a standard SVM. The ITC-S3VM method can be easily implemented using freely available software libraries. The datasets used in this study include hyperspectral imagery and laser scanning data acquired over two boreal forest areas characterized by the presence of three information classes (Pine, Spruce, and Broadleaves). The experimental results quantify the effectiveness of the proposed approach, which provides classification accuracies significantly higher (from 2% to above 27%) than those obtained by the standard supervised SVM and by a state-of-the-art semi-supervised SVM (S3VM). Particularly, by reducing the number of training samples (i.e. from 100% to 25%, and from 100% to 5% for the two datasets, respectively) the proposed method still exhibits results comparable to the ones of a supervised SVM trained with the full available training set. This property of the method makes it particularly suitable for practical forest inventory applications in which collection of in situ information can be very expensive both in terms of cost and time.

  2. Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

    PubMed Central

    Satler, Jordan D.; Starrett, James; Hayashi, Cheryl Y.; Hedin, Marshal

    2011-01-01

    Background The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. Methodology/Principal Findings We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general “3 clade” structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. Conclusions/Significance This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages

  3. Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

    PubMed

    Brienen, Roel J W; Zuidema, Pieter A

    2005-11-01

    Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate-growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines. PMID:16012820

  4. Urban Tree Species Show the Same Hydraulic Response to Vapor Pressure Deficit across Varying Tree Size and Environmental Conditions

    PubMed Central

    Chen, Lixin; Zhang, Zhiqiang; Ewers, Brent E.

    2012-01-01

    Background The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations. Methodology/Principal Findings We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP). The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1) the influence of tree species and size on transpiration, and 2) the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH) and tree canopy transpiration amount (Ec) was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between Gc at VPD = 1 kPa (Gcref) and the Gc sensitivity to VPD (−dGc/dlnVPD) across studied species as well as under contrasting soil water and Rs conditions in the urban area. Conclusions/Significance We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of Gcref. PMID:23118904

  5. Lianas suppress seedling growth and survival of 14 tree species in a Panamanian tropical forest.

    PubMed

    Martínez-Izquierdo, Laura; García, María M; Powers, Jennifer S; Schnitzer, Stefan A

    2016-01-01

    Lianas are a common plant growth form in tropical forests, where they compete intensely with trees, decreasing tree recruitment, growth, and survival. If the detrimental effects of lianas vary significantly with tree species identity, as is often assumed, then lianas may influence tree species diversity and community composition. Furthermore, recent studies have shown that liana abundance and biomass are increasing relative to trees in neotropical forests, which will likely magnify the detrimental effects of lianas and may ultimately alter tree species diversity, relative abundances, and community composition. Few studies, however, have tested the responses of multiple tree species to the presence of lianas in robust, well-replicated experiments. We tested the hypotheses that lianas reduce tree seedling growth and survival, and that the effect of lianas varies with tree species identity. We used a large-scale liana removal experiment in Central Panama in which we planted 14 replicate seedlings of 14 different tree species that varied in shade tolerance in each of 16 80 x 80 m plots (eight liana-removal and eight unmanipulated controls; 3136 total seedlings). Over a nearly two-yr period, we found that tree seedlings survived 75% more, grew 300% taller, and had twice the aboveground biomass in liana-removal plots than seedlings in control plots, consistent with strong competition between lianas and tree seedlings. There were no significant differences in the response of tree species to liana competition (i.e., there was no species by treatment interaction), indicating that lianas had a similar negative effect on all 14 tree species. Furthermore, the effect of lianas did not vary with tree species shade tolerance classification, suggesting that the liana effect was not solely based on light. Based on these findings, recently observed increases in liana abundance in neotropical forests will substantially reduce tree regeneration, but will not significantly alter

  6. Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

    PubMed Central

    Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

    2014-01-01

    The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

  7. The Impact of Missing Data on Species Tree Estimation.

    PubMed

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2016-03-01

    Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amount of missing data, there remains no consensus on their impact to species tree estimation. Here, using several simulated and empirical data sets, we assess the effects of missing data on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and gene rate heterogeneity. We demonstrate that concatenation (RAxML), gene-tree-based coalescent (ASTRAL, MP-EST, and STAR), and supertree (matrix representation with parsimony [MRP]) methods perform reliably, so long as missing data are randomly distributed (by gene and/or by species) and that a sufficiently large number of genes are sampled. When data sets are indecisive sensu Sanderson et al. (2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155) and/or ILS is high, however, high amounts of missing data that are randomly distributed require exhaustive levels of gene sampling, likely exceeding most empirical studies to date. Moreover, missing data become especially problematic when they are nonrandomly distributed. We demonstrate that STAR produces inconsistent results when the amount of nonrandom missing data is high, regardless of the degree of ILS and gene rate heterogeneity. Similarly, concatenation methods using maximum likelihood can be misled by nonrandom missing data in the presence of gene rate heterogeneity, which becomes further exacerbated when combined with high ILS. In contrast, ASTRAL, MP-EST, and MRP are more robust under all of these scenarios. These results underscore the importance of understanding the influence of missing data in the phylogenomics era. PMID:26589995

  8. Interannual Variation in Stand Transpiration is Dependent Upon Tree Species

    NASA Astrophysics Data System (ADS)

    Ewers, B. E.; Mackay, D. S.; Burrows, S. N.; Ahl, D. E.; Samanta, S.

    2003-12-01

    In order to successfully predict transpirational water fluxes from forested watersheds, interannual variability in transpiration must be quantified and understood. In a heterogeneous forested landscape in northern Wisconsin, we quantified stand transpiration across four forest cover types representing more than 80 percent of the land area in order to 1) quantify differences in stand transpiration and leaf area over two years and 2) determine the mechanisms governing the changes in transpiration over two years. We measured sap flux in eight trees of each tree species in the four cover types. We found that in northern hardwoods, the leaf area of sugar maple increased between the two measurement years with transpiration per unit ground area increasing even more than could be explained by leaf area. In an aspen stand, tent caterpillars completely defoliated the stand for approximately a month until a new set of leaves flushed out. The new set of leaves resulted in a lower leaf area but the same transpiration per unit leaf area indicating there was no physiological compensation for the lower leaf area. At the same time, balsam fir growing underneath the aspen increased their transpiration rate in response to greater light penetration through the dominant aspen canopy Red pine had a thirty percent change in leaf area within a growing season due to multiple cohorts of leaves and transpiration followed this leaf area dynamic. In a forested wetland, white cedar transpiration was proportional to surface water depth between the two years. Despite the specific tree species' effects on stand transpiration, all species displayed a minimum water potential regulation resulting in a saturating response of transpiration to vapor pressure deficit that did not vary across the two years. This physiological set point will allow future water flux models to explain mechanistically interannual variability in transpiration of this and similar forests.

  9. Nitrogen and phosphorus additions negatively affect tree species diversity in tropical forest regrowth trajectories.

    PubMed

    Siddique, Ilyas; Vieira, Ima Célia Guimarães; Schmidt, Susanne; Lamb, David; Carvalho, Cláudio José Reis; Figueiredo, Ricardo de Oliveira; Blomberg, Simon; Davidson, Eric A

    2010-07-01

    Nutrient enrichment is increasingly affecting many tropical ecosystems, but there is no information on how this affects tree biodiversity. To examine dynamics in vegetation structure and tree species biomass and diversity, we annually remeasured tree species before and for six years after repeated additions of nitrogen (N) and phosphorus (P) in permanent plots of abandoned pasture in Amazonia. Nitrogen and, to a lesser extent, phosphorus addition shifted growth among woody species. Nitrogen stimulated growth of two common pioneer tree species and one common tree species adaptable to both high- and low-light environments, while P stimulated growth only of the dominant pioneer tree Rollinia exsucca (Annonaceae). Overall, N or P addition reduced tree assemblage evenness and delayed tree species accrual over time, likely due to competitive monopolization of other resources by the few tree species responding to nutrient enrichment with enhanced establishment and/or growth rates. Absolute tree growth rates were elevated for two years after nutrient addition. However, nutrient-induced shifts in relative tree species growth and reduced assemblage evenness persisted for more than three years after nutrient addition, favoring two nutrient-responsive pioneers and one early-secondary tree species. Surprisingly, N + P effects on tree biomass and species diversity were consistently weaker than N-only and P-only effects, because grass biomass increased dramatically in response to N + P addition. The resulting intensified competition probably prevented an expected positive N + P synergy in the tree assemblage. Thus, N or P enrichment may favor unknown tree functional response types, reduce the diversity of coexisting species, and delay species accrual during structurally and functionally complex tropical rainforest secondary succession. PMID:20715634

  10. Tree Species Specific Soil Moisture Patterns and Dynamics

    NASA Astrophysics Data System (ADS)

    Heidbuechel, I.; Dreibrodt, J.; Guntner, A.; Blume, T.

    2014-12-01

    Land use has a major influence on the hydrologic processes that take place in soils. Soil compaction on pastures for example leads to infiltration patterns that differ considerably from the ones observable in forests. It is not clear, however, how different forest stands influence soil infiltration and soil moisture distributions. Factors that that vary amongst different stands and potentially affect soil moisture processes in forests are, amongst others, canopy density, throughfall patterns, the intensity and frequency of stem flow, litter type, root distributions and rooting depth. To investigate how different tree species influence the way soils partition, store and conduct incoming precipitation we selected 15 locations under different tree stands within the TERENO observatory in north-east Germany. The forest stands under investigation were mature oak, young pine, mature pine, young beech and mature beech. At each location we installed 30 FDR soil moisture sensors grouped into five depth profiles (monitoring soil moisture from 10 cm to 200 cm) and 5 additional near surface sensors. The profile locations within each forest stand covered most of the anticipated variability by ranging from minimum to maximum distance to the trees including locations under more and less dense canopy. Supplementary to the FDR sensors, throughfall measurements, tensiometers and groundwater data were available to observe dynamics of tree water availability, water fluxes within the soils and percolation towards the groundwater. To identify patterns in space and time we referred to the statistical methods of wavelet analysis and temporal stability analysis. Finally, we tried to link the results from these analyses to specific hydrologic processes at the different locations.

  11. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure.

    PubMed

    DeGiorgio, Michael; Rosenberg, Noah A

    2016-08-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure. PMID:27086043

  12. Neogene origins and implied warmth tolerance of Amazon tree species

    PubMed Central

    Dick, Christopher W; Lewis, Simon L; Maslin, Mark; Bermingham, Eldredge

    2013-01-01

    Tropical rain forest has been a persistent feature in South America for at least 55 million years. The future of the contemporary Amazon forest is uncertain, however, as the region is entering conditions with no past analogue, combining rapidly increasing air temperatures, high atmospheric carbon dioxide concentrations, possible extreme droughts, and extensive removal and modification by humans. Given the long-term Cenozoic cooling trend, it is unknown whether Amazon forests can tolerate air temperature increases, with suggestions that lowland forests lack warm-adapted taxa, leading to inevitable species losses. In response to this uncertainty, we posit a simple hypothesis: the older the age of a species prior to the Pleistocene, the warmer the climate it has previously survived, with Pliocene (2.6–5 Ma) and late-Miocene (8–10 Ma) air temperature across Amazonia being similar to 2100 temperature projections under low and high carbon emission scenarios, respectively. Using comparative phylogeographic analyses, we show that 9 of 12 widespread Amazon tree species have Pliocene or earlier lineages (>2.6 Ma), with seven dating from the Miocene (>5.6 Ma) and three >8 Ma. The remarkably old age of these species suggest that Amazon forests passed through warmth similar to 2100 levels and that, in the absence of other major environmental changes, near-term high temperature-induced mass species extinction is unlikely. PMID:23404439

  13. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

    PubMed

    Mirarab, Siavash; Bayzid, Md Shamsuzzoha; Warnow, Tandy

    2016-05-01

    Species tree estimation is complicated by processes, such as gene duplication and loss and incomplete lineage sorting (ILS), that cause discordance between gene trees and the species tree. Furthermore, while concatenation, a traditional approach to tree estimation, has excellent performance under many conditions, the expectation is that the best accuracy will be obtained through the use of species tree estimation methods that are specifically designed to address gene tree discordance. In this article, we report on a study to evaluate MP-EST-one of the most popular species tree estimation methods designed to address ILS-as well as concatenation under maximum likelihood, the greedy consensus, and two supertree methods (Matrix Representation with Parsimony and Matrix Representation with Likelihood). Our study shows that several factors impact the absolute and relative accuracy of methods, including the number of gene trees, the accuracy of the estimated gene trees, and the amount of ILS. Concatenation can be more accurate than the best summary methods in some cases (mostly when the gene trees have poor phylogenetic signal or when the level of ILS is low), but summary methods are generally more accurate than concatenation when there are an adequate number of sufficiently accurate gene trees. Our study suggests that coalescent-based species tree methods may be key to estimating highly accurate species trees from multiple loci. PMID:25164915

  14. The complex biogeographic history of a widespread tropical tree species.

    PubMed

    Dick, Christopher W; Heuertz, Myriam

    2008-11-01

    Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P < 0.001) and allele-size mutations contributed significantly (R(ST) > F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal. PMID:18764917

  15. Firewood crops: shrub and tree species for energy production

    SciTech Connect

    Not Available

    1980-01-01

    In the face of global concern over the dwindling supply of fuelwood, the rate of forest decimation to provide basic human necessities in developing countries is alarming. We must look upon woody plants as renewable resources that, if effectively managed, could alleviate the problem not only for the present,but for posterity. This report suggests potential significant fuelwood species for introduction to suitable environments, although it does not suggest a solution for the fuelwood crisis. The emphasis is on species suitable for individual crops, but species suited to plantation cultivation for fueling small industrial factories, electric generators, and crop driers are also considered. Most of the plants are little known in traditional forest production. Some are woody shrubs rather than trees, but all are aggressive and quick growing. They should be introduced with care in areas where the climate and soil conditions are not harsh. The substitution of well-designed stoves, kilns, or boilers could improve fuel efficiency. Each species is illustrated with photographs and diagrams. (Refs. 420).

  16. Biogenic volatile organic compound emissions from nine tree species used in an urban tree-planting program

    NASA Astrophysics Data System (ADS)

    Curtis, A. J.; Helmig, D.; Baroch, C.; Daly, R.; Davis, S.

    2014-10-01

    The biogenic volatile organic compound (BVOC) emissions of nine urban tree species were studied to assess the air quality impacts from planting a large quantity of these trees in the City and County of Denver, Colorado, through the Mile High Million tree-planting initiative. The deciduous tree species studied were Sugar maple, Ohio buckeye, northern hackberry, Turkish hazelnut, London planetree, American basswood, Littleleaf linden, Valley Forge elm, and Japanese zelkova. These tree species were selected using the i-Tree Species Selector (itreetools.org). BVOC emissions from the selected tree species were investigated to evaluate the Species Selector data under the Colorado climate and environmental growing conditions. Individual tree species were subjected to branch enclosure experiments in which foliar emissions of BVOC were collected onto solid adsorbent cartridges. The cartridge samples were analyzed for monoterpenes (MT), sesquiterpenes (SQT), and other C10-C15 BVOC using thermal desorption-gas chromatography-flame ionization detection/mass spectroscopy (GC-FID/MS). Individual compounds and their emission rates (ER) were identified. MT were observed in all tree species, exhibiting the following total MT basal emission rates (BER; with a 1-σ lower bound, upper bound uncertainty window): Sugar maple, 0.07 (0.02, 0.11) μg g-1 h-1; London planetree, 0.15 (0.02, 0.27) μg g-1 h-1; northern hackberry, 0.33 (0.09, 0.57) μg g-1 h-1; Japanese zelkova, 0.42 (0.26, 0.58) μg g-1 h-1; Littleleaf linden, 0.71 (0.33, 1.09) μg g-1 h-1; Valley Forge elm, 0.96 (0.01, 1.92) μg g-1 h-1; Turkish hazelnut, 1.30 (0.32, 2.23) μg g-1 h-1; American basswood, 1.50 (0.40, 2.70) μg g-1 h-1; and Ohio buckeye, 6.61 (1.76, 11.47) μg g-1 h-1. SQT emissions were seen in five tree species with total SQT BER of: London planetree, 0.11 (0.01, 0.20) μg g-1 h-1; Japanese zelkova, 0.11 (0.05, 0.16) μg g-1 h-1; Littleleaf linden, 0.13 (0.06, 0.21) μg g-1 h-1; northern hackberry, 0.20 (0

  17. Tree species and functional traits but not species richness affect interrill erosion processes in young subtropical forests

    NASA Astrophysics Data System (ADS)

    Seitz, S.; Goebes, P.; Song, Z.; Bruelheide, H.; Härdtle, W.; Kühn, P.; Li, Y.; Scholten, T.

    2016-01-01

    Soil erosion is seriously threatening ecosystem functioning in many parts of the world. In this context, it is assumed that tree species richness and functional diversity of tree communities can play a critical role in improving ecosystem services such as erosion control. An experiment with 170 micro-scale run-off plots was conducted to investigate the influence of tree species and tree species richness as well as functional traits on interrill erosion in a young forest ecosystem. An interrill erosion rate of 47.5 Mg ha-1 a-1 was calculated. This study provided evidence that different tree species affect interrill erosion differently, while tree species richness did not affect interrill erosion in young forest stands. Thus, different tree morphologies have to be considered, when assessing soil erosion under forest. High crown cover and leaf area index reduced interrill erosion in initial forest ecosystems, whereas rising tree height increased it. Even if a leaf litter cover was not present, the remaining soil surface cover by stones and biological soil crusts was the most important driver for soil erosion control. Furthermore, soil organic matter had a decreasing influence on interrill erosion. Long-term monitoring of soil erosion under closing tree canopies is necessary, and a wide range of functional tree traits should be considered in future research.

  18. Higher levels of multiple ecosystem services are found in forests with more tree species.

    PubMed

    Gamfeldt, Lars; Snäll, Tord; Bagchi, Robert; Jonsson, Micael; Gustafsson, Lena; Kjellander, Petter; Ruiz-Jaen, María C; Fröberg, Mats; Stendahl, Johan; Philipson, Christopher D; Mikusiński, Grzegorz; Andersson, Erik; Westerlund, Bertil; Andrén, Henrik; Moberg, Fredrik; Moen, Jon; Bengtsson, Jan

    2013-01-01

    Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000 km(2), we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests. PMID:23299890

  19. Higher levels of multiple ecosystem services are found in forests with more tree species

    PubMed Central

    Gamfeldt, Lars; Snäll, Tord; Bagchi, Robert; Jonsson, Micael; Gustafsson, Lena; Kjellander, Petter; Ruiz-Jaen, María C.; Fröberg, Mats; Stendahl, Johan; Philipson, Christopher D.; Mikusiński, Grzegorz; Andersson, Erik; Westerlund, Bertil; Andrén, Henrik; Moberg, Fredrik; Moen, Jon; Bengtsson, Jan

    2013-01-01

    Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000 km2, we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests. PMID:23299890

  20. Temporal changes of soil respiration under different tree species.

    PubMed

    Akburak, Serdar; Makineci, Ender

    2013-04-01

    Soil respiration rates were measured monthly (from April 2007 to March 2008) under four adjacent coniferous plantation sites [Oriental spruce (Picea orientalis L.), Austrian pine (Pinus nigra Arnold), Turkish fir (Abies bornmulleriana L.), and Scots pine (Pinus sylvestris L.)] and adjacent natural Sessile oak forest (Quercus petraea L.) in Belgrad Forest-Istanbul/Turkey. Also, soil moisture, soil temperature, and fine root biomass were determined to identify the underlying environmental variables among sites which are most likely causing differences in soil respiration. Mean annual soil moisture was determined to be between 6.3 % and 8.1 %, and mean annual temperature ranged from 13.0°C to 14.2°C under all species. Mean annual fine root biomass changed between 368.09 g/m(2) and 883.71 g/m(2) indicating significant differences among species. Except May 2007, monthly soil respiration rates show significantly difference among species. However, focusing on tree species, differences of mean annual respiration rates did not differ significantly. Mean annual soil respiration ranged from 0.56 to 1.09 g C/m(2)/day. The highest rates of soil respiration reached on autumn months and the lowest rates were determined on summer season. Soil temperature, soil moisture, and fine root biomass explain mean annual soil respiration rates at the highest under Austrian pine (R (2) = 0.562) and the lowest (R (2) = 0.223) under Turkish fir. PMID:22828980

  1. Tree species composition affects the abundance of rowan (Sorbus aucuparia L.) in urban forests in Finland.

    PubMed

    Hamberg, Leena; Lehvävirta, Susanna; Kotze, D Johan; Heikkinen, Juha

    2015-03-15

    Recent studies have shown a considerable increase in the abundance of rowan (Sorbus aucuparia) saplings in urban forests in Finland, yet the reasons for this increase are not well understood. Here we investigated whether canopy cover or tree species composition, i.e., the basal areas of different tree species in Norway spruce dominated urban forests, affects the abundances of rowan seedlings, saplings and trees. Altogether 24 urban forest patches were investigated. We sampled the number of rowan and other saplings, and calculated the basal areas of trees. We showed that rowan abundance was affected by tree species composition. The basal area of rowan trees (≥ 5 cm in diameter at breast height, dbh) decreased with increasing basal area of Norway spruce, while the cover of rowan seedlings increased with an increase in Norway spruce basal area. However, a decrease in the abundance of birch (Betula pendula) and an increase in the broad-leaved tree group (Acer platanoides, Alnus glutinosa, Alnus incana, Amelanchier spicata, Prunus padus, Quercus robur, Rhamnus frangula and Salix caprea) coincided with a decreasing number of rowans. Furthermore, rowan saplings were scarce in the vicinity of mature rowan trees. Although it seems that tree species composition has an effect on rowan, the relationship between rowan saplings and mature trees is complex, and therefore we conclude that regulating tree species composition is not an easy way to keep rowan thickets under control in urban forests in Finland. PMID:25588119

  2. Tree species identity and functional traits but not species richness affect interrill erosion processes in young subtropical forests

    NASA Astrophysics Data System (ADS)

    Seitz, S.; Goebes, P.; Song, Z.; Bruelheide, H.; Härdtle, W.; Kühn, P.; Li, Y.; Scholten, T.

    2015-06-01

    Soil erosion is seriously threatening ecosystem functioning in many parts of the world. In this context, it is assumed that tree species richness and functional diversity of tree communities can play a critical role in improving ecosystem services such as erosion control. An experiment with 170 micro-scale runoff plots was conducted to investigate the influence of tree species richness and identity as well as tree functional traits on interrill erosion in a young forest ecosystem. An interrill erosion rate of 47.5 t ha-1 a-1 was calculated. This study provided evidence that different tree species affect interrill erosion, but higher tree species richness did not mitigate soil losses in young forest stands. Thus, different tree morphologies have to be considered, when assessing erosion under forest. High crown cover and leaf area index reduced soil losses in initial forest ecosystems, whereas rising tree height increased them. Even if a leaf litter cover was not present, remaining soil surface cover by stones and biological soil crusts was the most important driver for soil erosion control. Furthermore, soil organic matter had a decreasing influence on soil loss. Long-term monitoring of soil erosion under closing tree canopies is necessary and a wide range of functional tree traits should be taken into consideration in future research.

  3. Species identity and neighbor size surpass the impact of tree species diversity on productivity in experimental broad-leaved tree sapling assemblages under dry and moist conditions

    PubMed Central

    Lübbe, Torben; Schuldt, Bernhard; Leuschner, Christoph

    2015-01-01

    Species diversity may increase the productivity of tree communities through complementarity (CE) and/or selection effects (SE), but it is not well known how this relationship changes under water limitation. We tested the stress-gradient hypothesis, which predicts that resource use complementarity and facilitation are more important under water-limited conditions. We conducted a growth experiment with saplings of five temperate broad-leaved tree species that were grown in assemblages of variable diversity (1, 3, or 5 species) and species composition under ample and limited water supply to examine effects of species richness and species identity on stand- and tree-level productivity. Special attention was paid to effects of neighbor identity on the growth of target trees in mixture as compared to growth in monoculture. Stand productivity was strongly influenced by species identity while a net biodiversity effect (NE) was significant in the moist treatment (mostly assignable to CE) but of minor importance. The growth performance of some of the species in the mixtures was affected by tree neighborhood characteristics with neighbor size likely being more important than neighbor species identity. Diversity and neighbor identity effects visible in the moist treatment mostly disappeared in the dry treatment, disproving the stress-gradient hypothesis. The mixtures were similarly sensitive to drought-induced growth reduction as the monocultures, which may relate to the decreased CE on growth upon drought in the mixtures. PMID:26579136

  4. Species identity and neighbor size surpass the impact of tree species diversity on productivity in experimental broad-leaved tree sapling assemblages under dry and moist conditions.

    PubMed

    Lübbe, Torben; Schuldt, Bernhard; Leuschner, Christoph

    2015-01-01

    Species diversity may increase the productivity of tree communities through complementarity (CE) and/or selection effects (SE), but it is not well known how this relationship changes under water limitation. We tested the stress-gradient hypothesis, which predicts that resource use complementarity and facilitation are more important under water-limited conditions. We conducted a growth experiment with saplings of five temperate broad-leaved tree species that were grown in assemblages of variable diversity (1, 3, or 5 species) and species composition under ample and limited water supply to examine effects of species richness and species identity on stand- and tree-level productivity. Special attention was paid to effects of neighbor identity on the growth of target trees in mixture as compared to growth in monoculture. Stand productivity was strongly influenced by species identity while a net biodiversity effect (NE) was significant in the moist treatment (mostly assignable to CE) but of minor importance. The growth performance of some of the species in the mixtures was affected by tree neighborhood characteristics with neighbor size likely being more important than neighbor species identity. Diversity and neighbor identity effects visible in the moist treatment mostly disappeared in the dry treatment, disproving the stress-gradient hypothesis. The mixtures were similarly sensitive to drought-induced growth reduction as the monocultures, which may relate to the decreased CE on growth upon drought in the mixtures. PMID:26579136

  5. Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

    PubMed Central

    Blair, Jaime E.; Coffey, Michael D.; Martin, Frank N.

    2012-01-01

    To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred. PMID:22615869

  6. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    PubMed Central

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  7. Remnant Trees Affect Species Composition but Not Structure of Tropical Second-Growth Forest

    PubMed Central

    Sandor, Manette E.; Chazdon, Robin L.

    2014-01-01

    Remnant trees, spared from cutting when tropical forests are cleared for agriculture or grazing, act as nuclei of forest regeneration following field abandonment. Previous studies on remnant trees were primarily conducted in active pasture or old fields abandoned in the previous 2–3 years, and focused on structure and species richness of regenerating forest, but not species composition. Our study is among the first to investigate the effects of remnant trees on neighborhood forest structure, biodiversity, and species composition 20 years post-abandonment. We compared the woody vegetation around individual remnant trees to nearby plots without remnant trees in the same second-growth forests (“control plots”). Forest structure beneath remnant trees did not differ significantly from control plots. Species richness and species diversity were significantly higher around remnant trees. The species composition around remnant trees differed significantly from control plots and more closely resembled the species composition of nearby old-growth forest. The proportion of old-growth specialists and generalists around remnant trees was significantly greater than in control plots. Although previous studies show that remnant trees may initially accelerate secondary forest growth, we found no evidence that they locally affect stem density, basal area, and seedling density at later stages of regrowth. Remnant trees do, however, have a clear effect on the species diversity, composition, and ecological groups of the surrounding woody vegetation, even after 20 years of forest regeneration. To accelerate the return of diversity and old-growth forest species into regrowing forest on abandoned land, landowners should be encouraged to retain remnant trees in agricultural or pastoral fields. PMID:24454700

  8. The contribution of seed dispersers to tree species diversity in tropical rainforests.

    PubMed

    Kakishima, Satoshi; Morita, Satoru; Yoshida, Katsuhiko; Ishida, Atsushi; Hayashi, Saki; Asami, Takahiro; Ito, Hiromu; Miller, Donald G; Uehara, Takashi; Mori, Shigeta; Hasegawa, Eisuke; Matsuura, Kenji; Kasuya, Eiiti; Yoshimura, Jin

    2015-10-01

    Tropical rainforests are known for their extreme biodiversity, posing a challenging problem in tropical ecology. Many hypotheses have been proposed to explain the diversity of tree species, yet our understanding of this phenomenon remains incomplete. Here, we consider the contribution of animal seed dispersers to the species diversity of trees. We built a multi-layer lattice model of trees whose animal seed dispersers are allowed to move only in restricted areas to disperse the tree seeds. We incorporated the effects of seed dispersers in the traditional theory of allopatric speciation on a geological time scale. We modified the lattice model to explicitly examine the coexistence of new tree species and the resulting high biodiversity. The results indicate that both the coexistence and diversified evolution of tree species can be explained by the introduction of animal seed dispersers. PMID:26587246

  9. The contribution of seed dispersers to tree species diversity in tropical rainforests

    PubMed Central

    Kakishima, Satoshi; Morita, Satoru; Yoshida, Katsuhiko; Ishida, Atsushi; Hayashi, Saki; Asami, Takahiro; Ito, Hiromu; Miller, Donald G.; Uehara, Takashi; Mori, Shigeta; Hasegawa, Eisuke; Matsuura, Kenji; Kasuya, Eiiti; Yoshimura, Jin

    2015-01-01

    Tropical rainforests are known for their extreme biodiversity, posing a challenging problem in tropical ecology. Many hypotheses have been proposed to explain the diversity of tree species, yet our understanding of this phenomenon remains incomplete. Here, we consider the contribution of animal seed dispersers to the species diversity of trees. We built a multi-layer lattice model of trees whose animal seed dispersers are allowed to move only in restricted areas to disperse the tree seeds. We incorporated the effects of seed dispersers in the traditional theory of allopatric speciation on a geological time scale. We modified the lattice model to explicitly examine the coexistence of new tree species and the resulting high biodiversity. The results indicate that both the coexistence and diversified evolution of tree species can be explained by the introduction of animal seed dispersers. PMID:26587246

  10. Landscape Variation in Tree Species Richness in Northern Iran Forests

    PubMed Central

    Bourque, Charles P.-A.; Bayat, Mahmoud

    2015-01-01

    Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area’s unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area’s digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to

  11. Landscape variation in tree species richness in northern Iran forests.

    PubMed

    Bourque, Charles P-A; Bayat, Mahmoud

    2015-01-01

    Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area's unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area's digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to be

  12. The description of Paramblynotus delaneyi (Hymenoptera: Liopteridae), a new species from Joshua Tree National Park

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species, Paramblynotus delaneyi (Hymenoptera: Liopteridae), is described and characters separating it from the Nearctic species P. zonatus Weld and P. virginianus Liu are discussed. A discussion of the insect biodiversity survey at Joshua Tree National Park is provided....

  13. ECOLOGICAL RESPONSE SURFACES FOR NORTH AMERICAN BOREAL TREE SPECIES AND THEIR USE IN FOREST CLASSIFICATION

    EPA Science Inventory

    Empirical ecological response surfaces were derived for eight dominant tree species in the boreal forest region of Canada. tepwise logistic regression was used to model species dominance as a response to five climatic predictor variables. he predictor variables (annual snowfall, ...

  14. Fire controls population structure in four dominant tree species in a tropical savanna.

    PubMed

    Lehmann, Caroline E R; Prior, Lynda D; Bowman, David M J S

    2009-09-01

    The persistence of mesic savannas has been theorised as being dependent on disturbances that restrict the number of juveniles growing through the sapling size class to become fire-tolerant trees. We analysed the population structures of four dominant tropical savanna tree species from 30 locations in Kakadu National Park (KNP), northern Australia. We found that across KNP as a whole, the population size structures of these species do not exhibit recruitment bottlenecks. However, individual stands had multimodal size-class distributions and mixtures of tree species consistent with episodic and individualistic recruitment of co-occurring tree species. Using information theory and multimodel inference, we examined the relative importance of fire frequency, stand basal area and elevation difference between a site and permanent water in explaining variations in the proportion of sapling to adult stems in four dominant tree species. This showed that the proportion of the tree population made up of saplings was negatively related to both fire frequencies and stand basal area. Overall, fire frequency has density-dependent effects in the regulation of the transition of saplings to trees in this Australian savanna, due to interactions with stem size, regeneration strategies, growth rates and tree-tree competition. Although stable at the regional scale, the spatiotemporal variability of fire can result in structural and floristic diversity of savanna tree populations. PMID:19629532

  15. Indicator species of essential forest tree species in the Burdur district.

    PubMed

    Negiz, Mehmet Güvenç; Eser, Yunus; Kuzugüdenll, Emre; Izkan, Kürşad

    2015-01-01

    The forests of Burdur district for long have been subjected to over grazing and individual selection. As a result of this, majority of the forest areas in the district were degraded. In the district, afforestation efforts included majority of forestry implementations. It is well known that selecting suitable species plays an important role for achieving afforestation efforts. In this context, knowing the indicator species among the target species would be used in afforestation efforts, studies on the interrelationships between environmental factors and target species distribution is vital for selecting suitable species for a given area. In this study, Anatolian Black pine (Pinus nigra), Red pine (Pinus brutia), Crimean juniper (Juniperus excelsa) and Taurus cedar (Cedrus libani), essential tree species, were considered as target species. The data taken from 100 sample plots in Burdur district was used. Interspecific correlation analysis was performed to determine the positive and negative indicator species among each of the target species. As a result of ICA, 2 positive (Berberis crataegina, Juniperus oxycedrus), 2 negative (Phillyrea latifolia, Quercus coccifera) for Crimean Juniper, I positive (Juniperus oxycedrus), 3 negative (Onopordium acanthium, Fraxinus ornus, Phillyrea latifolia) for Anatolian black pine, 3 positive (Paliurus spina-christi, Quercus coccifer, Crataegus orientalis), 2 negative (Berberis crataegina, Astragalus nanus) for Red pine and 3 positive (Berberis crataegina, Rhamnus oleoides, Astragalus prusianus) 2 negative (Paliurus spina-christi, Quercus cerris) for Taurus cedarwere defined as indicator plant species. In this way, practical information was obtained for selecting the most suitable species, among the target species, for afforestation efforts in Burdur district. PMID:26591889

  16. Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

    PubMed Central

    Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

    2015-01-01

    The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P

  17. Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

    PubMed

    Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

    2015-01-01

    The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P

  18. Characterizing tropical tree species growth strategies: learning from inter-individual variability and scale invariance.

    PubMed

    Le Bec, Jimmy; Courbaud, Benoit; Le Moguédec, Gilles; Pélissier, Raphaël

    2015-01-01

    Understanding how tropical tree species differ in their growth strategies is critical to predict forest dynamics and assess species coexistence. Although tree growth is highly variable in tropical forests, species maximum growth is often considered as a major axis synthesizing species strategies, with fast-growing pioneer and slow-growing shade tolerant species as emblematic representatives. We used a hierarchical linear mixed model and 21-years long tree diameter increment series in a monsoon forest of the Western Ghats, India, to characterize species growth strategies and question whether maximum growth summarizes these strategies. We quantified both species responses to biotic and abiotic factors and individual tree effects unexplained by these factors. Growth responses to competition and tree size appeared highly variable among species which led to reversals in performance ranking along those two gradients. However, species-specific responses largely overlapped due to large unexplained variability resulting mostly from inter-individual growth differences consistent over time. On average one-third of the variability captured by our model was explained by covariates. This emphasizes the high dimensionality of the tree growth process, i.e. the fact that trees differ in many dimensions (genetics, life history) influencing their growth response to environmental gradients, some being unmeasured or unmeasurable. In addition, intraspecific variability increased as a power function of species maximum growth partly as a result of higher absolute responses of fast-growing species to competition and tree size. However, covariates explained on average the same proportion of intraspecific variability for slow- and fast-growing species, which showed the same range of relative responses to competition and tree size. These results reflect a scale invariance of the growth process, underlining that slow- and fast-growing species exhibit the same range of growth strategies. PMID

  19. Characterizing Tropical Tree Species Growth Strategies: Learning from Inter-Individual Variability and Scale Invariance

    PubMed Central

    Le Bec, Jimmy; Courbaud, Benoit; Le Moguédec, Gilles; Pélissier, Raphaël

    2015-01-01

    Understanding how tropical tree species differ in their growth strategies is critical to predict forest dynamics and assess species coexistence. Although tree growth is highly variable in tropical forests, species maximum growth is often considered as a major axis synthesizing species strategies, with fast-growing pioneer and slow-growing shade tolerant species as emblematic representatives. We used a hierarchical linear mixed model and 21-years long tree diameter increment series in a monsoon forest of the Western Ghats, India, to characterize species growth strategies and question whether maximum growth summarizes these strategies. We quantified both species responses to biotic and abiotic factors and individual tree effects unexplained by these factors. Growth responses to competition and tree size appeared highly variable among species which led to reversals in performance ranking along those two gradients. However, species-specific responses largely overlapped due to large unexplained variability resulting mostly from inter-individual growth differences consistent over time. On average one-third of the variability captured by our model was explained by covariates. This emphasizes the high dimensionality of the tree growth process, i.e. the fact that trees differ in many dimensions (genetics, life history) influencing their growth response to environmental gradients, some being unmeasured or unmeasurable. In addition, intraspecific variability increased as a power function of species maximum growth partly as a result of higher absolute responses of fast-growing species to competition and tree size. However, covariates explained on average the same proportion of intraspecific variability for slow- and fast-growing species, which showed the same range of relative responses to competition and tree size. These results reflect a scale invariance of the growth process, underlining that slow- and fast-growing species exhibit the same range of growth strategies. PMID

  20. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    PubMed

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  1. The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community, Mexico

    PubMed Central

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions

  2. Tree species richness promotes productivity in temperate forests through strong complementarity between species.

    PubMed

    Morin, Xavier; Fahse, Lorenz; Scherer-Lorenzen, Michael; Bugmann, Harald

    2011-12-01

    Understanding the link between biodiversity and ecosystem functioning (BEF) is pivotal in the context of global biodiversity loss. Yet, long-term effects have been explored only weakly, especially for forests, and no clear evidence has been found regarding the underlying mechanisms. We explore the long-term relationship between diversity and productivity using a forest succession model. Extensive simulations show that tree species richness promotes productivity in European temperate forests across a large climatic gradient, mostly through strong complementarity between species. We show that this biodiversity effect emerges because increasing species richness promotes higher diversity in shade tolerance and growth ability, which results in forests responding faster to small-scale mortality events. Our study generalises results from short-term experiments in grasslands to forest ecosystems and demonstrates that competition for light alone induces a positive effect of biodiversity on productivity, thus providing a new angle for explaining BEF relationships. PMID:21955682

  3. Mortality rates associated with crown health for eastern forest tree species.

    PubMed

    Morin, Randall S; Randolph, KaDonna C; Steinman, Jim

    2015-03-01

    The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during inventories of the US Forest Service Forest Inventory and Analysis (FIA) program since 1999. In this study, remeasured data from 55,013 trees on 2616 FIA plots in the eastern USA were used to assess the probability of survival among various tree species using the suite of FIA crown condition variables. Logistic regression procedures were employed to develop models for predicting tree survival. Results of the regression analyses indicated that crown dieback was the most important crown condition variable for predicting tree survival for all species combined and for many of the 15 individual species in the study. The logistic models were generally successful in representing recent tree mortality responses to multiyear infestations of beech bark disease and hemlock woolly adelgid. Although our models are only applicable to trees growing in a forest setting, the utility of models that predict impending tree mortality goes beyond forest inventory or traditional forestry growth and yield models and includes any application where managers need to assess tree health or predict tree mortality including urban forest, recreation, wildlife, and pest management. PMID:25655130

  4. Independent domestications of cultivated tree peonies from different wild peony species.

    PubMed

    Yuan, Jun-Hui; Cornille, Amandine; Giraud, Tatiana; Cheng, Fang-Yun; Hu, Yong-Hong

    2014-01-01

    An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants. PMID:24138195

  5. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus).

    PubMed

    Leaché, Adam D

    2009-12-01

    I investigated the impacts of phylogeographic sampling decisions on species tree estimation in the Sceloporus undulatus species group, a recent radiation of small, insectivorous lizards connected by parapatric and peripatric distribution across North America, using a variety of species tree inference methods (Bayesian estimation of species trees, Bayesian untangling of concordance knots, and minimize deep coalescences). Phylogenetic analyses of 16 specimens representing 4 putative species within S. "undulatus" using complete (8 loci, >5.5 kb) and incomplete (29 loci, >23.6 kb) nuclear data sets result in species trees that share features with the mitochondrial DNA (mtDNA) genealogy at the phylogeographic level but provide new insights into the evolutionary history of the species group. The concatenated nuclear data and mtDNA data both recover 4 major clades connecting populations across North America; however, instances of discordance are localized at the contact zones between adjacent phylogeographic groups. A random sub-sampling experiment designed to vary the phylogeographic samples included across hundreds of replicate species tree inferences suggests that inaccurate species assignments can result in inferred phylogenetic relationships that are dependent upon which particular populations are used as exemplars to represent species and can lead to increased estimates of effective population size. For the phylogeographic data presented here, reassigning specimens with introgressed mtDNA genomes to their prospective species, or excluding them from the analysis altogether, produces species tree topologies that are distinctly different from analyses that utilize mtDNA-based species assignments. Evolutionary biologists working at the interface of phylogeography and phylogenetics are likely to encounter multiple processes influencing gene trees congruence, which increases the relevance of estimating species trees with multilocus nuclear data and models that accommodate

  6. Species-specific effects on throughfall kinetic energy below 12 subtropical tree species are related to leaf traits and tree architecture

    NASA Astrophysics Data System (ADS)

    Goebes, Philipp; Seitz, Steffen; Kühn, Peter; Kröber, Wenzel; Bruelheide, Helge; Li, Ying; von Oheimb, Goddert; Scholten, Thomas

    2015-04-01

    Soil erosion impacts environmental systems widely, especially in subtropical China where high erosion rates occur. The comprehension about the mechanisms that induce soil erosion on agricultural land is broad, but erosion processes below forests are only rarely understood. Especially throughfall kinetic energy (TKE) is influenced by forests and their structure as well as their succession in many ways. Today, many forests are monoculture tree stands due to economic reasons by providing timber, fuel and pulp wood. Therefore, this study investigates the role of different monoculture forest stands on TKE that were afforestated in 2008. The main questions are: Is TKE species-specific? What are characteristic leaf traits and tree architectural parameters that induce a species-specific effect on TKE and by what extend do they contribute to a mediation of species-specific effects on TKE? We measured TKE of 12 different species in subtropical China using sand-filled splash cups during five rainfall events in summer 2013. In addition, 14 leaf traits and tree architectural parameters were registered to link species-specific effects on TKE to vegetation parameters. Our results show that TKE is highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus mukorossi, while Schima superba showed lowest TKE. The latter species can be regarded as key species for reduced erosion occurrence. This species effect is mediated by leaf habit, leaf area, leaf pinnation, leaf margin, tree ground diameter, crown base height, tree height, number of branches and LAI as biotic factors and rainfall amount as abiotic factor. Moreover, leaf habit, tree height and LA show high effect sizes on TKE and can be considered as major drivers evoking TKE differences below vegetation.

  7. Surface Water Storage Capacity of Twenty Tree Species in Davis, California.

    PubMed

    Xiao, Qingfu; McPherson, E Gregory

    2016-01-01

    Urban forestry is an important green infrastructure strategy because healthy trees can intercept rainfall, reducing stormwater runoff and pollutant loading. Surface saturation storage capacity, defined as the thin film of water that must wet tree surfaces before flow begins, is the most important variable influencing rainfall interception processes. Surface storage capacity is known to vary widely among tree species, but it is little studied. This research measured surface storage capacities of 20 urban tree species in a rainfall simulator. The measurement system included a rainfall simulator, digital balance, digital camera, and computer. Eight samples were randomly collected from each tree species. Twelve rainfall intensities (3.5-139.5 mm h) were simulated. Leaf-on and leaf-off simulations were conducted for deciduous species. Stem and foliar surface areas were estimated using an image analysis method. Results indicated that surface storage capacities varied threefold among tree species, 0.59 mm for crape myrtle ( L.) and 1.81 mm for blue spruce ( Engelm.). The mean value across all species was 0.86 mm (0.11 mm SD). To illustrate application of the storage values, interception was simulated and compared across species for a 40-yr period with different rainfall intensities and durations. By quantifying the potential for different tree species to intercept rainfall under a variety of meteorological conditions, this study provides new knowledge that is fundamental to validating the cost-effectiveness of urban forestry as a green infrastructure strategy and designing functional plantings. PMID:26828174

  8. No evidence for consistent long-term growth stimulation of 13 tropical tree species: results from tree-ring analysis.

    PubMed

    Groenendijk, Peter; van der Sleen, Peter; Vlam, Mart; Bunyavejchewin, Sarayudh; Bongers, Frans; Zuidema, Pieter A

    2015-10-01

    The important role of tropical forests in the global carbon cycle makes it imperative to assess changes in their carbon dynamics for accurate projections of future climate-vegetation feedbacks. Forest monitoring studies conducted over the past decades have found evidence for both increasing and decreasing growth rates of tropical forest trees. The limited duration of these studies restrained analyses to decadal scales, and it is still unclear whether growth changes occurred over longer time scales, as would be expected if CO2 -fertilization stimulated tree growth. Furthermore, studies have so far dealt with changes in biomass gain at forest-stand level, but insights into species-specific growth changes - that ultimately determine community-level responses - are lacking. Here, we analyse species-specific growth changes on a centennial scale, using growth data from tree-ring analysis for 13 tree species (~1300 trees), from three sites distributed across the tropics. We used an established (regional curve standardization) and a new (size-class isolation) growth-trend detection method and explicitly assessed the influence of biases on the trend detection. In addition, we assessed whether aggregated trends were present within and across study sites. We found evidence for decreasing growth rates over time for 8-10 species, whereas increases were noted for two species and one showed no trend. Additionally, we found evidence for weak aggregated growth decreases at the site in Thailand and when analysing all sites simultaneously. The observed growth reductions suggest deteriorating growth conditions, perhaps due to warming. However, other causes cannot be excluded, such as recovery from large-scale disturbances or changing forest dynamics. Our findings contrast growth patterns that would be expected if elevated CO2 would stimulate tree growth. These results suggest that commonly assumed growth increases of tropical forests may not occur, which could lead to erroneous

  9. Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini).

    PubMed

    Perez, S Ivan; Klaczko, Julia; dos Reis, Sérgio F

    2012-11-01

    The estimation of a robust phylogeny is a necessary first step in understanding the biological diversification of the platyrrhines. Although the most recent phylogenies are generally robust, they differ from one another in the relationship between Aotus and other genera as well as in the relationship between Pitheciidae and other families. Here, we used coding and non-coding sequences to infer the species tree and embedded gene trees of the platyrrhine genera using the Bayesian Markov chain Monte Carlo method for the multispecies coalescent (*BEAST) for the first time and to compared the results with those of a Bayesian concatenated phylogenetic analysis. Our species tree, based on all available sequences, shows a closer phylogenetic relationship between Atelidae and Cebidae and a closer relationship between Aotus and the Cebidae clade. The posterior probabilities are lower for these conflictive tree nodes compared to those in the concatenated analysis; this finding could be explained by some gene trees showing no concordant topologies between Aotus and the other genera. Moreover, the topology of our species tree also differs from the findings of previous molecular and morphological studies regarding the position of Aotus. The existence of discrepancies between morphological data, gene trees and the species tree is widely reported and can be related to processes such as incomplete lineage sorting or selection. Although these processes are common in species trees with low divergence, they can also occur in species trees with deep and rapid divergence. The sources of the inconsistency of morphological and molecular traits with the species tree could be a main focus of further research on platyrrhines. PMID:22841656

  10. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

    PubMed Central

    2015-01-01

    Background Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT). Mathematical theory about reconstructing species trees in the presence of HGT alone or ILS alone suggests that quartet-based species tree methods (known to be statistically consistent under ILS, or under bounded amounts of HGT) might be effective techniques for estimating species trees when both HGT and ILS are present. Results We evaluated several publicly available coalescent-based methods and concatenation under maximum likelihood on simulated datasets with moderate ILS and varying levels of HGT. Our study shows that two quartet-based species tree estimation methods (ASTRAL-2 and weighted Quartets MaxCut) are both highly accurate, even on datasets with high rates of HGT. In contrast, although NJst and concatenation using maximum likelihood are highly accurate under low HGT, they are less robust to high HGT rates. Conclusion Our study shows that quartet-based species-tree estimation methods can be highly accurate under the presence of both HGT and ILS. The study suggests the possibility that some quartet-based methods might be statistically consistent under phylogenomic models of gene tree heterogeneity with both HGT and ILS. PMID:26450506

  11. Seasonal variations of isoprene emissions from five oak tree species in East Asia

    NASA Astrophysics Data System (ADS)

    Lim, Yong-Jae; Armendariz, Al; Son, Youn-Suk; Kim, Jo-Chun

    2011-04-01

    Emissions of biogenic volatile organic compounds (BVOC) from trees can enhance the photochemical production of tropospheric ozone. Isoprene is one of the most environmentally important BVOCs, since its emission rate from certain tree species can be high and its chemical structure gives it high ozone forming potential. Understanding of isoprene emission rates from many tree species is limited, including influences of tree age, season, and other factors. Five oak species were studied which represent approximately 85 percent of the deciduous trees in South Korean forests. In general, there were obvious seasonal variations of isoprene emissions from five oak trees. Especially, Quercus aliena B. and Quercus mongolica F showed substantial seasonal variations of isoprene emissions; However, Quercus serrata T. and Quercus acutissima C. generally did not. It was found that Q. serrata T. showed the highest isoprene emission rates among the species tested (up to 130.5 μgC gdw -1 h -1) and its emission rates were highest during spring followed by summer and fall. The emission rates from two ( Q. acutissima C., Quercus variabilis B.) of the other tested oak species were lower by more than 3 orders of magnitude. Besides, two oak species, Q. aliena B. and Q. mongolica F. were chosen to determine the effect of tree age on isoprene emissions. Trees at the age of 21˜30 years had significantly higher isoprene emission rates than those at the age of 41˜50.

  12. Soil magnetic susceptibility reflects soil moisture regimes and the adaptability of tree species to these regimes

    USGS Publications Warehouse

    Wang, J.-S.; Grimley, D.A.; Xu, C.; Dawson, J.O.

    2008-01-01

    Flooded, saturated or poorly drained soils are frequently anaerobic, leading to dissolution of the strongly magnetic minerals, magnetite and maghemite, and a corresponding decrease in soil magnetic susceptibility (MS). In this study of five temperate deciduous forests in east-central Illinois, USA, mean surface soil MS was significantly higher adjacent to upland tree species (31 ?? 10-5 SI) than adjacent to floodplain or lowland tree species (17 ?? 10-5 SI), when comparing regional soils with similar parent material of loessal silt. Although the sites differ in average soil MS for each tree species, the relative order of soil MS means for associated tree species at different locations is similar. Lowland tree species, Celtis occidentalis L., Ulmus americana L., Acer saccharinum L., Carya laciniosa (Michx. f.) Loud., and Fraxinus pennsylvanica Marsh. were associated with the lowest measured soil MS mean values overall and at each site. Tree species' flood tolerance rankings increased significantly, as soil MS values declined, the published rankings having significant correlations with soil MS values for the same species groups. The three published classifications of tree species' flood tolerance were significantly correlated with associated soil MS values at all sites, but most strongly at Allerton Park, the site with the widest range of soil drainage classes and MS values. Using soil MS measurements in forests with soil parent material containing similar initial levels of strongly magnetic minerals can provide a simple, rapid and quantitative method to classify soils according to hydric regimes, including dry conditions, and associated plant composition. Soil MS values thus have the capacity to quantify the continuum of hydric tolerances of tree species and guide tree species selection for reforestation. ?? 2007 Elsevier B.V. All rights reserved.

  13. Species-environment relationships and vegetation patterns: Effects of spatial scale and tree life-stage

    USGS Publications Warehouse

    Stohlgren, T.J.; Bachand, R.R.; Onami, Y.; Binkley, D.

    1998-01-01

    Do relationships between species and environmental gradients strengthen or weaken with tree life-stage (i.e., small seedlings, large seedlings, saplings, and mature trees)? Strengthened relationships may lead to distinct forest type boundaries, or weakening connections could lead to gradual ecotones and heterogeneous forest landscapes. We quantified the changes in forest dominance (basal area of tree species by life-stage) and environmental factors (elevation, slope, aspect, intercepted photosynthetically active radiation (PAR), summer soil moisture, and soil depth and texture) across 14 forest ecotones (n = 584, 10 m x 10 m plots) in Rocky Mountain National Park, Colorado, U.S.A. Local, ecotone-specific species-environment relationships, based on multiple regression techniques, generally strengthened from the small seedling stage (multiple R2 ranged from 0.00 to 0.26) to the tree stage (multiple R2 ranged from 0.20 to 0.61). At the landscape scale, combined canonical correspondence analysis (CCA) among species and for all tree life-stages suggested that the seedlings of most species became established in lower-elevation, drier sites than where mature trees of the same species dominated. However, conflicting evidence showed that species-environment relationships may weaken with tree life-stage. Seedlings were only found in a subset of plots (habitats) occupied by mature trees of the same species. At the landscape scale, CCA results showed that species-environment relationships weakened somewhat from the small seedling stage (86.4% of the variance explained by the first two axes) to the tree stage (76.6% of variance explained). The basal area of tree species co-occurring with Pinus contorta Doug. ex. Loud declined more gradually than P. contorta basal area declined across ecotones, resulting in less-distinct forest type boundaries. We conclude that broad, gradual ecotones and heterogeneous forest landscapes are created and maintained by: (1) sporadic establishment

  14. Tissue culture and top-fruit tree species.

    PubMed

    Ochatt, S J; Davey, M R; Power, J B

    1990-01-01

    The commercial cultivation of rosaceous fruit trees (e.g., pear, apple, cherry, peach, plum) relies heavily upon the quality and performance of the rootstocks. This is even more the case now that self-rooted scions produce larger trees with a longer juvenile phase (1). It would, therefore, be of special interest for the fruit breeder to have general purpose rootstocks with a wide ecophysiological adaptation and high compatibility coupled with early cropping. In addition, many of the older and highly adapted scion varieties of fruit trees could benefit greatly from the introduction of stable, yet minor changes in their genome. Fruit trees are generally highly heterozygous, outbreeding, and thus are asexually propagated (see Chapter 10 , this vol.). Consequently, genetic improvement is likely to be based on protoplast technology, and achieved mainly through somatic methods, such as somaclonal variation or somatic hybridization. PMID:21390607

  15. Designing Mixed Species Tree Plantations for the Tropics: Balancing Ecological Attributes of Species with Landholder Preferences in the Philippines

    PubMed Central

    Nguyen, Huong; Lamb, David; Herbohn, John; Firn, Jennifer

    2014-01-01

    A mixed species reforestation program known as the Rainforestation Farming system was undertaken in the Philippines to develop forms of farm forestry more suitable for smallholders than the simple monocultural plantations commonly used then. In this study, we describe the subsequent changes in stand structure and floristic composition of these plantations in order to learn from the experience and develop improved prescriptions for reforestation systems likely to be attractive to smallholders. We investigated stands aged from 6 to 11 years old on three successive occasions over a 6 year period. We found the number of species originally present in the plots as trees >5 cm dbh decreased from an initial total of 76 species to 65 species at the end of study period. But, at the same time, some new species reached the size class threshold and were recruited into the canopy layer. There was a substantial decline in tree density from an estimated stocking of about 5000 trees per ha at the time of planting to 1380 trees per ha at the time of the first measurement; the density declined by a further 4.9% per year. Changes in composition and stand structure were indicated by a marked shift in the Importance Value Index of species. Over six years, shade-intolerant species became less important and the native shade-tolerant species (often Dipterocarps) increased in importance. Based on how the Rainforestation Farming plantations developed in these early years, we suggest that mixed-species plantations elsewhere in the humid tropics should be around 1000 trees per ha or less, that the proportion of fast growing (and hence early maturing) trees should be about 30–40% of this initial density and that any fruit tree component should only be planted on the plantation margin where more light and space are available for crowns to develop. PMID:24751720

  16. Designing mixed species tree plantations for the tropics: balancing ecological attributes of species with landholder preferences in the Philippines.

    PubMed

    Nguyen, Huong; Lamb, David; Herbohn, John; Firn, Jennifer

    2014-01-01

    A mixed species reforestation program known as the Rainforestation Farming system was undertaken in the Philippines to develop forms of farm forestry more suitable for smallholders than the simple monocultural plantations commonly used then. In this study, we describe the subsequent changes in stand structure and floristic composition of these plantations in order to learn from the experience and develop improved prescriptions for reforestation systems likely to be attractive to smallholders. We investigated stands aged from 6 to 11 years old on three successive occasions over a 6 year period. We found the number of species originally present in the plots as trees >5 cm dbh decreased from an initial total of 76 species to 65 species at the end of study period. But, at the same time, some new species reached the size class threshold and were recruited into the canopy layer. There was a substantial decline in tree density from an estimated stocking of about 5000 trees per ha at the time of planting to 1380 trees per ha at the time of the first measurement; the density declined by a further 4.9% per year. Changes in composition and stand structure were indicated by a marked shift in the Importance Value Index of species. Over six years, shade-intolerant species became less important and the native shade-tolerant species (often Dipterocarps) increased in importance. Based on how the Rainforestation Farming plantations developed in these early years, we suggest that mixed-species plantations elsewhere in the humid tropics should be around 1000 trees per ha or less, that the proportion of fast growing (and hence early maturing) trees should be about 30-40% of this initial density and that any fruit tree component should only be planted on the plantation margin where more light and space are available for crowns to develop. PMID:24751720

  17. CpDNA-based species identification and phylogeography: application to African tropical tree species.

    PubMed

    Duminil, J; Heuertz, M; Doucet, J-L; Bourland, N; Cruaud, C; Gavory, F; Doumenge, C; Navascués, M; Hardy, O J

    2010-12-01

    Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations. PMID:21091558

  18. Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions

    PubMed Central

    Tonini, João; Moore, Andrew; Stern, David; Shcheglovitova, Maryia; Ortí, Guillermo

    2015-01-01

    Phylogeneticists have long understood that several biological processes can cause a gene tree to disagree with its species tree. In recent years, molecular phylogeneticists have increasingly foregone traditional supermatrix approaches in favor of species tree methods that account for one such source of error, incomplete lineage sorting (ILS). While gene tree-species tree discordance no doubt poses a significant challenge to phylogenetic inference with molecular data, researchers have only recently begun to systematically evaluate the relative accuracy of traditional and ILS-sensitive methods. Here, we report on simulations demonstrating that concatenation can perform as well or better than methods that attempt to account for sources of error introduced by ILS. Based on these and similar results from other researchers, we argue that concatenation remains a useful component of the phylogeneticist’s toolbox and highlight that phylogeneticists should continue to make explicit comparisons of results produced by contemporaneous and classical methods. PMID:25901289

  19. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

    2016-02-01

    Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

  20. Leapfrogging of tree species provenances? Interaction of microclimate and genetics on upward shifts in tree species' range limits

    NASA Astrophysics Data System (ADS)

    Reinhardt, K.; Castanha, C.; Germino, M. J.; Kueppers, L. M.

    2011-12-01

    The elevation limit of tree growth (alpine treeline) is considered to be constrained by environmental (i.e., thermal) and genetic (i.e., inability to adapt to climatic conditions) limitations to growth. Warming conditions due to climate change are predicted to cause upward shifts in the elevation of alpine treelines, through relief of cold-induced physiological limitations on seedling recruitment beyond current treeline boundaries. To determine how genetics and climate may interact to affect seedling establishment, we transplanted recently germinated seedlings from high- and low-elevation provenances (HI and LO, respectively) of Pinus flexilis in common gardens arrayed along an elevation and canopy gradient from subalpine forest into the alpine zone at Niwot Ridge, CO. We compared differences in microclimate and seedling ecophysiology among sites and between provenances. During the first summer of growth, frequently cloudy skies resulted in similar solar radiation incidence and air and soil temperatures among sites, despite nearly a 500 m-span in elevation across all sites. Preliminary findings suggest that survival of seedlings was similar between the lowest and highest elevations, with greater survival of LO (60%) compared to HI (40%) seedlings at each of these sites. Photosynthesis, carbon balance (photosynthesis/respiration), and conductance increased more than 2X with elevation for both provenances, and were 35-77% greater in LO seedlings compared to HI seedlings. There were no differences in dark-adapted chlorophyll fluorescence (Fv/Fm) among sites or between provenances. However, in a common-garden study at low elevation, we observed no differences in carbon or water relations between two naturally-germinated mitochondrial haplotypes of P. flexilis (of narrow and wide-ranging distributions). We did observe water-related thresholds on seedling carbon balance and survival that occurred when soil volumetric water content dropped below 10% and seedling water

  1. Coordination between water transport capacity, biomass growth, metabolic scaling and species stature in co-occurring shrub and tree species.

    PubMed

    Smith, Duncan D; Sperry, John S

    2014-12-01

    The significance of xylem function and metabolic scaling theory begins from the idea that water transport is strongly coupled to growth rate. At the same time, coordination of water transport and growth seemingly should differ between plant functional types. We evaluated the relationships between water transport, growth and species stature in six species of co-occurring trees and shrubs. Within species, a strong proportionality between plant hydraulic conductance (K), sap flow (Q) and shoot biomass growth (G) was generally supported. Across species, however, trees grew more for a given K or Q than shrubs, indicating greater growth-based water-use efficiency (WUE) in trees. Trees also showed slower decline in relative growth rate (RGR) than shrubs, equivalent to a steeper G by mass (M) scaling exponent in trees (0.77-0.98). The K and Q by M scaling exponents were common across all species (0.80, 0.82), suggesting that the steeper G scaling in trees reflects a size-dependent increase in their growth-based WUE. The common K and Q by M exponents were statistically consistent with the 0.75 of ideal scaling theory. A model based upon xylem anatomy and branching architecture consistently predicted the observed K by M scaling exponents but only when deviations from ideal symmetric branching were incorporated. PMID:25041417

  2. SIMULATION OF OZONE EFFECTS ON EIGHT TREE SPECIES AT SHENANDOAH NATIONAL PARK

    EPA Science Inventory

    As part of an assessment of potential effects of air pollutants on the vegetation of Shenandoah National Park (SHEN), we simulated the growth of eight important tree species using TREGRO, a mechanistic model of individual tree growth. Published TREGRO parameters for black cherry...

  3. Assessing the potential of native tree species for carbon sequestration forestry in Northeast China.

    PubMed

    Thomas, S C; Malczewski, G; Saprunoff, M

    2007-11-01

    Although the native forests of China are exceptionally diverse, only a small number of tree species have been widely utilized in forest plantations and reforestation efforts. We used dendrochronological sampling methods to assess the potential growth and carbon sequestration of native tree species in Jilin Province, Northeast China. Trees were sampled in and near the Changbaishan Biosphere Reserve, with samples encompassing old-growth, disturbed forest, and plantations. To approximate conditions for planted trees, sampling focused on trees with exposed crowns (dominant and co-dominant individuals). A log-linear relationship was found between diameter increment and tree diameter, with a linear decrease in increment with increasing local basal area; no significant differences in these patterns between plantations and natural stands were detected for two commonly planted species (Pinus koraiensis and Larix olgensis). A growth model that incorporates observed feedbacks with individual tree size and local basal area (in conjunction with allometric models for tree biomass), was used to project stand-level biomass increment. Predicted growth trajectories were then linked to the carbon process model InTEC to provide estimates of carbon sequestration potential. Results indicate substantial differences among species, and suggest that certain native hardwoods (in particular Fraxinus mandshurica and Phellodendron amurense), have high potential for use in carbon forestry applications. Increased use of native hardwoods in carbon forestry in China is likely to have additional benefits in terms of economic diversification and enhanced provision of "ecosystem services", including biodiversity protection. PMID:17188419

  4. Slope variation and population structure of tree species from different ecological groups in South Brazil.

    PubMed

    Bianchini, Edmilson; Garcia, Cristina C; Pimenta, José A; Torezan, José M D

    2010-09-01

    Size structure and spatial arrangement of 13 abundant tree species were determined in a riparian forest fragment in Paraná State, South Brazil (23°16'S and 51°01'W). The studied species were Aspidosperma polyneuron Müll. Arg., Astronium graveolens Jacq. and Gallesia integrifolia (Spreng) Harms (emergent species); Alseis floribunda Schott, Ruprechtia laxiflora Meisn. and Bougainvillea spectabilis Willd. (shade-intolerant canopy species); Machaerium paraguariense Hassl, Myroxylum peruiferum L. and Chrysophyllum gonocarpum (Mart. & Eichler ex Miq.) Engl. (shade-tolerant canopy species); Sorocea bonplandii (Baill.) Bürger, Trichilia casaretti C. Dc, Trichilia catigua A. Juss. and Actinostemon concolor (Spreng.) Müll. Arg. (understory small trees species). Height and diameter structures and basal area of species were analyzed. Spatial patterns and slope correlation were analyzed by Moran's / spatial autocorrelation coefficient and partial Mantel test, respectively. The emergent and small understory species showed the highest and the lowest variations in height, diameter and basal area. Size distribution differed among emergent species and also among canopy shade-intolerant species. The spatial pattern ranged among species in all groups, except in understory small tree species. The slope was correlated with spatial pattern for A. polyneuron, A. graveolens, A. floribunda, R. laxiflora, M. peruiferum and T. casaretti. The results indicated that most species occurred in specific places, suggesting that niche differentiation can be an important factor in structuring the tree community. PMID:21562693

  5. Method for estimating potential tree-grade distributions for northeastern forest species. Forest Service research paper (Final)

    SciTech Connect

    Yaussy, D.A.

    1993-03-01

    The generalized logistic regression was used to distribute trees into four potential tree grades for 20 northeastern species groups. The potential tree grade is defined as the tree grade based on the length and amount of clear cuttings and defects only, disregarding minimum grading diameter. The algorithms described use site index and tree diameter as the predictive variables, allowing the equations to be incorporated into individual-tree growth and yield simulators such as NE-TWIGS.

  6. Pythium species Associated with Forest Tree Nurseries of Oregon and Washington

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pythium species are one of several pathogen genera responsible for damping off of conifer seedlings in forest tree nurseries. Species identification has been traditionally based on morphology. However, DNA-based identification methods may allow more accurate identification of species associated wi...

  7. Herbs versus Trees: Influences on Teenagers' Knowledge of Plant Species

    ERIC Educational Resources Information Center

    Lückmann, Katrin; Menzel, Susanne

    2014-01-01

    The study reports on species knowledge among German adolescents (n = 507) as: (1) self-assessed evaluation of one's species knowledge; and (2) factual knowledge about popular local herbs and trees. Besides assessing species knowledge, we were interested in whether selected demographic factors, environmental attitude (as measured through the…

  8. Predicting spatial variations of tree species richness in tropical forests from high-resolution remote sensing.

    PubMed

    Fricker, Geoffrey A; Wolf, Jeffrey A; Saatchi, Sassan S; Gillespie, Thomas W

    2015-10-01

    There is an increasing interest in identifying theories, empirical data sets, and remote-sensing metrics that can quantify tropical forest alpha diversity at a landscape scale. Quantifying patterns of tree species richness in the field is time consuming, especially in regions with over 100 tree species/ha. We examine species richness in a 50-ha plot in Barro Colorado Island in Panama and test if biophysical measurements of canopy reflectance from high-resolution satellite imagery and detailed vertical forest structure and topography from light detection and ranging (lidar) are associated with species richness across four tree size classes (>1, 1-10, >10, and >20 cm dbh) and three spatial scales (1, 0.25, and 0.04 ha). We use the 2010 tree inventory, including 204,757 individuals belonging to 301 species of freestanding woody plants or 166 ± 1.5 species/ha (mean ± SE), to compare with remote-sensing data. All remote-sensing metrics became less correlated with species richness as spatial resolution decreased from 1.0 ha to 0.04 ha and tree size increased from 1 cm to 20 cm dbh. When all stems with dbh > 1 cm in 1-ha plots were compared to remote-sensing metrics, standard deviation in canopy reflectance explained 13% of the variance in species richness. The standard deviations of canopy height and the topographic wetness index (TWI) derived from lidar were the best metrics to explain the spatial variance in species richness (15% and 24%, respectively). Using multiple regression models, we made predictions of species richness across Barro Colorado Island (BCI) at the 1-ha spatial scale for different tree size classes. We predicted variation in tree species richness among all plants (adjusted r² = 0.35) and trees with dbh > 10 cm (adjusted r² = 0.25). However, the best model results were for understory trees and shrubs (dbh 1-10 cm) (adjusted r² = 0.52) that comprise the majority of species richness in tropical forests. Our results indicate that high

  9. Supercooling Capacity Increases from Sea Level to Tree Line in the Hawaiian Tree Species Metrosideros polymorpha.

    PubMed

    Melcher; Cordell; Jones; Scowcroft; Niemczura; Giambelluca; Goldstein

    2000-05-01

    Population-specific differences in the freezing resistance of Metrosideros polymorpha leaves were studied along an elevational gradient from sea level to tree line (located at ca. 2500 m above sea level) on the east flank of the Mauna Loa volcano in Hawaii. In addition, we also studied 8-yr-old saplings grown in a common garden from seeds collected from the same field populations. Leaves of low-elevation field plants exhibited damage at -2 degrees C, before the onset of ice formation, which occurred at -5.7 degrees C. Leaves of high-elevation plants exhibited damage at ca. -8.5 degrees C, concurrent with ice formation in the leaf tissue, which is typical of plants that avoid freezing in their natural environment by supercooling. Nuclear magnetic resonance studies revealed that water molecules of both extra- and intracellular leaf water fractions from high-elevation plants had restricted mobility, which is consistent with their low water content and their high levels of osmotically active solutes. Decreased mobility of water molecules may delay ice nucleation and/or ice growth and may therefore enhance the ability of plant tissues to supercool. Leaf traits that correlated with specific differences in supercooling capacity were in part genetically determined and in part environmentally induced. Evidence indicated that lower apoplastic water content and smaller intercellular spaces were associated with the larger supercooling capacity of the plant's foliage at tree line. The irreversible tissue-damage temperature decreased by ca. 7 degrees C from sea level to tree line in leaves of field populations. However, this decrease appears to be only large enough to allow M. polymorpha trees to avoid leaf tissue damage from freezing up to a level of ca. 2500 m elevation, which is also the current tree line location on the east flank of Mauna Loa. The limited freezing resistance of M. polymorpha leaves may be partially responsible for the occurrence of tree line at a relatively

  10. Mountain landscapes offer few opportunities for high-elevation tree species migration.

    PubMed

    Bell, David M; Bradford, John B; Lauenroth, William K

    2014-05-01

    Climate change is anticipated to alter plant species distributions. Regional context, notably the spatial complexity of climatic gradients, may influence species migration potential. While high-elevation species may benefit from steep climate gradients in mountain regions, their persistence may be threatened by limited suitable habitat as land area decreases with elevation. To untangle these apparently contradictory predictions for mountainous regions, we evaluated the climatic suitability of four coniferous forest tree species of the western United States based on species distribution modeling (SDM) and examined changes in climatically suitable areas under predicted climate change. We used forest structural information relating to tree species dominance, productivity, and demography from an extensive forest inventory system to assess the strength of inferences made with a SDM approach. We found that tree species dominance, productivity, and recruitment were highest where climatic suitability (i.e., probability of species occurrence under certain climate conditions) was high, supporting the use of predicted climatic suitability in examining species risk to climate change. By predicting changes in climatic suitability over the next century, we found that climatic suitability will likely decline, both in areas currently occupied by each tree species and in nearby unoccupied areas to which species might migrate in the future. These trends were most dramatic for high elevation species. Climatic changes predicted over the next century will dramatically reduce climatically suitable areas for high-elevation tree species while a lower elevation species, Pinus ponderosa, will be well positioned to shift upslope across the region. Reductions in suitable area for high-elevation species imply that even unlimited migration would be insufficient to offset predicted habitat loss, underscoring the vulnerability of these high-elevation species to climatic changes. PMID:24353188

  11. Mountain landscapes offer few opportunities for high-elevation tree species migration

    USGS Publications Warehouse

    Bell, David M.; Bradford, John B.; Lauenroth, William K.

    2014-01-01

    Climate change is anticipated to alter plant species distributions. Regional context, notably the spatial complexity of climatic gradients, may influence species migration potential. While high-elevation species may benefit from steep climate gradients in mountain regions, their persistence may be threatened by limited suitable habitat as land area decreases with elevation. To untangle these apparently contradictory predictions for mountainous regions, we evaluated the climatic suitability of four coniferous forest tree species of the western United States based on species distribution modeling (SDM) and examined changes in climatically suitable areas under predicted climate change. We used forest structural information relating to tree species dominance, productivity, and demography from an extensive forest inventory system to assess the strength of inferences made with a SDM approach. We found that tree species dominance, productivity, and recruitment were highest where climatic suitability (i.e., probability of species occurrence under certain climate conditions) was high, supporting the use of predicted climatic suitability in examining species risk to climate change. By predicting changes in climatic suitability over the next century, we found that climatic suitability will likely decline, both in areas currently occupied by each tree species and in nearby unoccupied areas to which species might migrate in the future. These trends were most dramatic for high elevation species. Climatic changes predicted over the next century will dramatically reduce climatically suitable areas for high-elevation tree species while a lower elevation species, Pinus ponderosa, will be well positioned to shift upslope across the region. Reductions in suitable area for high-elevation species imply that even unlimited migration would be insufficient to offset predicted habitat loss, underscoring the vulnerability of these high-elevation species to climatic changes.

  12. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

    PubMed

    Perez, Manolo F; Carstens, Bryan C; Rodrigues, Gustavo L; Moraes, Evandro M

    2016-03-01

    Supportive data related to the article "Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America" (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. PMID:26900589

  13. Version 5 of Forecasts; Forecasts of Climate-Associated Shifts in Tree Species

    NASA Astrophysics Data System (ADS)

    Hargrove, W. W.; Kumar, J.; Potter, K. M.; Hoffman, F. M.

    2014-12-01

    Version 5 of the ForeCASTS tree range shift atlas (www.geobabble.org/~hnw/global/treeranges5/climate_change/atlas.html) now predicts global shifts in the suitable ranges of 335 tree species (essentially all woody species measured in Forest Inventory Analysis (FIA)) under forecasts from the Parallel Climate Model, and the Hadley Model, each under future climatic scenarios A1 and B1, each at two future dates (2050 and 2100). Version 5 includes more Global Biodiversity Information Facility (GBIF) occurrence points, uses improved heuristics for occurrence training, and recovers occurrence points that fall in water. A multivariate clustering procedure was used to quantitatively delineate 30 thousand environmentally homogeneous ecoregions across present and 8 potential future global locations at once, using global maps of 17 environmental characteristics describing temperature, precipitation, soils, topography and solar insolation. Occurrence of each tree species on FIA plots and in GBIF samples was used to identify a subset of suitable ecoregions from the full set of 30 thousand. This subset of suitable ecoregions was compared to the known current present range of the tree species. Predicted present ranges correspond well with existing ranges for all but a few of the 335 tree species. The subset of suitable ecoregions can then be tracked into the future to determine whether the suitable home range remains the same, moves, grows, shrinks, or disappears under each model/scenario combination. A quantitative niche breadth analysis allows sorting of the 17 environmental variables from the narrowest, most important, to the broadest, least restrictive environmental factors limiting each tree species. Potential tree richness maps were produced, along with a quantitative potential tree endemism map for present and future CONUS. Using a new empirical imputation method which associates sparse measurements of dependent variables with particular clustered combinations of the

  14. Extending the dormant bud cryopreservation method to new tree species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In cryopreservation of germplasm, using dormant winter buds (DB) as source plant material is economically favorable over tissue culture options. Although the DB cryopreservation method has been known for many years, the approach is feasible only for cryopreserving a select number of temperate tree s...

  15. North American tree squirrels and ground squirrels with overlapping ranges host different Cryptosporidium species and genotypes.

    PubMed

    Stenger, Brianna L S; Clark, Mark E; Kváč, Martin; Khan, Eakalak; Giddings, Catherine W; Prediger, Jitka; McEvoy, John M

    2015-12-01

    Wildlife-associated Cryptosporidium are an emerging cause of cryptosporidiosis in humans. The present study was undertaken to determine the extent to which North American tree squirrels and ground squirrels host zoonotic Cryptosporidium species and genotypes. Fragments of the Cryptosporidium 18S rRNA and actin genes were amplified and sequenced from fecal samples obtained from three tree squirrel and three ground squirrel species. In tree squirrels, Cryptosporidium was identified in 40.5% (17/42) of American red squirrels (Tamiasciurus hudsonicus), 40.4% (55/136) of eastern gray squirrels (Sciurus carolinensis), and 28.6% (2/7) of fox squirrels (Sciurus niger). Human-pathogenic Cryptosporidium ubiquitum and Cryptosporidium skunk genotype were the most prevalent species/genotypes in tree squirrels. Because tree squirrels live in close proximity to humans and are frequently infected with potentially zoonotic Cryptosporidium species/genotypes, they may be a significant reservoir of infection in humans. In ground squirrels, Cryptosporidium was detected in 70.2% (33/47) of 13-lined ground squirrels (Ictidomys tridecemlineatus), 35.1% (27/77) of black-tailed prairie dogs (Cynomys ludovicianus), and the only golden-mantled ground squirrel (Callospermophilus lateralis) that was sampled. Cryptosporidium rubeyi and ground squirrel genotypes I, II, and III were identified in isolates from these ground squirrel species. In contrast to the Cryptosporidium infecting tree squirrels, these species/genotypes appear to be specific for ground squirrels and are not associated with human disease. PMID:26437239

  16. Long range correlations in tree ring chronologies of the USA: Variation within and across species

    NASA Astrophysics Data System (ADS)

    Bowers, M. C.; Gao, J. B.; Tung, W. W.

    2013-02-01

    Abstract <span class="hlt">Tree</span> ring width data are among the best proxies for reconstructing past temperature and precipitation records. The discovery of fractal scaling and long-memory in meteorological and hydrological signals motivates us to investigate such properties in <span class="hlt">tree</span> ring chronologies. Detrended fluctuation analysis and adaptive fractal analysis are utilized to estimate the Hurst parameter values of 697 <span class="hlt">tree</span> ring chronologies from the continental United States. We find significant differences in the Hurst parameter values across the 10 <span class="hlt">species</span> studied in the work. The long-range scaling relations found here suggest that the behavior of <span class="hlt">tree</span> ring growth observed in a short calibration period may be similar to the general behavior of <span class="hlt">tree</span> ring growth in a much longer period, and therefore, the limited calibration period may be more useful than originally thought. The variations of the long-range correlations within and across <span class="hlt">species</span> may be further explored in future to better reconstruct paleoclimatic records.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3178650','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3178650"><span id="translatedtitle">Growth Strategies of Tropical <span class="hlt">Tree</span> <span class="hlt">Species</span>: Disentangling Light and Size Effects</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Rüger, Nadja; Berger, Uta; Hubbell, Stephen P.; Vieilledent, Ghislain; Condit, Richard</p> <p>2011-01-01</p> <p>An understanding of the drivers of <span class="hlt">tree</span> growth at the <span class="hlt">species</span> level is required to predict likely changes of carbon stocks and biodiversity when environmental conditions change. Especially in <span class="hlt">species</span>-rich tropical forests, it is largely unknown how <span class="hlt">species</span> differ in their response of growth to resource availability and individual size. We use a hierarchical Bayesian approach to quantify the impact of light availability and <span class="hlt">tree</span> diameter on growth of 274 woody <span class="hlt">species</span> in a 50-ha long-term forest census plot in Barro Colorado Island, Panama. Light reaching each individual <span class="hlt">tree</span> was estimated from yearly vertical censuses of canopy density. The hierarchical Bayesian approach allowed accounting for different sources of error, such as negative growth observations, and including rare <span class="hlt">species</span> correctly weighted by their abundance. All <span class="hlt">species</span> grew faster at higher light. Exponents of a power function relating growth to light were mostly between 0 and 1. This indicates that nearly all <span class="hlt">species</span> exhibit a decelerating increase of growth with light. In contrast, estimated growth rates at standardized conditions (5 cm dbh, 5% light) varied over a 9-fold range and reflect strong growth-strategy differentiation between the <span class="hlt">species</span>. As a consequence, growth rankings of the <span class="hlt">species</span> at low (2%) and high light (20%) were highly correlated. Rare <span class="hlt">species</span> tended to grow faster and showed a greater sensitivity to light than abundant <span class="hlt">species</span>. Overall, <span class="hlt">tree</span> size was less important for growth than light and about half the <span class="hlt">species</span> were predicted to grow faster in diameter when bigger or smaller, respectively. Together light availability and <span class="hlt">tree</span> diameter only explained on average 12% of the variation in growth rates. Thus, other factors such as soil characteristics, herbivory, or pathogens may contribute considerably to shaping <span class="hlt">tree</span> growth in the tropics. PMID:21966498</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JHyd..537....1S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JHyd..537....1S&link_type=ABSTRACT"><span id="translatedtitle">Inter- and intra-specific variation in stemflow for evergreen <span class="hlt">species</span> and deciduous <span class="hlt">tree</span> <span class="hlt">species</span> in a subtropical forest</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Su, Lei; Xu, Wenting; Zhao, Changming; Xie, Zongqiang; Ju, Hua</p> <p>2016-06-01</p> <p>Quantification of stemflow is necessary for the assessment of forest ecosystem hydrological effects. Nevertheless, variation of stemflow among plant functional groups is currently not well understood. Stemflow production of co-occurring evergreen broadleaved <span class="hlt">trees</span> (Cyclobalanopsis multinervis and Cyclobalanopsis oxyodon) and deciduous broadleaved <span class="hlt">trees</span> (Fagus engleriana and Quercus serrata var. brevipetiolata) was quantified through field observations in a mixed evergreen and deciduous broadleaved forest. The research results revealed that stemflow increased linearly with increasing rainfall magnitude, with precipitation depths of 6.9, 7.2, 10.0 and 14.8 mm required for the initiation of stemflow for C. multinervis, C. oxyodon, F. engleriana and Q. serrata, respectively. Stemflow percentage and funneling ratio (FR) increased with increasing rainfall in a logarithmic fashion. Stemflow percentage and FR tended to grow rapidly with increasing rainfall magnitude up to a rainfall threshold of 50 mm, above which, further rainfall increases brought about only small increases. For C. multinervis, C. oxyodon, F. engleriana and Q. serrata, FR averaged 19.8, 14.8, 8.9 and 2.8, respectively. The stemflow generating rainfall thresholds for evergreen <span class="hlt">species</span> were smaller than for deciduous <span class="hlt">species</span>. Furthermore, stemflow percentage and FR of the former was greater than the latter. For both evergreen <span class="hlt">species</span> and deciduous <span class="hlt">species</span>, overall funneling ratio (FRs) decreased with increasing basal area. We concluded that: (1) although stemflow partitioning represented a fairly low percentage of gross rainfall in mixed evergreen and deciduous broadleaved forests, it was capable of providing substantial amount of rainwater to <span class="hlt">tree</span> boles; (2) the evergreen <span class="hlt">species</span> were more likely to generate stemflow than deciduous <span class="hlt">species</span>, and directed more intercepted rainwater to the root zone; (3) small <span class="hlt">trees</span> were more productive in funneling stemflow than larger <span class="hlt">trees</span>, which may provide a favorable</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2694365','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2694365"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">Species</span> Traits Influence Soil Physical, Chemical, and Biological Properties in High Elevation Forests</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Ayres, Edward; Steltzer, Heidi; Berg, Sarah; Wallenstein, Matthew D.; Simmons, Breana L.; Wall, Diana H.</p> <p>2009-01-01</p> <p>Background Previous studies have shown that plants often have <span class="hlt">species</span>-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single <span class="hlt">tree</span> <span class="hlt">species</span> are often adjacent to areas dominated by another <span class="hlt">tree</span> <span class="hlt">species</span>. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant <span class="hlt">tree</span> <span class="hlt">species</span> in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different <span class="hlt">tree</span> <span class="hlt">species</span> and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. Methodology/Principal Findings We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the <span class="hlt">tree</span> <span class="hlt">species</span>, with the highest nitrogen (N) concentration and lowest lignin∶N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin∶N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among <span class="hlt">tree</span> <span class="hlt">species</span>, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the <span class="hlt">tree</span> <span class="hlt">species</span>, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64306&keyword=Taxonomy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=65294418&CFTOKEN=71908534','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64306&keyword=Taxonomy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=65294418&CFTOKEN=71908534"><span id="translatedtitle">ISOPRENE EMISSION CAPACITY FOR U.S. <span class="hlt">TREE</span> <span class="hlt">SPECIES</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Isoprene emission capacity measurements are presented from 18 North American oak <I>(Quercus)</I> <span class="hlt">species</span> and <span class="hlt">species</span> from six other genera previously found to emit significant quantities of isoprene. Sampling was conducted at physiographically diverse locations in North Carolina...</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_5");'>5</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li class="active"><span>7</span></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_7 --> <div id="page_8" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li class="active"><span>8</span></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="141"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24233419','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24233419"><span id="translatedtitle">Ozone exposure : Areas of potential ozone risk for selected <span class="hlt">tree</span> <span class="hlt">species</span> in Austria.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Loibl, W; Smidt, S</p> <p>1996-12-01</p> <p>Increased tropospheric ozone concentrations cause damage to both human health and the environment. To assess the exposure of forest areas and selected <span class="hlt">tree</span> <span class="hlt">species</span> to ozone, it is necessary to calculate the ozone exposure distribution. The present article describes the application of an ozone interpolation model to the calculation of the ozone exposure distribution in combination with forest inventory data.The exposure of forest regions to ozone was assessed by means of an AOT40 map (accumulated ozone exposure over a threshold of 40 ppb). The calculation was performed by hourly running of the model during the summer term and accumulation of the patterns that exceeded 40 ppb.The exposure of the primary Austrian <span class="hlt">tree</span> <span class="hlt">species</span> to ozone can be assessed due to the spatial relation of ozone exposure and <span class="hlt">tree</span> <span class="hlt">species</span> patterns. This spatial relation also allows the verification of assumptions concerning ozone-related <span class="hlt">tree</span> damage. PMID:24233419</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..17.8279L&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..17.8279L&link_type=ABSTRACT"><span id="translatedtitle">Temporal and Spatial Dynamics of <span class="hlt">Tree</span> <span class="hlt">Species</span> Composition in Temperate Mountains of South Korea</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lee, Boknam; Park, Juhan; Cho, Sungsik; Ryu, Daun; Zaw Wynn, Khine; Park, Minji; Cho, Sunhee; Yoon, Jongguk; Park, Jongyoung; Kim, Hyun Seok</p> <p>2015-04-01</p> <p>Long term studies on vegetation dynamics are important to identify changes of ecosystem-level responses to climate change. To learn how <span class="hlt">tree</span> <span class="hlt">species</span> composition and stand structure change across temperate mountains, the temporal and spatial variations in <span class="hlt">tree</span> <span class="hlt">species</span> diversity and structure were investigated using the <span class="hlt">species</span> composition and DBH size collected over the fourteen-year period across 134 sites in Jiri and Baekoon Mountains, South Korea. The overall temporal changes over fourteen years showed significant increase in stand density, <span class="hlt">species</span> diversity and evenness according to the indices of Shannon-Weiner diversity, Bray-Curtis dissimilarity, and Pielou's evenness, contributing to the increase of basal area and biomass growth. The change of <span class="hlt">tree</span> <span class="hlt">species</span> composition could be categorized into five <span class="hlt">species</span> communities, representing gradual increase or decrease, establishment, extinction, fluctuation of <span class="hlt">species</span> population. However, in general, the change in <span class="hlt">species</span> composition appeared to have consistent and directional patterns of increase in the annual rate of change in the mean <span class="hlt">species</span> traits including <span class="hlt">species</span> richness, pole growth rate, adult growth rate, and adult stature with five common dominant <span class="hlt">species</span> (Quercus mongolica, Quercus variabilis, Quercus serrata, Carpinus laxiflora, and Styrax japonicus). The spatial patterns of <span class="hlt">species</span> composition appeared to have a higher stand density and <span class="hlt">species</span> diversity along with the low latitude and high slope ecosystem. The climate change was another main driver to vary the distribution of <span class="hlt">species</span> abundance. Overall, both temporal and spatial changes of composition in <span class="hlt">tree</span> <span class="hlt">species</span> community was clear and further analysis to clarify the reasons for such fast and <span class="hlt">species</span>-specific changes is underway especially to separate the effect of successional change and climate change. Keywords <span class="hlt">species</span> composition; climate change; temporal and spatial variation ; forest structure; temperate forest</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25761711','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25761711"><span id="translatedtitle">Glacial refugia and modern genetic diversity of 22 western North American <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Roberts, David R; Hamann, Andreas</p> <p>2015-04-01</p> <p>North American <span class="hlt">tree</span> <span class="hlt">species</span>, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American <span class="hlt">trees</span> since the last glacial maximum using <span class="hlt">species</span> distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 <span class="hlt">tree</span> <span class="hlt">species</span>. We find that <span class="hlt">species</span> with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas <span class="hlt">species</span> with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4375868','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4375868"><span id="translatedtitle">Glacial refugia and modern genetic diversity of 22 western North American <span class="hlt">tree</span> <span class="hlt">species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Roberts, David R.; Hamann, Andreas</p> <p>2015-01-01</p> <p>North American <span class="hlt">tree</span> <span class="hlt">species</span>, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American <span class="hlt">trees</span> since the last glacial maximum using <span class="hlt">species</span> distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 <span class="hlt">tree</span> <span class="hlt">species</span>. We find that <span class="hlt">species</span> with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas <span class="hlt">species</span> with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r2 = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/1015692','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/1015692"><span id="translatedtitle">Relationships among environmental variables and distribution of <span class="hlt">tree</span> <span class="hlt">species</span> at high elevation in the Olympic Mountains</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Woodward, Andrea</p> <p>1998-01-01</p> <p>Relationships among environmental variables and occurrence of <span class="hlt">tree</span> <span class="hlt">species</span> were investigated at Hurricane Ridge in Olympic National Park, Washington, USA. A transect consisting of three plots was established down one north-and one south-facing slope in stands representing the typical elevational sequence of <span class="hlt">tree</span> <span class="hlt">species</span>. <span class="hlt">Tree</span> <span class="hlt">species</span> included subalpine fir (Abies lasiocarpa), Douglas-fir (Pseudotsuga menziesii), mountain hemlock (Tsuga mertensiana), and Pacific silver fir (Abies amabilis). Air and soil temperature, precipitation, and soil moisture were measured during three growing seasons. Snowmelt patterns, soil carbon and moisture release curves were also determined. The plots represented a wide range in soil water potential, a major determinant of <span class="hlt">tree</span> <span class="hlt">species</span> distribution (range of minimum values = -1.1 to -8.0 MPa for Pacific silver fir and Douglas-fir plots, respectively). Precipitation intercepted at plots depended on topographic location, storm direction and storm type. Differences in soil moisture among plots was related to soil properties, while annual differences at each plot were most often related to early season precipitation. Changes in climate due to a doubling of atmospheric CO2 will likely shift <span class="hlt">tree</span> <span class="hlt">species</span> distributions within, but not among aspects. Change will be buffered by innate tolerance of adult <span class="hlt">trees</span> and the inertia of soil properties.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25712048','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25712048"><span id="translatedtitle">Regional-scale directional changes in abundance of <span class="hlt">tree</span> <span class="hlt">species</span> along a temperature gradient in Japan.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Suzuki, Satoshi N; Ishihara, Masae I; Hidaka, Amane</p> <p>2015-09-01</p> <p>Climate changes are assumed to shift the ranges of <span class="hlt">tree</span> <span class="hlt">species</span> and forest biomes. Such range shifts result from changes in abundances of <span class="hlt">tree</span> <span class="hlt">species</span> or functional types. Owing to global warming, the abundance of a <span class="hlt">tree</span> <span class="hlt">species</span> or functional type is expected to increase near the colder edge of its range and decrease near the warmer edge. This study examined directional changes in abundance and demographic parameters of forest <span class="hlt">trees</span> along a temperature gradient, as well as a successional gradient, in Japan. Changes in the relative abundance of each of four functional types (evergreen broad-leaved, deciduous broad-leaved, evergreen temperate conifer, and evergreen boreal conifer) and the demography of each <span class="hlt">species</span> (recruitment rate, mortality, and population growth rate) were analyzed in 39 permanent forest plots across the Japanese archipelago. Directional changes in the relative abundance of functional types were detected along the temperature gradient. Relative abundance of evergreen broad-leaved <span class="hlt">trees</span> increased near their colder range boundaries, especially in secondary forests, coinciding with the decrease in deciduous broad-leaved <span class="hlt">trees</span>. Similarly, relative abundance of deciduous broad-leaved <span class="hlt">trees</span> increased near their colder range boundaries, coinciding with the decrease in boreal conifers. These functional-type-level changes were mainly due to higher recruitment rates and partly to the lower mortality of individual <span class="hlt">species</span> at colder sites. This is the first report to show that <span class="hlt">tree</span> <span class="hlt">species</span> abundances in temperate forests are changing directionally along a temperature gradient, which might be due to current or past climate changes as well as recovery from past disturbances. PMID:25712048</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/12620063','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/12620063"><span id="translatedtitle">Identification, measurement and interpretation of <span class="hlt">tree</span> rings in woody <span class="hlt">species</span> from mediterranean climates.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cherubini, Paolo; Gartner, Barbara L; Tognetti, Roberto; Bräker, Otto U; Schoch, Werner; Innes, John L</p> <p>2003-02-01</p> <p>We review the literature dealing with mediterranean climate, vegetation, phenology and ecophysiology relevant to the understanding of <span class="hlt">tree</span>-ring formation in mediterranean regions. <span class="hlt">Tree</span> rings have been used extensively in temperate regions to reconstruct responses of forests to past environmental changes. In mediterranean regions, studies of <span class="hlt">tree</span> rings are scarce, despite their potential for understanding and predicting the effects of global change on important ecological processes such as desertification. In mediterranean regions, due to the great spatio-temporal variability of mediterranean environmental conditions, <span class="hlt">tree</span> rings are sometimes not formed. Often, clear seasonality is lacking, and vegetation activity is not always associated with regular dormancy periods. We present examples of <span class="hlt">tree</span>-ring morphology of five <span class="hlt">species</span> (Arbutus unedo, Fraxinus ornus, Quercus cerris, Q. ilex, Q. pubescens) sampled in Tuscany, Italy, focusing on the difficulties we encountered during the dating. We present an interpretation of anomalies found in the wood structure and, more generally, of cambial activity in such environments. Furthermore, we propose a classification of <span class="hlt">tree</span>-ring formation in mediterranean environments. Mediterranean <span class="hlt">tree</span> rings can be dated and used for dendrochronological purposes, but great care should be taken in selecting sampling sites, <span class="hlt">species</span> and sample <span class="hlt">trees</span>. PMID:12620063</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..1712601J&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..1712601J&link_type=ABSTRACT"><span id="translatedtitle">Does deciduous <span class="hlt">tree</span> <span class="hlt">species</span> identity affect carbon storage in temperate soils?</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Jungkunst, Hermann; Schleuß, Per; Heitkamp, Felix</p> <p>2015-04-01</p> <p>Forest soils contribute roughly 70 % to the global terrestrial soil organic carbon (SOC) pool and thus play a vital role in the global carbon cycle. It is less clear, however, whether temperate <span class="hlt">tree</span> <span class="hlt">species</span> identity affects SOC storage beyond the coarse differentiation between coniferous and deciduous <span class="hlt">trees</span>. The most important driver for soil SOC storage definitely is the fine mineral fraction (clay and fine silt) because of its high sorption ability. It is difficult to disentangle any additional biotic effects since clay and silt vary considerably in nature. For experimental approaches, the process of soil carbon accumulation is too slow and, therefore, sound results cannot be expected for decades. Here we will present our success to distinguish between the effects of fine particle content (abiotic) and <span class="hlt">tree</span> <span class="hlt">species</span> composition (biotic) on the SOC pool in an old-growth broad-leaved forest plots along a <span class="hlt">tree</span> diversity gradient , i.e., 1- (beech), 3- (plus ash and lime <span class="hlt">tree</span>)- and 5-(plus maple and hornbeam) <span class="hlt">species</span>. The particle size fractions were separated first and then the carbon concentrations of each fraction was measured. Hence, the carbon content per unit clay was not calculated, as usually done, but directly measured. As expected, the variation in SOC content was mainly explained by the variations in clay content but not entirely. We found that the carbon concentration per unit clay and fine silt in the subsoil was by 30-35% higher in mixed than in monospecific stands indicating a significant <span class="hlt">species</span> identity or <span class="hlt">species</span> diversity effect on C stabilization. In contrast to the subsoil, no <span class="hlt">tree</span> <span class="hlt">species</span> effects was identified for the topsoil. Indications are given that the mineral phase was already carbon saturated and thus left no more room for a possible biotic effect. Underlying processes must remain speculative, but we will additionally present our latest microcosm results, including isotopic signatures, to underpin the proposed deciduous <span class="hlt">tree</span> <span class="hlt">species</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/861330','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/861330"><span id="translatedtitle">Ambrosia Beetle (Coleoptera: Scolytidae) <span class="hlt">Species</span>, Flight, and Attack on Living Eastern Cottonwood <span class="hlt">Trees</span>.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Coyle, D R; D.C. Booth: M.S. Wallace</p> <p>2005-12-01</p> <p>ABSTRACT In spring 2002, ambrosia beetles (Coleoptera: Scolytidae) infested an intensively managed 22-ha <span class="hlt">tree</span> plantation on the upper coastal plain of South Carolina. Nearly 3,500 scolytids representing 28 <span class="hlt">species</span> were captured in ethanol-baited traps from 18 June 2002 to 18 April 2004. More than 88% of total captures were exotic <span class="hlt">species</span>. Five <span class="hlt">species</span> [Dryoxylon onoharaensum (Murayama), Euwallacea validus (Eichhoff), Pseudopityophthorus minutissimus (Zimmermann), Xyleborus atratus Eichhoff, and Xyleborus impressus Eichhoff]) were collected in South Carolina for the first time. Of four <span class="hlt">tree</span> <span class="hlt">species</span> in the plantation, eastern cottonwood, Populus deltoides Bartram, was the only one attacked, with nearly 40% of the <span class="hlt">trees</span> sustaining ambrosia beetle damage. Clone ST66 sustained more damage than clone S7C15. ST66 <span class="hlt">trees</span> receiving fertilization were attacked more frequently than <span class="hlt">trees</span> receiving irrigation, irrigation_fertilization, or controls, although the number of S7C15 <span class="hlt">trees</span> attacked did not differ among treatments. The study location is near major shipping ports; our results demonstrate the necessity for intensive monitoring programs to determine the arrival, spread, ecology, and impact of exotic scolytids.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17665219','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17665219"><span id="translatedtitle">Population structure, physiology and ecohydrological impacts of dioecious riparian <span class="hlt">tree</span> <span class="hlt">species</span> of western North America.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hultine, K R; Bush, S E; West, A G; Ehleringer, J R</p> <p>2007-11-01</p> <p>The global water cycle is intimately linked to vegetation structure and function. Nowhere is this more apparent than in the arid west where riparian forests serve as ribbons of productivity in otherwise mostly unproductive landscapes. Dioecy is common among <span class="hlt">tree</span> <span class="hlt">species</span> that make up western North American riparian forests. There are intrinsic physiological differences between male and female dioecious riparian <span class="hlt">trees</span> that may influence population structure (i.e., the ratio of male to female <span class="hlt">trees</span>) and impact ecohydrology at large scales. In this paper, we review the current literature on sex ratio patterns and physiology of dioecious riparian <span class="hlt">tree</span> <span class="hlt">species</span>. Then develop a conceptual framework of the mechanisms that underlie population structure of dominant riparian <span class="hlt">tree</span> <span class="hlt">species</span>. Finally, we identify linkages between population structure and ecohydrological processes such as evapotranspiration and streamflow. A more thorough understanding of the mechanisms that underlie population structure of dominant riparian <span class="hlt">tree</span> <span class="hlt">species</span> will enable us to better predict global change impacts on vegetation and water cycling at multiple scales. PMID:17665219</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20010004212','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20010004212"><span id="translatedtitle">BOREAS TE-4 Branch Bag Data From Boreal <span class="hlt">Tree</span> <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hall, Forrest G. (Editor); Papagno, Andrea (Editor); Berry, Joseph A.; Fu, Wei; Fredeen, Art; Gamon, John</p> <p>2000-01-01</p> <p>The BOREAS TE-4 team collected continuous records of gas exchange under ambient conditions from intact boreal forest <span class="hlt">trees</span> in the BOREAS NSA from 23-Jul-1996 until 14-Aug-1996. These measurements can be used to test models of photosynthesis, stomatal conductance, and leaf respiration, such as SiB2 (Sellers et al., 1996) or the leaf model (Collatz et al., 1991), and programs can be obtained from the investigators. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010AGUFM.B13B0476R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010AGUFM.B13B0476R"><span id="translatedtitle">Wind Disturbance Produced Changes in <span class="hlt">Tree</span> <span class="hlt">Species</span> Assemblage in the Peruvian Amazon</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Rifai, S. W.; Chambers, J. Q.; Negron Juarez, R. I.; Ramirez, F.; Tello, R.; Alegria Muñoz, W.</p> <p>2010-12-01</p> <p>Wind disturbance has been a frequently overlooked abiotic cause of mass <span class="hlt">tree</span> mortality in the Amazon basin. In the Peruvian Amazon these wind disturbances are produced by meteorological events such as convective systems. Downbursts for example produce short term descendent wind speeds that can be in excess of 30 m s-1. These are capable of producing <span class="hlt">tree</span> blowdowns which have been reported to be as large as 33 km2 in the Amazon basin. We used the chronosequence of Landsat Satellite imagery to find and locate where these blowdowns have occurred in the Loreto region of the Peruvian Amazon. Spectral Mixture Analysis was used to estimate the proportion landcover of green vegetation, non-photosynthetic vegetation (NPV), soil and shade in each pixel. The change in NPV was calculated by subtracting the NPV signal in the Landsat image prior to the blowdown occurrence, from the image following the disturbance. Our prior research has established a linear relationship between <span class="hlt">tree</span> mortality and change in NPV. It is hypothesized that these mass <span class="hlt">tree</span> mortality events result in changes in the <span class="hlt">tree</span> <span class="hlt">species</span> assemblage of affected forests. Here we present preliminary <span class="hlt">tree</span> <span class="hlt">species</span> assemblage data from two sites in the Peruvian Amazon near Iquitos, Peru. The site (ALP) at the Allpahuayo Mishana reserve (3.945 S, 73.455 W) is 30 km south of Iquitos, Peru, and hosts the remnants of a 50 ha blowdown that occurred in either 1992 or 1993. Another site (NAPO) on the Napo river about 60 km north of Iquitos, is the location of an approximately 300 ha blowdown that occurred in 1998. At each site, a 3000 m x 10 m transect encompassing non disturbed and disturbed areas was installed, and <span class="hlt">trees</span> greater than 10 cm diameter at breast height were measured for diameter, height and were identified to the <span class="hlt">species</span>. Stem density of <span class="hlt">trees</span> with diameter at breast height > 10 cm, and <span class="hlt">tree</span> height appear to be similar both inside and outside the blowdown affected areas of the forests at both sites. At the ALP</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=238475','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=238475"><span id="translatedtitle">Impact of Fumigation on Pythium <span class="hlt">Species</span> Associated with Forest <span class="hlt">Tree</span> Nurseries of Oregon and Washington</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Pythium <span class="hlt">species</span> cause damping off of conifer seedlings in forest <span class="hlt">tree</span> nurseries. Identification of the <span class="hlt">species</span> responsible for the disease has been traditionally based on morphology. However, newer DNA-based identification methods may allow more accurate identification and assessment of soil popul...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26936241','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26936241"><span id="translatedtitle">Selective logging in tropical forests decreases the robustness of liana-<span class="hlt">tree</span> interaction networks to the loss of host <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Magrach, Ainhoa; Senior, Rebecca A; Rogers, Andrew; Nurdin, Deddy; Benedick, Suzan; Laurance, William F; Santamaria, Luis; Edwards, David P</p> <p>2016-03-16</p> <p>Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in <span class="hlt">species</span> composition. Whether such changes modify interactions between <span class="hlt">species</span> 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 <span class="hlt">tree</span> hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher <span class="hlt">species</span> richness, and different <span class="hlt">species</span> compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growing <span class="hlt">tree</span> <span class="hlt">species</span>, which could exacerbate the loss of timber value and carbon storage already associated with logging. Moreover, simulation scenarios of host <span class="hlt">tree</span> local <span class="hlt">species</span> loss indicated that logging might decrease the robustness of liana-<span class="hlt">tree</span> interaction networks if heavily infested <span class="hlt">trees</span> (i.e. the most connected ones) were more likely to disappear. This effect is partially mitigated in the short term by the colonization of host <span class="hlt">trees</span> by a greater diversity of liana <span class="hlt">species</span> within logged forests, yet this might not compensate for the loss of preferred <span class="hlt">tree</span> hosts in the long term. As a consequence, <span class="hlt">species</span> interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in <span class="hlt">species</span> richness and ecosystem function in response to additional disturbances, representing a new type of 'extinction debt'. PMID:26936241</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3460976','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3460976"><span id="translatedtitle">Spatial Distribution and Interspecific Associations of <span class="hlt">Tree</span> <span class="hlt">Species</span> in a Tropical Seasonal Rain Forest of China</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lan, Guoyu; Getzin, Stephan; Wiegand, Thorsten; Hu, Yuehua; Xie, Guishui; Zhu, Hua; Cao, Min</p> <p>2012-01-01</p> <p>Studying the spatial pattern and interspecific associations of plant <span class="hlt">species</span> may provide valuable insights into processes and mechanisms that maintain <span class="hlt">species</span> coexistence. Point pattern analysis was used to analyze the spatial distribution patterns of twenty dominant <span class="hlt">tree</span> <span class="hlt">species</span>, their interspecific spatial associations and changes across life stages in a 20-ha permanent plot of seasonal tropical rainforest in Xishuangbanna, China, to test mechanisms maintaining <span class="hlt">species</span> coexistence. Torus-translation tests were used to quantify positive or negative associations of the <span class="hlt">species</span> to topographic habitats. The results showed: (1) fourteen of the twenty <span class="hlt">tree</span> <span class="hlt">species</span> were negatively (or positively) associated with one or two of the topographic variables, which evidences that the niche contributes to the spatial pattern of these <span class="hlt">species</span>. (2) Most saplings of the study <span class="hlt">species</span> showed a significantly clumped distribution at small scales (0–10 m) which was lost at larger scales (10–30 m). (3) The degree of spatial clumping deceases from saplings, to poles, to adults indicates that density-dependent mortality of the offspring is ubiquitous in <span class="hlt">species</span>. (4) It is notable that a high number of positive small-scale interactions were found among the twenty <span class="hlt">species</span>. For saplings, 42.6% of all combinations of <span class="hlt">species</span> pairs showed positive associations at neighborhood scales up to five meters, but only 38.4% were negative. For poles and adults, positive associations at these distances still made up 45.5% and 29.5%, respectively. In conclusion, there is considerable evidence for the presence of positive interactions among the <span class="hlt">tree</span> <span class="hlt">species</span>, which suggests that <span class="hlt">species</span> herd protection may occur in our plot. In addition, niche assembly and limited dispersal (likely) contribute to the spatial patterns of <span class="hlt">tree</span> <span class="hlt">species</span> in the tropical seasonal rain forest in Xishuangbanna, China. PMID:23029394</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/12625013','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/12625013"><span id="translatedtitle">[Feasibility to introduce rare <span class="hlt">tree</span> <span class="hlt">species</span> Pinus sibirica into China].</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Liu, Guifeng; Yang, Chuanping; Zhao, Guangyi</p> <p>2002-11-01</p> <p>Pinus sibirica growing mainly in Siberia of Russia is distributed over the Euro-Asia Taiga forest belt. There are many high-quality populations due to a great deal of variations. This kind of <span class="hlt">tree</span> has an advantage of standing up to frigid environment, and can spread out in such places that have cold weather and high altitude. In China, boreal forest is a wide-spreaded type of forest that has the largest area and high volume. For this reason, it is feasible to introduce Pinus sibirica into the region that the condition is suitable. Introducing this kind of <span class="hlt">tree</span> is a strategic project that can improve the structure and quality of our boreal forest. Introducing it can not only meet the demands of improved variety in short time, but also do the experiment of producing edible seeds and build up the developing center of nut, which can be a way of getting rid of poverty of forest region in heavy frigid area where is regarded as infertile area for farming formerly. PMID:12625013</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26364482','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26364482"><span id="translatedtitle">Fuel wood properties of some oak <span class="hlt">tree</span> <span class="hlt">species</span> of Manipur, India.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Meetei, Shougrakpam Bijen; Singh, E J; Das, Ashesh Kumar</p> <p>2015-07-01</p> <p>Five indigenous oak <span class="hlt">tree</span> <span class="hlt">species</span>, i.e., Castanopsis indica (Roxb. ex Lindl.) A.DC., Lithocarpus fenestratus (Roxb.) Rehder, Lithocarpus pachyphyllus (Kurz) Rehder, Lithocarpus polystachyus (Wall. ex A.DC.) Rehder and Quercus serrata Murray were estimated for their wood properties such as calorific value, density, moisture content and ash content from a sub-tropical forest of Haraothel hill, Senapati District, Manipur. Wood biomass components were found to have higher calorific value (kJ g(-)) than bark components. The calorific values for <span class="hlt">tree</span> <span class="hlt">species</span> were found highest in L. pachyphyllus (17.99 kJ g(-1)) followed by C. indica (17.98 kJ g1), L. fenestratus (17.96 kJ g"), L. polystachyus (17.80 kJ g(-1)) and Q. serrata (17.49 kJ g(-1)). Calorific values for bole bark, bole wood and branch bark were found significantly different (F > 3.48 at p = 0.05) in five oak <span class="hlt">tree</span> <span class="hlt">species</span>. Percentage of ash on dry weight basis was found to be highest in Q. serrata (4.73%) and lowest in C. indica (2.19%). Ash content of <span class="hlt">tree</span> components gives a singnificant factor in determining fuelwood value index (FVI). Of all the five oak <span class="hlt">tree</span> <span class="hlt">species</span>, Q. serrata exhibited highest value of wood density (0.78 g cm-) and lowest was observed in C. indica (0.63 g cm(-3)). There was significant correlation between wood density (p<0.05), ash content (p<0.01) with calorific value in oak <span class="hlt">tree</span> <span class="hlt">species</span>. Fuelwood value index (FVI) was in the following order: C. indica (1109.70) > L. pachyphyllus (898.41)> L. polystachyus (879.02)> L. fenestratus (824.61)> Q. serrata (792.50). Thus, the present study suggests that C. indica may be considered as a fuelwood oak <span class="hlt">tree</span> <span class="hlt">species</span> in Manipur. PMID:26364482</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988811','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988811"><span id="translatedtitle">Early establishment of <span class="hlt">trees</span> at the alpine treeline: idiosyncratic <span class="hlt">species</span> responses to temperature-moisture interactions</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Loranger, Hannah; Zotz, Gerhard; Bader, Maaike Y.</p> <p>2016-01-01</p> <p>On a global scale, temperature is the main determinant of arctic and alpine treeline position. However on a local scale, treeline form and position vary considerably due to other climatic factors, <span class="hlt">tree</span> <span class="hlt">species</span> ecology and life-stage-dependent responses. For treelines to advance poleward or uphill, the first steps are germination and seedling establishment. These earliest life stages may be major bottlenecks for treeline <span class="hlt">tree</span> populations and will depend differently on climatic conditions than adult <span class="hlt">trees</span>. We investigated the effect of soil temperature and moisture on germination and early seedling survival in a field experiment in the French Alps near the local treeline (2100 m a.s.l.) using passive temperature manipulations and two watering regimes. Five European treeline <span class="hlt">tree</span> <span class="hlt">species</span> were studied: Larix decidua, Picea abies, Pinus cembra, Pinus uncinata and Sorbus aucuparia. In addition, we monitored the germination response of three of these <span class="hlt">species</span> to low temperatures under controlled conditions in growth chambers. The early establishment of these <span class="hlt">trees</span> at the alpine treeline was limited either by temperature or by moisture, the sensitivity to one factor often depending on the intensity of the other. The results showed that the relative importance of the two factors and the direction of the effects are highly <span class="hlt">species</span>-specific, while both factors tend to have consistent effects on both germination and early seedling survival within each <span class="hlt">species</span>. We show that temperature and water availability are both important contributors to establishment patterns of treeline <span class="hlt">trees</span> and hence to <span class="hlt">species</span>-specific forms and positions of alpine treelines. The observed idiosyncratic <span class="hlt">species</span> responses highlight the need for studies including several <span class="hlt">species</span> and life-stages to create predictive power concerning future treeline dynamics. PMID:27402618</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27402618','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27402618"><span id="translatedtitle">Early establishment of <span class="hlt">trees</span> at the alpine treeline: idiosyncratic <span class="hlt">species</span> responses to temperature-moisture interactions.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Loranger, Hannah; Zotz, Gerhard; Bader, Maaike Y</p> <p>2016-01-01</p> <p>On a global scale, temperature is the main determinant of arctic and alpine treeline position. However on a local scale, treeline form and position vary considerably due to other climatic factors, <span class="hlt">tree</span> <span class="hlt">species</span> ecology and life-stage-dependent responses. For treelines to advance poleward or uphill, the first steps are germination and seedling establishment. These earliest life stages may be major bottlenecks for treeline <span class="hlt">tree</span> populations and will depend differently on climatic conditions than adult <span class="hlt">trees</span>. We investigated the effect of soil temperature and moisture on germination and early seedling survival in a field experiment in the French Alps near the local treeline (2100 m a.s.l.) using passive temperature manipulations and two watering regimes. Five European treeline <span class="hlt">tree</span> <span class="hlt">species</span> were studied: Larix decidua, Picea abies, Pinus cembra, Pinus uncinata and Sorbus aucuparia In addition, we monitored the germination response of three of these <span class="hlt">species</span> to low temperatures under controlled conditions in growth chambers. The early establishment of these <span class="hlt">trees</span> at the alpine treeline was limited either by temperature or by moisture, the sensitivity to one factor often depending on the intensity of the other. The results showed that the relative importance of the two factors and the direction of the effects are highly <span class="hlt">species</span>-specific, while both factors tend to have consistent effects on both germination and early seedling survival within each <span class="hlt">species</span>. We show that temperature and water availability are both important contributors to establishment patterns of treeline <span class="hlt">trees</span> and hence to <span class="hlt">species</span>-specific forms and positions of alpine treelines. The observed idiosyncratic <span class="hlt">species</span> responses highlight the need for studies including several <span class="hlt">species</span> and life-stages to create predictive power concerning future treeline dynamics. PMID:27402618</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3436813','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3436813"><span id="translatedtitle">Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary <span class="hlt">species</span> <span class="hlt">trees</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie</p> <p>2012-01-01</p> <p>Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and <span class="hlt">species</span> <span class="hlt">trees</span>, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. Results: We present an algorithm to reconcile a binary gene <span class="hlt">tree</span> with a nonbinary <span class="hlt">species</span> <span class="hlt">tree</span> under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving <span class="hlt">tree</span> incongruence and the first to reconcile non-binary <span class="hlt">species</span> <span class="hlt">trees</span> with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and <span class="hlt">species</span> lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum <span class="hlt">species</span> outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Availability: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. Contact: mstolzer@andrew.cmu.edu PMID:22962460</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li class="active"><span>8</span></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_8 --> <div id="page_9" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li class="active"><span>9</span></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="161"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25377453','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25377453"><span id="translatedtitle">Multiple <span class="hlt">species</span> of wild <span class="hlt">tree</span> peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhou, Shi-Liang; Zou, Xin-Hui; Zhou, Zhi-Qin; Liu, Jing; Xu, Chao; Yu, Jing; Wang, Qiang; Zhang, Da-Ming; Wang, Xiao-Quan; Ge, Song; Sang, Tao; Pan, Kai-Yu; Hong, De-Yuan</p> <p>2014-12-22</p> <p>The origin of cultivated <span class="hlt">tree</span> peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of <span class="hlt">tree</span> peonies and all wild <span class="hlt">species</span> from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild <span class="hlt">species</span> inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast <span class="hlt">trees</span> suggested that there had been gene flow between the wild <span class="hlt">species</span>. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated <span class="hlt">tree</span> peonies originated from homoploid hybridization among five wild <span class="hlt">species</span>. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental <span class="hlt">species</span> are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in <span class="hlt">tree</span> peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication. PMID:25377453</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4657984','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4657984"><span id="translatedtitle">Discrimination of Deciduous <span class="hlt">Tree</span> <span class="hlt">Species</span> from Time Series of Unmanned Aerial System Imagery</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lisein, Jonathan; Michez, Adrien; Claessens, Hugues; Lejeune, Philippe</p> <p>2015-01-01</p> <p>Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at <span class="hlt">tree</span> level. This paper addresses the question of how and particularly when Unmanned Aerial System (UAS) should be used in order to efficiently discriminate deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. The goal of this research is to determine when is the best time window to achieve an optimal <span class="hlt">species</span> discrimination. A time series of high resolution UAS imagery was collected to cover the growing season from leaf flush to leaf fall. Full benefit was taken of the temporal resolution of UAS acquisition, one of the most promising features of small drones. The disparity in forest <span class="hlt">tree</span> phenology is at the maximum during early spring and late autumn. But the phenology state that optimized the classification result is the one that minimizes the spectral variation within <span class="hlt">tree</span> <span class="hlt">species</span> groups and, at the same time, maximizes the phenologic differences between <span class="hlt">species</span>. Sunlit <span class="hlt">tree</span> crowns (5 deciduous <span class="hlt">species</span> groups) were classified using a Random Forest approach for monotemporal, two-date and three-date combinations. The end of leaf flushing was the most efficient single-date time window. Multitemporal datasets definitely improve the overall classification accuracy. But single-date high resolution orthophotomosaics, acquired on optimal time-windows, result in a very good classification accuracy (overall out of bag error of 16%). PMID:26600422</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26600422','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26600422"><span id="translatedtitle">Discrimination of Deciduous <span class="hlt">Tree</span> <span class="hlt">Species</span> from Time Series of Unmanned Aerial System Imagery.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lisein, Jonathan; Michez, Adrien; Claessens, Hugues; Lejeune, Philippe</p> <p>2015-01-01</p> <p>Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at <span class="hlt">tree</span> level. This paper addresses the question of how and particularly when Unmanned Aerial System (UAS) should be used in order to efficiently discriminate deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. The goal of this research is to determine when is the best time window to achieve an optimal <span class="hlt">species</span> discrimination. A time series of high resolution UAS imagery was collected to cover the growing season from leaf flush to leaf fall. Full benefit was taken of the temporal resolution of UAS acquisition, one of the most promising features of small drones. The disparity in forest <span class="hlt">tree</span> phenology is at the maximum during early spring and late autumn. But the phenology state that optimized the classification result is the one that minimizes the spectral variation within <span class="hlt">tree</span> <span class="hlt">species</span> groups and, at the same time, maximizes the phenologic differences between <span class="hlt">species</span>. Sunlit <span class="hlt">tree</span> crowns (5 deciduous <span class="hlt">species</span> groups) were classified using a Random Forest approach for monotemporal, two-date and three-date combinations. The end of leaf flushing was the most efficient single-date time window. Multitemporal datasets definitely improve the overall classification accuracy. But single-date high resolution orthophotomosaics, acquired on optimal time-windows, result in a very good classification accuracy (overall out of bag error of 16%). PMID:26600422</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4604832','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4604832"><span id="translatedtitle">PoMo: An Allele Frequency-Based Approach for <span class="hlt">Species</span> <span class="hlt">Tree</span> Estimation</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin</p> <p>2015-01-01</p> <p>Incomplete lineage sorting can cause incongruencies of the overall <span class="hlt">species</span>-level phylogenetic <span class="hlt">tree</span> with the phylogenetic <span class="hlt">trees</span> for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in <span class="hlt">species</span> <span class="hlt">tree</span> estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-<span class="hlt">species</span> variation data. We extend this model to perform efficient estimation of <span class="hlt">species</span> <span class="hlt">trees</span>. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide <span class="hlt">species</span> <span class="hlt">tree</span> estimation and that on such data it is more accurate than previous approaches. PMID:26209413</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21910838','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21910838"><span id="translatedtitle">Fruit availability, frugivore satiation and seed removal in 2 primate-dispersed <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ratiarison, Sandra; Forget, Pierre-Michel</p> <p>2011-09-01</p> <p>During a mast-fruiting event we investigated spatial variability in fruit availability, consumption, and seed removal at two sympatric <span class="hlt">tree</span> <span class="hlt">species</span>, Manilkara bidentata and M. huberi (Sapotaceae) at Nouragues Natural Reserve, French Guiana. We addressed the question of how Manilkara density and fruits at the community level might be major causes of variability in feeding assemblages between <span class="hlt">tree</span> <span class="hlt">species</span>. We thus explored how the frugivore assemblages differed between forest patches with contrasting relative Manilkara density and fruiting context. During the daytime, Alouatta seniculus was more often observed in M. huberi crowns at Petit Plateau (PP) with the greatest density of Manilkara spp. and the lowest fruit diversity and availability, whereas Cebus apella and Saguinus midas were more often observed in M. bidentata crowns at both Grand Plateau (GP), with a lowest density of M. bidentata and overall greater fruit supply, and PP. Overall, nearly 53% and 15% of the M. bidentata seed crop at GP and PP, respectively, and about 47% of the M. huberi seed crop were removed, otherwise either spit out or defecated beneath <span class="hlt">trees</span>, or dropped in fruits. Small-bodied primates concentrated fallen seeds beneath parent <span class="hlt">trees</span> while large-bodied primate <span class="hlt">species</span> removed and dispersed more seeds away from parents. However, among the latter, satiated A. seniculus wasted seeds under conspecific <span class="hlt">trees</span> at PP. Variations in feeding assemblages, seed removal rates and fates possibly reflected interactions with extra-generic fruit <span class="hlt">species</span> at the community level, according to feeding choice, habitat preferences and ranging patterns of primate <span class="hlt">species</span>. PMID:21910838</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.treesearch.fs.fed.us/pubs/4893','USGSPUBS'); return false;" href="http://www.treesearch.fs.fed.us/pubs/4893"><span id="translatedtitle">Supplemental planting of early successional <span class="hlt">tree</span> <span class="hlt">species</span> during bottomland hardwood afforestation</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Twedt, D.J.; Wilson, R.R.</p> <p>2002-01-01</p> <p>Reforestation of former bottom land hardwood forests that have been cleared for agriculture (i.e., afforestation) has historically emphasized planting heavy-seeded oaks (Quercus spp.) and pecans (Carya spp.). These <span class="hlt">species</span> are slow to develop vertical forest structure. However, vertical forest structure is key to colonization of afforested sites by forest birds. Although early-successional <span class="hlt">tree</span> <span class="hlt">species</span> often enhance vertical structure, few of these <span class="hlt">species</span> invade afforested sites that are distant from seed sources. Furthermore, many land mangers are reluctant to establish and maintain stands of fast-growing plantation <span class="hlt">trees</span>. Therefore, on 40 afforested bottomland sites, we supplemented heavy-seeded seedlings with 8 patches of fast-growing <span class="hlt">trees</span>: 4 patches of 12 eastern cottonwood (Populus deltoides) stem cuttings and 4 patches of 12 American sycamore (Platanus occidentalis) seedlings. To enhance survival and growth, <span class="hlt">tree</span> patches were subjected to 4 weed control treatments: (1) physical weed barriers, (2) chemical herbicide, (3) both physical and chemical weed control, or (4) no weed control. Overall, first-year survival of cottonwood and sycamore was 25 percent and 47 percent, respectively. Second-year survival of extant <span class="hlt">trees</span> was 52 percent for cottonwood and 77 percent for sycamore. Physical weed barriers increased survival of cottonwoods to 30 percent versus 18 percent survival with no weed control. Similarly, sycamore survival was increased from 49 percent without weed control to 64 percent with physical weed barriers. Chemical weed control adversely impacted sycamore and reduced survival to 35 percent. <span class="hlt">Tree</span> heights did not differ between <span class="hlt">species</span> or among weed control treatments. Girdling of <span class="hlt">trees</span> by deer often destroyed saplings. Thus, little increase in vertical structure was detected between growing seasons. Application of fertilizer and protection via <span class="hlt">tree</span> shelters did not improve survival or vertical development of sycamore or cottonwood.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26153693','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26153693"><span id="translatedtitle">Operational <span class="hlt">Tree</span> <span class="hlt">Species</span> Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Baldeck, Claire A; Asner, Gregory P; Martin, Robin E; Anderson, Christopher B; Knapp, David E; Kellner, James R; Wright, S Joseph</p> <p>2015-01-01</p> <p>Remote identification and mapping of canopy <span class="hlt">tree</span> <span class="hlt">species</span> can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote <span class="hlt">species</span> mapping of non-flowering <span class="hlt">tree</span> crowns in these ecosystems. We set out to identify individuals of three focal canopy <span class="hlt">tree</span> <span class="hlt">species</span> amongst a diverse background of <span class="hlt">tree</span> and liana <span class="hlt">species</span> on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods--binary support vector machine (SVM) and biased SVM--for their performance in identifying pixels of a single focal <span class="hlt">species</span>. From this comparison we determined that biased SVM was more precise and created a multi-<span class="hlt">species</span> classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal <span class="hlt">species</span> and the prediction results were then processed to create a map of focal <span class="hlt">species</span> crown objects. Crown-level cross-validation of the training data indicated that the multi-<span class="hlt">species</span> classification model had pixel-level producer's accuracies of 94-97% for the three focal <span class="hlt">species</span>, and field validation of the predicted crown objects indicated that these had user's accuracies of 94-100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal <span class="hlt">species</span> within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to <span class="hlt">species</span> detection in diverse closed-canopy forests, which can pave the way for remote <span class="hlt">species</span> mapping in a wider variety of ecosystems. PMID:26153693</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4496029','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4496029"><span id="translatedtitle">Operational <span class="hlt">Tree</span> <span class="hlt">Species</span> Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph</p> <p>2015-01-01</p> <p>Remote identification and mapping of canopy <span class="hlt">tree</span> <span class="hlt">species</span> can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote <span class="hlt">species</span> mapping of non-flowering <span class="hlt">tree</span> crowns in these ecosystems. We set out to identify individuals of three focal canopy <span class="hlt">tree</span> <span class="hlt">species</span> amongst a diverse background of <span class="hlt">tree</span> and liana <span class="hlt">species</span> on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal <span class="hlt">species</span>. From this comparison we determined that biased SVM was more precise and created a multi-<span class="hlt">species</span> classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal <span class="hlt">species</span> and the prediction results were then processed to create a map of focal <span class="hlt">species</span> crown objects. Crown-level cross-validation of the training data indicated that the multi-<span class="hlt">species</span> classification model had pixel-level producer’s accuracies of 94–97% for the three focal <span class="hlt">species</span>, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal <span class="hlt">species</span> within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to <span class="hlt">species</span> detection in diverse closed-canopy forests, which can pave the way for remote <span class="hlt">species</span> mapping in a wider variety of ecosystems. PMID:26153693</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1461003','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1461003"><span id="translatedtitle">Effects of colonization processes on genetic diversity: differences between annual plants and <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Austerlitz, F; Mariette, S; Machon, N; Gouyon, P H; Godelle, B</p> <p>2000-01-01</p> <p><span class="hlt">Tree</span> <span class="hlt">species</span> are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than <span class="hlt">trees</span>. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for <span class="hlt">trees</span>. This explanation is problematic because it relies on equilibrium hypotheses. Because <span class="hlt">trees</span> have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest <span class="hlt">trees</span>, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of <span class="hlt">trees</span> are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in <span class="hlt">trees</span> and annual <span class="hlt">species</span> by much less diversity and much more differentiation than nuclear genes. PMID:10757772</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70041741','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70041741"><span id="translatedtitle">Quantifying <span class="hlt">tree</span> mortality in a mixed <span class="hlt">species</span> woodland using multitemporal high spatial resolution satellite imagery</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Garrity, Steven R.; Allen, Craig D.; Brumby, Steven P.; Gangodagamage, Chandana; McDowell, Nate G.; Cai, D. Michael</p> <p>2013-01-01</p> <p>Widespread <span class="hlt">tree</span> mortality events have recently been observed in several biomes. To effectively quantify the severity and extent of these events, tools that allow for rapid assessment at the landscape scale are required. Past studies using high spatial resolution satellite imagery have primarily focused on detecting green, red, and gray <span class="hlt">tree</span> canopies during and shortly after <span class="hlt">tree</span> damage or mortality has occurred. However, detecting <span class="hlt">trees</span> in various stages of death is not always possible due to limited availability of archived satellite imagery. Here we assess the capability of high spatial resolution satellite imagery for <span class="hlt">tree</span> mortality detection in a southwestern U.S. mixed <span class="hlt">species</span> woodland using archived satellite images acquired prior to mortality and well after dead <span class="hlt">trees</span> had dropped their leaves. We developed a multistep classification approach that uses: supervised masking of non-<span class="hlt">tree</span> image elements; bi-temporal (pre- and post-mortality) differencing of normalized difference vegetation index (NDVI) and red:green ratio (RGI); and unsupervised multivariate clustering of pixels into live and dead <span class="hlt">tree</span> classes using a Gaussian mixture model. Classification accuracies were improved in a final step by tuning the rules of pixel classification using the posterior probabilities of class membership obtained from the Gaussian mixture model. Classifications were produced for two images acquired post-mortality with overall accuracies of 97.9% and 98.5%, respectively. Classified images were combined with land cover data to characterize the spatiotemporal characteristics of <span class="hlt">tree</span> mortality across areas with differences in <span class="hlt">tree</span> <span class="hlt">species</span> composition. We found that 38% of <span class="hlt">tree</span> crown area was lost during the drought period between 2002 and 2006. The majority of <span class="hlt">tree</span> mortality during this period was concentrated in piñon-juniper (Pinus edulis-Juniperus monosperma) woodlands. An additional 20% of the <span class="hlt">tree</span> canopy died or was removed between 2006 and 2011, primarily in areas</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19880241','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19880241"><span id="translatedtitle">Estimating <span class="hlt">tree</span> bole volume using artificial neural network models for four <span class="hlt">species</span> in Turkey.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ozçelik, Ramazan; Diamantopoulou, Maria J; Brooks, John R; Wiant, Harry V</p> <p>2010-01-01</p> <p><span class="hlt">Tree</span> bole volumes of 89 Scots pine (Pinus sylvestris L.), 96 Brutian pine (Pinus brutia Ten.), 107 Cilicica fir (Abies cilicica Carr.) and 67 Cedar of Lebanon (Cedrus libani A. Rich.) <span class="hlt">trees</span> were estimated using Artificial Neural Network (ANN) models. Neural networks offer a number of advantages including the ability to implicitly detect complex nonlinear relationships between input and output variables, which is very helpful in <span class="hlt">tree</span> volume modeling. Two different neural network architectures were used and produced the Back propagation (BPANN) and the Cascade Correlation (CCANN) Artificial Neural Network models. In addition, <span class="hlt">tree</span> bole volume estimates were compared to other established <span class="hlt">tree</span> bole volume estimation techniques including the centroid method, taper equations, and existing standard volume tables. An overview of the features of ANNs and traditional methods is presented and the advantages and limitations of each one of them are discussed. For validation purposes, actual volumes were determined by aggregating the volumes of measured short sections (average 1 meter) of the <span class="hlt">tree</span> bole using Smalian's formula. The results reported in this research suggest that the selected cascade correlation artificial neural network (CCANN) models are reliable for estimating the <span class="hlt">tree</span> bole volume of the four examined <span class="hlt">tree</span> <span class="hlt">species</span> since they gave unbiased results and were superior to almost all methods in terms of error (%) expressed as the mean of the percentage errors. PMID:19880241</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015ISPAnII22..175M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015ISPAnII22..175M"><span id="translatedtitle">Identification and Mapping of <span class="hlt">Tree</span> <span class="hlt">Species</span> in Urban Areas Using WORLDVIEW-2 Imagery</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mustafa, Y. T.; Habeeb, H. N.; Stein, A.; Sulaiman, F. Y.</p> <p>2015-10-01</p> <p>Monitoring and mapping of urban <span class="hlt">trees</span> are essential to provide urban forestry authorities with timely and consistent information. Modern techniques increasingly facilitate these tasks, but require the development of semi-automatic <span class="hlt">tree</span> detection and classification methods. In this article, we propose an approach to delineate and map the crown of 15 <span class="hlt">tree</span> <span class="hlt">species</span> in the city of Duhok, Kurdistan Region of Iraq using WorldView-2 (WV-2) imagery. A <span class="hlt">tree</span> crown object is identified first and is subsequently delineated as an image object (IO) using vegetation indices and texture measurements. Next, three classification methods: Maximum Likelihood, Neural Network, and Support Vector Machine were used to classify IOs using selected IO features. The best results are obtained with Support Vector Machine classification that gives the best map of urban <span class="hlt">tree</span> <span class="hlt">species</span> in Duhok. The overall accuracy was between 60.93% to 88.92% and κ-coefficient was between 0.57 to 0.75. We conclude that fifteen <span class="hlt">tree</span> <span class="hlt">species</span> were identified and mapped at a satisfactory accuracy in urban areas of this study.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012EGUGA..14.9592I','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012EGUGA..14.9592I"><span id="translatedtitle">The response of European <span class="hlt">tree</span> <span class="hlt">species</span> to drought: a meta-analysis</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Irschick, C.; Mayr, S.; Wohlfahrt, G.</p> <p>2012-04-01</p> <p>Here we provide first results of a meta-analysis of the response of European <span class="hlt">tree</span> <span class="hlt">species</span> to drought. A literature search was conducted in order to collect available studies of the response of the gas exchange of European <span class="hlt">tree</span> <span class="hlt">species</span> to either natural or imposed water shortage. The resulting publications were screened and parameters at organ (e.g. leaf or shoot), individual (i.e. <span class="hlt">tree</span>) and ecosystem scale were transferred to a data base. Here we present preliminary results from queries of the data base aiming at identifying differences in the drought response between <span class="hlt">species</span> that may have implications for forest productivity and composition under likely future warmer and drier conditions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4840356','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4840356"><span id="translatedtitle">Warming effects on photosynthesis of subtropical <span class="hlt">tree</span> <span class="hlt">species</span>: a translocation experiment along an altitudinal gradient</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Yiyong; Liu, Juxiu; Zhou, Guoyi; Huang, Wenjuan; Duan, Honglang</p> <p>2016-01-01</p> <p>Ongoing climate warming induced by human activities may have great impacts on <span class="hlt">trees</span>, yet it remains unresolved how subtropical <span class="hlt">tree</span> <span class="hlt">species</span> respond to rising temperature in the field. Here, we used downward translocation to investigate the effects of climate warming on leaf photosynthesis of six common <span class="hlt">tree</span> <span class="hlt">species</span> in subtropical China. During the experimental period between 2012 and 2014, the mean average photosynthetic rates (Asat) under saturating light for Schima superba, Machilus breviflora, Pinus massoniana and Ardisia lindleyana in the warm site were7%, 19%, 20% and 29% higher than those in the control site. In contrast, seasonal Asat for Castanopsis hystrix in the warm site were lower compared to the control site. Changes in Asat in response to translocation were mainly associated with those in leaf stomatal conductance (gs) and photosynthetic capacity (RuBP carboxylation, RuBP regeneration capacity). Our results imply that climate warming could have potential impacts on <span class="hlt">species</span> composition and community structure in subtropical forests. PMID:27102064</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/EJ1099325.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/EJ1099325.pdf"><span id="translatedtitle"><span class="hlt">Trees</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Al-Khaja, Nawal</p> <p>2007-01-01</p> <p>This is a thematic lesson plan for young learners about palm <span class="hlt">trees</span> and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a <span class="hlt">tree</span>; the modal auxiliary, can; dialogues and a role play activity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4021425','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4021425"><span id="translatedtitle">An empirical evaluation of two-stage <span class="hlt">species</span> <span class="hlt">tree</span> inference strategies using a multilocus dataset from North American pines</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2014-01-01</p> <p>Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, <span class="hlt">species</span> <span class="hlt">trees</span> are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for <span class="hlt">species</span> <span class="hlt">tree</span> inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup <span class="hlt">species</span> from subsection Strobus and three outgroup <span class="hlt">species</span> from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring <span class="hlt">species</span> <span class="hlt">trees</span> consists of three features: a <span class="hlt">species</span> <span class="hlt">tree</span> construction method, a gene <span class="hlt">tree</span> inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify <span class="hlt">tree</span> characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce <span class="hlt">trees</span> with similar features. We find that strategies that construct <span class="hlt">species</span> <span class="hlt">trees</span> using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a <span class="hlt">species</span> to infer gene <span class="hlt">trees</span> tend to produce estimates of <span class="hlt">species</span> <span class="hlt">trees</span> that contain clades present in <span class="hlt">trees</span> estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct <span class="hlt">species</span> <span class="hlt">trees</span> tend to produce <span class="hlt">species</span> <span class="hlt">tree</span> estimates that contain clades that are not present in <span class="hlt">trees</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27348264','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27348264"><span id="translatedtitle">The role of selected <span class="hlt">tree</span> <span class="hlt">species</span> in industrial sewage sludge/flotation tailing management.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Mleczek, Mirosław; Rutkowski, Paweł; Niedzielski, Przemysław; Goliński, Piotr; Gąsecka, Monika; Kozubik, Tomisław; Dąbrowski, Jędrzej; Budzyńska, Sylwia; Pakuła, Jarosław</p> <p>2016-11-01</p> <p>The aim of the study was to estimate the ability of ten <span class="hlt">tree</span> and bush <span class="hlt">species</span> to tolerate and accumulate Cd, Cu, Pb, Zn, and As <span class="hlt">species</span> [As(III), As(V), and total organic arsenic] in industrial sewage sludge extremely contaminated with arsenic (almost 27.5 g kg(-1)) in a pot experiment. The premise being that it will then be possible to select the most promising <span class="hlt">tree</span>/bush <span class="hlt">species</span>, able to grow in the vicinity of dams where sewage sludge/flotation tailings are used as landfill. Six of the ten tested <span class="hlt">tree</span> <span class="hlt">species</span> were able to grow on the sludge. The highest content of total As was observed in Betula pendula roots (30.0 ± 1.3 mg kg(-1) DW), where the dominant As <span class="hlt">species</span> was the toxic As(V). The highest biomass of Quercus Q1 robur (77.3 § 2.6 g) and Acer platanoides (76.0 § 4.9 g) was observed. A proper planting of selected <span class="hlt">tree</span> <span class="hlt">species</span> that are able to thrive on sewage sludge/flotation tailings could be an interesting and promising way to protect dams. By utilizing differences in their root systems and water needs, we will be able to reduce the risk of fatal environmental disasters. PMID:27348264</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24620581','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24620581"><span id="translatedtitle">Diversity and utilization of <span class="hlt">tree</span> <span class="hlt">species</span> in Meitei homegardens of Barak Valley, Assam.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Devi, N Linthoingambi; Das, Ashesh Kumar</p> <p>2013-03-01</p> <p>An inventory of <span class="hlt">tree</span> diversity in traditional homegardens of Meitei community was conducted in a Bontarapur village in Cachar district of Barak Valley, Assam. Meitei homegarden locally called Ingkhol exhibits a wide diversity in size, shape, location and composition. Seventy one <span class="hlt">tree</span> <span class="hlt">species</span> were enumerated from 50 homegardens belonging to 60 genus and 35 families. Among the families encountered, Rutaceae was the dominant family (4 genus and 7 <span class="hlt">species</span>) followed by Meliaceae (5 genus and 5 <span class="hlt">species</span>), Arecaceae (4 genus and 4 <span class="hlt">species</span>) and Moraceae (3 genus and 5 <span class="hlt">species</span>). Total 7946 <span class="hlt">tree</span> individuals were recorded, with the density of 831 No ha(-1) of and total basal area of 9.54 m2 ha(-1). Areco catechu was the dominant <span class="hlt">species</span> with the maximum number of individuals. Other dominant <span class="hlt">trees</span> include Mangifera indica, Artocarpus heterophyllus, Citrus grandis, Parkia timoriana, Syzygium cumini and Psidium guajava. Being a cash crop, the intensification of betel nut has been preferred in many homegardens. Homegardens form an important component of land use of Meitei community which fulfills the socio-cultural and economic needs of the family and helps in conserving plant diversity through utilization. PMID:24620581</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25058660','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25058660"><span id="translatedtitle">Negative density dependence regulates two <span class="hlt">tree</span> <span class="hlt">species</span> at later life stage in a temperate forest.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Piao, Tiefeng; Chun, Jung Hwa; Yang, Hee Moon; Cheon, Kwangil</p> <p>2014-01-01</p> <p>Numerous studies have demonstrated that <span class="hlt">tree</span> survival is influenced by negative density dependence (NDD) and differences among <span class="hlt">species</span> in shade tolerance could enhance coexistence via resource partitioning, but it is still unclear how NDD affects <span class="hlt">tree</span> <span class="hlt">species</span> with different shade-tolerance guilds at later life stages. In this study, we analyzed the spatial patterns for <span class="hlt">trees</span> with dbh (diameter at breast height) ≥2 cm using the pair-correlation g(r) function to test for NDD in a temperate forest in South Korea after removing the effects of habitat heterogeneity. The analyses were implemented for the most abundant shade-tolerant (Chamaecyparis obtusa) and shade-intolerant (Quercus serrata) <span class="hlt">species</span>. We found NDD existed for both <span class="hlt">species</span> at later life stages. We also found Quercus serrata experienced greater NDD compared with Chamaecyparis obtusa. This study indicates that NDD regulates the two abundant <span class="hlt">tree</span> <span class="hlt">species</span> at later life stages and it is important to consider variation in <span class="hlt">species</span>' shade tolerance in NDD study. PMID:25058660</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26094447','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26094447"><span id="translatedtitle">[Biomass allometric equations of nine common <span class="hlt">tree</span> <span class="hlt">species</span> in an evergreen broadleaved forest of subtropical China].</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zuo, Shu-di; Ren, Yin; Weng, Xian; Ding, Hong-feng; Luo, Yun-jian</p> <p>2015-02-01</p> <p>Biomass allometric equation (BAE) considered as a simple and reliable method in the estimation of forest biomass and carbon was used widely. In China, numerous studies focused on the BAEs for coniferous forest and pure broadleaved forest, and generalized BAEs were frequently used to estimate the biomass and carbon of mixed broadleaved forest, although they could induce large uncertainty in the estimates. In this study, we developed the <span class="hlt">species</span>-specific and generalized BAEs using biomass measurement for 9 common broadleaved <span class="hlt">trees</span> (Castanopsis fargesii, C. lamontii, C. tibetana, Lithocarpus glaber, Sloanea sinensis, Daphniphyllum oldhami, Alniphyllum fortunei, Manglietia yuyuanensis, and Engelhardtia fenzlii) of subtropical evergreen broadleaved forest, and compared differences in <span class="hlt">species</span>-specific and generalized BAEs. The results showed that D (diameter at breast height) was a better independent variable in estimating the biomass of branch, leaf, root, aboveground section and total <span class="hlt">tree</span> than a combined variable (D2 H) of D and H (<span class="hlt">tree</span> height) , but D2H was better than D in estimating stem biomass. R2 (coefficient of determination) values of BAEs for 6 <span class="hlt">species</span> decreased when adding H as the second independent variable into D- only BAEs, where R2 value for S. sinensis decreased by 5.6%. Compared with generalized D- and D2H-based BAEs, standard errors of estimate (SEE) of BAEs for 8 <span class="hlt">tree</span> <span class="hlt">species</span> decreased, and similar decreasing trend was observed for different components, where SEEs of the branch decreased by 13.0% and 20.3%. Therefore, the biomass carbon storage and its dynamic estimates were influenced largely by <span class="hlt">tree</span> <span class="hlt">species</span> and model types. In order to improve the accuracy of the estimates of biomass and carbon, we should consider the differences in <span class="hlt">tree</span> <span class="hlt">species</span> and model types. PMID:26094447</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li class="active"><span>9</span></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_9 --> <div id="page_10" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li class="active"><span>10</span></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="181"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70028562','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70028562"><span id="translatedtitle">Effects of sample survey design on the accuracy of classification <span class="hlt">tree</span> models in <span class="hlt">species</span> distribution models</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Edwards, T.C., Jr.; Cutler, D.R.; Zimmermann, N.E.; Geiser, L.; Moisen, G.G.</p> <p>2006-01-01</p> <p>We evaluated the effects of probabilistic (hereafter DESIGN) and non-probabilistic (PURPOSIVE) sample surveys on resultant classification <span class="hlt">tree</span> models for predicting the presence of four lichen <span class="hlt">species</span> in the Pacific Northwest, USA. Models derived from both survey forms were assessed using an independent data set (EVALUATION). Measures of accuracy as gauged by resubstitution rates were similar for each lichen <span class="hlt">species</span> irrespective of the underlying sample survey form. Cross-validation estimates of prediction accuracies were lower than resubstitution accuracies for all <span class="hlt">species</span> and both design types, and in all cases were closer to the true prediction accuracies based on the EVALUATION data set. We argue that greater emphasis should be placed on calculating and reporting cross-validation accuracy rates rather than simple resubstitution accuracy rates. Evaluation of the DESIGN and PURPOSIVE <span class="hlt">tree</span> models on the EVALUATION data set shows significantly lower prediction accuracy for the PURPOSIVE <span class="hlt">tree</span> models relative to the DESIGN models, indicating that non-probabilistic sample surveys may generate models with limited predictive capability. These differences were consistent across all four lichen <span class="hlt">species</span>, with 11 of the 12 possible <span class="hlt">species</span> and sample survey type comparisons having significantly lower accuracy rates. Some differences in accuracy were as large as 50%. The classification <span class="hlt">tree</span> structures also differed considerably both among and within the modelled <span class="hlt">species</span>, depending on the sample survey form. Overlap in the predictor variables selected by the DESIGN and PURPOSIVE <span class="hlt">tree</span> models ranged from only 20% to 38%, indicating the classification <span class="hlt">trees</span> fit the two evaluated survey forms on different sets of predictor variables. The magnitude of these differences in predictor variables throws doubt on ecological interpretation derived from prediction models based on non-probabilistic sample surveys. ?? 2006 Elsevier B.V. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25371435','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25371435"><span id="translatedtitle">Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of <span class="hlt">species</span> <span class="hlt">tree</span>-aware gene <span class="hlt">trees</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo</p> <p>2015-01-01</p> <p>The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on <span class="hlt">species</span> history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the <span class="hlt">tree</span> topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the <span class="hlt">species</span> phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using <span class="hlt">species</span> <span class="hlt">tree</span>-aware gene <span class="hlt">trees</span> on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify. PMID:25371435</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.springerlink.com/content/g4295k8x56wj20g0/','USGSPUBS'); return false;" href="http://www.springerlink.com/content/g4295k8x56wj20g0/"><span id="translatedtitle">Complementary models of <span class="hlt">tree</span> <span class="hlt">species</span>-soil relationships in old-growth temperate forests</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Cross, Alison; Perakis, Steven S.</p> <p>2011-01-01</p> <p>Ecosystem level studies identify plant soil feed backs as important controls on soil nutrient availability,particularly for nitrogen and phosphorus. Although site and <span class="hlt">species</span> specific studies of <span class="hlt">tree</span> <span class="hlt">species</span> soil relationships are relatively common,comparatively fewer studies consider multiple coexisting speciesin old-growth forests across a range of sites that vary underlying soil fertility. We characterized patterns in forest floor and mineral soil nutrients associated with four common <span class="hlt">tree</span> <span class="hlt">species</span> across eight undisturbed old-growth forests in Oregon, USA, and used two complementary conceptual models to assess <span class="hlt">tree</span> <span class="hlt">species</span> soil relationships. Plant soil feedbacks that could reinforce sitelevel differences in nutrient availability were assessed using the context dependent relationships model, where by relative <span class="hlt">species</span> based differences in each soil nutrient divergedorconvergedas nutrient status changed across sites. <span class="hlt">Tree</span> <span class="hlt">species</span> soil relationships that did not reflect strong feedbacks were evaluated using a site independent relationships model, where by forest floor and surface mineral soil nutrient tools differed consistently by <span class="hlt">tree</span> <span class="hlt">species</span> across sites,without variation in deeper mineral soils. We found that theorganically cycled elements carbon, nitrogen, and phosphorus exhibited context-dependent differences among <span class="hlt">species</span> in both forest floor and mineral soil, and most of ten followed adivergence model,where by <span class="hlt">species</span> differences were greatest at high-nutrient sites. These patterns are consistent with the oryemphasizing biotic control of these elements through plant soil feedback mechanisms. Site independent <span class="hlt">species</span> differences were strongest for pool so if the weather able cations calcium, magnesium, potassium,as well as phosphorus, in mineral soils. Site independent <span class="hlt">species</span> differences in forest floor nutrients we reattributable too nespecies that displayed significant greater forest floor mass accumulation. Our finding confirmed that site-independent and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4407066','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4407066"><span id="translatedtitle">How <span class="hlt">tree</span> <span class="hlt">species</span> fill geographic and ecological space in eastern North America</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Ricklefs, Robert E.</p> <p>2015-01-01</p> <p>Background and Aims Ecologists broadly accept that the number of <span class="hlt">species</span> present within a region balances regional processes of immigration and speciation against competitive and other interactions between populations that limit distribution and constrain diversity. Although ecological theory has, for a long time, addressed the premise that ecological space can be filled to ‘capacity’ with <span class="hlt">species</span>, only with the availability of time-calibrated phylogenies has it been possible to test the hypothesis that diversification slows as the number of <span class="hlt">species</span> in a region increases. Focusing on the deciduous <span class="hlt">trees</span> of eastern North America, this study tested predictions from competition theory concerning the distribution and abundance of <span class="hlt">species</span>. Methods Local assemblages of <span class="hlt">trees</span> tabulated in a previous study published in 1950 were analysed. Assemblages were ordinated with respect to <span class="hlt">species</span> composition by non-metric multidimensional scaling (NMS). Distributions of <span class="hlt">trees</span> were analysed by taxonomically nested analysis of variance, discriminant analysis based on NMS scores, and canonical correlation analysis of NMS scores and Bioclim climate variables. Key Results Most of the variance in <span class="hlt">species</span> abundance and distribution was concentrated among closely related (i.e. congeneric) <span class="hlt">species</span>, indicating evolutionary lability. <span class="hlt">Species</span> distribution and abundance were unrelated to the number of close relatives, suggesting that competitive effects are diffuse. Distances between pairs of congeneric <span class="hlt">species</span> in NMS space did not differ significantly from distances between more distantly related <span class="hlt">species</span>, in contrast to the predictions of both competitive habitat partitioning and ecological sorting of <span class="hlt">species</span>. Conclusions Eastern deciduous forests of North America do not appear to be saturated with <span class="hlt">species</span>. The distributions and abundances of individual <span class="hlt">species</span> provide little evidence of being shaped by competition from related (i.e. ecologically similar) <span class="hlt">species</span> and, by inference, that</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25292455','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25292455"><span id="translatedtitle">Stem CO2 efflux in six co-occurring <span class="hlt">tree</span> <span class="hlt">species</span>: underlying factors and ecological implications.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Rodríguez-Calcerrada, Jesús; López, Rosana; Salomón, Roberto; Gordaliza, Guillermo G; Valbuena-Carabaña, María; Oleksyn, Jacek; Gil, Luis</p> <p>2015-06-01</p> <p>Stem respiration plays a role in <span class="hlt">species</span> coexistence and forest dynamics. Here we examined the intra- and inter-specific variability of stem CO2 efflux (E) in dominant and suppressed <span class="hlt">trees</span> of six deciduous <span class="hlt">species</span> in a mixed forest stand: Fagus sylvatica L., Quercus petraea [Matt.] Liebl, Quercus pyrenaica Willd., Prunus avium L., Sorbus aucuparia L. and Crataegus monogyna Jacq. We conducted measurements in late autumn. Within <span class="hlt">species</span>, dominants had higher E per unit stem surface area (Es ) mainly because sapwood depth was higher than in suppressed <span class="hlt">trees</span>. Across <span class="hlt">species</span>, however, differences in Es corresponded with differences in the proportion of living parenchyma in sapwood and concentration of non-structural carbohydrates (NSC). Across <span class="hlt">species</span>, Es was strongly and NSC marginally positively related with an index of drought tolerance, suggesting that slow growth of drought-tolerant <span class="hlt">trees</span> is related to higher NSC concentration and Es . We conclude that, during the leafless period, E is indicative of maintenance respiration and is related with some ecological characteristics of the <span class="hlt">species</span>, such as drought resistance; that sapwood depth is the main factor explaining variability in Es within <span class="hlt">species</span>; and that the proportion of NSC in the sapwood is the main factor behind variability in Es among <span class="hlt">species</span>. PMID:25292455</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EnMan..53..783S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EnMan..53..783S&link_type=ABSTRACT"><span id="translatedtitle">The Right <span class="hlt">Tree</span> for the Job? Perceptions of <span class="hlt">Species</span> Suitability for the Provision of Ecosystem Services</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Smaill, Simeon J.; Bayne, Karen M.; Coker, Graham W. R.; Paul, Thomas S. H.; Clinton, Peter W.</p> <p>2014-04-01</p> <p>Stakeholders in plantation forestry are increasingly aware of the importance of the ecosystem services and non-market values associated with forests. In New Zealand, there is significant interest in establishing <span class="hlt">species</span> other than Pinus radiata D. Don (the dominant plantation <span class="hlt">species</span>) in the belief that alternative <span class="hlt">species</span> are better suited to deliver these services. Significant risk is associated with this position as there is little objective data to support these views. To identify which <span class="hlt">species</span> were likely to be planted to deliver ecosystem services, a survey was distributed to examine stakeholder perceptions. Stakeholders were asked which of 15 <span class="hlt">tree</span> attributes contributed to the provision of five ecosystem services (amenity value, bioenergy production, carbon capture, the diversity of native habitat, and erosion control/water quality) and to identify which of 22 candidate <span class="hlt">tree</span> <span class="hlt">species</span> possessed those attributes. These data were combined to identify the <span class="hlt">species</span> perceived most suitable for the delivery of each ecosystem service. Sequoia sempervirens (D.Don) Endl. closely matched the stakeholder derived ideotypes associated with all five ecosystem services. Comparisons to data from growth, physiological and ecological studies demonstrated that many of the opinions held by stakeholders were inaccurate, leading to erroneous assumptions regarding the suitability of most candidate <span class="hlt">species</span>. Stakeholder perceptions substantially influence <span class="hlt">tree</span> <span class="hlt">species</span> selection, and plantations established on the basis of inaccurate opinions are unlikely to deliver the desired outcomes. Attitudinal surveys associated with engagement campaigns are essential to improve stakeholder knowledge, advancing the development of fit-for-purpose forest management that provides the required ecosystem services.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21362638','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21362638"><span id="translatedtitle">Detecting phylogenetic breakpoints and discordance from genome-wide alignments for <span class="hlt">species</span> <span class="hlt">tree</span> reconstruction.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ané, Cécile</p> <p>2011-01-01</p> <p>With the easy acquisition of sequence data, it is now possible to obtain and align whole genomes across multiple related <span class="hlt">species</span> or populations. In this work, I assess the performance of a statistical method to reconstruct the whole distribution of phylogenetic <span class="hlt">trees</span> along the genome, estimate the proportion of the genome for which a given clade is true, and infer a concordance <span class="hlt">tree</span> that summarizes the dominant vertical inheritance pattern. There are two main issues when dealing with whole-genome alignments, as opposed to multiple genes: the size of the data and the detection of recombination breakpoints. These breakpoints partition the genomic alignment into phylogenetically homogeneous loci, where sites within a given locus all share the same phylogenetic <span class="hlt">tree</span> topology. To delimitate these loci, I describe here a method based on the minimum description length (MDL) principle, implemented with dynamic programming for computational efficiency. Simulations show that combining MDL partitioning with Bayesian concordance analysis provides an efficient and robust way to estimate both the vertical inheritance signal and the horizontal phylogenetic signal. The method performed well both in the presence of incomplete lineage sorting and in the presence of horizontal gene transfer. A high level of systematic bias was found here, highlighting the need for good individual <span class="hlt">tree</span> building methods, which form the basis for more elaborate gene <span class="hlt">tree/species</span> <span class="hlt">tree</span> reconciliation methods. PMID:21362638</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4538783','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4538783"><span id="translatedtitle"><span class="hlt">Tree</span> cover at fine and coarse spatial grains interacts with shade tolerance to shape plant <span class="hlt">species</span> distributions across the Alps</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Svenning, Jens-Christian</p> <p>2015-01-01</p> <p>The role of competition for light among plants has long been recognised at local scales, but its importance for plant <span class="hlt">species</span> distributions at larger spatial scales has generally been ignored. <span class="hlt">Tree</span> cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of <span class="hlt">species</span> that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of <span class="hlt">tree</span> cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 <span class="hlt">species</span> of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and <span class="hlt">tree</span> cover) at both spatial grains for each <span class="hlt">species</span>. We used partial regressions to evaluate the independent effects of plot- and landscape-grain <span class="hlt">tree</span> cover on plot-level plant communities. Finally, the effects on <span class="hlt">species</span>-specific elevational range limits were assessed by simulating a removal experiment comparing the <span class="hlt">species</span> distributions under high and low <span class="hlt">tree</span> cover. Accounting for <span class="hlt">tree</span> cover improved the model performance, with the probability of the presence of shade-tolerant <span class="hlt">species</span> increasing with increasing <span class="hlt">tree</span> cover, whereas shade-intolerant <span class="hlt">species</span> showed the opposite pattern. The <span class="hlt">tree</span> cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, <span class="hlt">tree</span> cover at the two grain sizes had partially independent effects on plot-level plant communities. With high <span class="hlt">tree</span> cover, shade-intolerant <span class="hlt">species</span> exhibited narrower elevational ranges than with low <span class="hlt">tree</span> cover whereas shade-tolerant <span class="hlt">species</span> showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23376521','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23376521"><span id="translatedtitle">Forest floor leachate fluxes under six different <span class="hlt">tree</span> <span class="hlt">species</span> on a metal contaminated site.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Van Nevel, Lotte; Mertens, Jan; De Schrijver, An; Baeten, Lander; De Neve, Stefaan; Tack, Filip M G; Meers, Erik; Verheyen, Kris</p> <p>2013-03-01</p> <p><span class="hlt">Trees</span> play an important role in the biogeochemical cycling of metals, although the influence of different <span class="hlt">tree</span> <span class="hlt">species</span> on the mobilization of metals is not yet clear. This study examined effects of six <span class="hlt">tree</span> <span class="hlt">species</span> on fluxes of Cd, Zn, DOC, H(+) and base cations in forest floor leachates on a metal polluted site in Belgium. Forest floor leachates were sampled with zero-tension lysimeters in a 12-year-old post-agricultural forest on a sandy soil. The <span class="hlt">tree</span> <span class="hlt">species</span> included were silver birch (Betula pendula), oak (Quercus robur and Q. petraea), black locust (Robinia pseudoacacia), aspen (Populus tremula), Scots pine (Pinus sylvestris) and Douglas fir (Pseudotsuga menziesii). We show that total Cd fluxes in forest floor leachate under aspen were slightly higher than those in the other <span class="hlt">species</span>' leachates, yet the relative differences between the <span class="hlt">species</span> were considerably smaller when looking at dissolved Cd fluxes. The latter was probably caused by extremely low H(+) amounts leaching from aspen's forest floor. No <span class="hlt">tree</span> <span class="hlt">species</span> effect was found for Zn leachate fluxes. We expected higher metal leachate fluxes under aspen as its leaf litter was significantly contaminated with Cd and Zn. We propose that the low amounts of Cd and Zn leaching under aspen's forest floor were possibly caused by high activity of soil biota, for example burrowing earthworms. Furthermore, our results reveal that Scots pine and oak were characterized by high H(+) and DOC fluxes as well as low base cation fluxes in their forest floor leachates, implying that those <span class="hlt">species</span> might enhance metal mobilization in the soil profile and thus bear a potential risk for belowground metal dispersion. PMID:23376521</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27220216','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27220216"><span id="translatedtitle">Interspecific variation in growth responses to climate and competition of five eastern <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Rollinson, Christine R; Kaye, Margot W; Canham, Charles D</p> <p>2016-04-01</p> <p>Climate and competition are often presented from two opposing views of the dominant driver of individual <span class="hlt">tree</span> growth and <span class="hlt">species</span> distribution in temperate forests, such as those in the eastern United States. Previous studies have provided abundant evidence indicating that both factors influence <span class="hlt">tree</span> growth, and we argue that these effects are not independent of one another and rather that interactions between climate, competition, and size best describe <span class="hlt">tree</span> growth. To illustrate this point, we describe the growth responses of five common eastern <span class="hlt">tree</span> <span class="hlt">species</span> to interacting effects of temperature, precipitation, competition, and individual size using maximum likelihood estimation. Models that explicitly include interactions among these four factors explained over half of the variance in annual growth for four out of five <span class="hlt">species</span> using annual climate. Expanding temperature and precipitation analyses to include seasonal interactions resulted in slightly improved models with a mean R2 of 0.61 (SD 0.10). Growth responses to individual factors as well their interactions varied greatly among <span class="hlt">species</span>. For example, growth sensitivity to temperature for Quercus rubra increased with maximum annual precipitation, but other <span class="hlt">species</span> showed no change in sensitivity or slightly reduced annual growth. Our results also indicate that three-way interactions among individual stem size, competition, and temperature may determine which of the five co-occurring <span class="hlt">species</span> in our study could have the highest growth rate in a given year. Continued consideration and quantification of interactions among climate, competition, and individual-based characteristics are likely to increase understanding of key biological processes such as <span class="hlt">tree</span> growth. Greater parameterization of interactions between traditionally segregated factors such as climate and competition may also help build a framework to reconcile drivers of individual-based processes such as growth with larger-scale patterns of <span class="hlt">species</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23572941','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23572941"><span id="translatedtitle">Improved method of in vitro regeneration in Leucaena leucocephala - a leguminous pulpwood <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Shaik, Noor M; Arha, Manish; Nookaraju, A; Gupta, Sushim K; Srivastava, Sameer; Yadav, Arun K; Kulkarni, Pallavi S; Abhilash, O U; Vishwakarma, Rishi K; Singh, Somesh; Tatkare, Rajeshri; Chinnathambi, Kannan; Rawal, Shuban K; Khan, Bashir M</p> <p>2009-10-01</p> <p>Leucaena leucocephala is a fast growing <span class="hlt">multipurpose</span> legume <span class="hlt">tree</span> used for forage, leaf manure, paper and pulp. Lignin in Leucaena pulp adversely influences the quality of paper produced. Developing transgenic Leucaena with altered lignin by genetic engineering demands an optimized regeneration system. The present study deals with optimization of regeneration system for L. leucocephala cv. K636. Multiple shoot induction from the cotyledonary nodes of L. leucocephala was studied in response to cytokinins, thidiazuron (TDZ) and N(6)-benzyladenine (BA) supplemented in half strength MS (½-MS) medium and also their effect on in vitro rooting of the regenerated shoots. Multiple shoots were induced from cotyledonary nodes at varied frequencies depending on the type and concentration of cytokinin used in the medium. TDZ was found to induce more number of shoots per explant than BA, with a maximum of 7 shoots at an optimum concentration of 0.23 µM. Further increase in TDZ concentration resulted in reduced shoot length and fasciation of the shoots. Liquid pulse treatment of the explants with TDZ did not improve the shoot production further but improved the subsequent rooting of the shoots that regenerated. Regenerated shoots successfully rooted on ½-MS medium supplemented with 0.54 µM α-naphthaleneacetic acid (NAA). Rooted shoots of Leucaena were transferred to coco-peat and hardened plantlets showed ≥ 90 % establishment in the green house. PMID:23572941</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFM.B43C0563C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFM.B43C0563C"><span id="translatedtitle">A Section-based Method For <span class="hlt">Tree</span> <span class="hlt">Species</span> Classification Using Airborne LiDAR Discrete Points In Urban Areas</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chunjing, Y. C.; Hui, T.; Zhongjie, R.; Guikai, B.</p> <p>2015-12-01</p> <p>As a new approach to forest inventory utilizing, LiDAR remote sensing has become an important research issue in the past. Lidar researches initially concentrate on the investigation for mapping forests at the <span class="hlt">tree</span> level and identifying important structural parameters, such as <span class="hlt">tree</span> height, crown size, crown base height, individual <span class="hlt">tree</span> <span class="hlt">species</span>, and stem volume etc. But for the virtual city visualization and mapping, the traditional methods of <span class="hlt">tree</span> classification can't satisfy the more complex conditions. Recently, the advanced LiDAR technology has generated new full waveform scanners that provide a higher point density and additional information about the reflecting characteristics of <span class="hlt">trees</span>. Subsequently, it was demonstrated that it is feasible to detect individual overstorey <span class="hlt">trees</span> in forests and classify <span class="hlt">species</span>. But the important issues like the calibration and the decomposition of full waveform data with a series of Gaussian functions usually take a lot of works. What's more, the detection and classification of vegetation results relay much on the prior outcomes. From all above, the section-based method for <span class="hlt">tree</span> <span class="hlt">species</span> classification using small footprint and high sampling density lidar data is proposed in this paper, which can overcome the <span class="hlt">tree</span> <span class="hlt">species</span> classification issues in urban areas. More specific objectives are to: (1)use local maximum height decision and four direction sections certification methods to get the precise locations of the <span class="hlt">trees</span>;(2) develop new lidar-derived features processing techniques for characterizing the section structure of individual <span class="hlt">tree</span> crowns;(3) investigate several techniques for filtering and analyzing vertical profiles of individual <span class="hlt">trees</span> to classify the <span class="hlt">trees</span>, and using the expert decision skills based on percentile analysis;(4) assess the accuracy of estimating <span class="hlt">tree</span> <span class="hlt">species</span> for each <span class="hlt">tree</span>, and (5) investigate which type of lidar data, point frequency or intensity, provides the most accurate estimate of <span class="hlt">tree</span> <span class="hlt">species</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26828175','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26828175"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">Species</span> Suitability to Bioswales and Impact on the Urban Water Budget.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Scharenbroch, Bryant C; Morgenroth, Justin; Maule, Brian</p> <p>2016-01-01</p> <p>Water movement between soil and the atmosphere is restricted by hardscapes in the urban environment. Some green infrastructure is intended to increase infiltration and storage of water, thus decreasing runoff and discharge of urban stormwater. Bioswales are a critical component of a water-sensitive urban design (or a low-impact urban design), and incorporation of <span class="hlt">trees</span> into these green infrastructural components is believed to be a novel way to return stored water to the atmosphere via transpiration. This research was conducted in The Morton Arboretum's main parking lot, which is one of the first and largest green infrastructure installations in the midwestern United States. The parking lot is constructed of permeable pavers and <span class="hlt">tree</span> bioswales. <span class="hlt">Trees</span> in bioswales were evaluated for growth and condition and for their effects on water cycling via transpiration. Our data indicate that <span class="hlt">trees</span> in bioswales accounted for 46 to 72% of total water outputs via transpiration, thereby reducing runoff and discharge from the parking lot. By evaluating the stomatal conductance, diameter growth, and condition of a variety of <span class="hlt">tree</span> <span class="hlt">species</span> in these bioswales, we found that not all <span class="hlt">species</span> are equally suited for bioswales and that not all are equivalent in their transpiration and growth rates, thereby contributing differentially to the functional capacity of bioswales. We conclude that <span class="hlt">species</span> with high stomatal conductance and large mature form are likely to contribute best to bioswale function. PMID:26828175</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/22864803','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/22864803"><span id="translatedtitle">The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic <span class="hlt">tree</span> <span class="hlt">species</span>: a case study from the Forest Reserve of Bandia, Senegal.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Sene, Godar; Thiao, Mansour; Samba-Mbaye, Ramatoulaye; Khasa, Damase; Kane, Aboubacry; Mbaye, Mame Samba; Beaulieu, Marie-Ève; Manga, Anicet; Sylla, Samba Ndao</p> <p>2013-01-01</p> <p>Several fast-growing and <span class="hlt">multipurpose</span> <span class="hlt">tree</span> <span class="hlt">species</span> have been widely used in West Africa to both reverse the tendency of land degradation and restore soil productivity. Although beneficial effects have been reported on soil stabilization, there still remains a lack of information about their impact on soil microorganisms. Our investigation has been carried out in exotic and native <span class="hlt">tree</span> plantations of 28 years and aimed to survey and compare the abundance and genetic diversity of natural legume-nodulating rhizobia (LNR). The study of LNR is supported by the phylogenetic analysis which clustered the isolates into three genera: Bradyrhizobium, Mesorhizobium, and Sinorhizobium. The results showed close positive correlations between the sizes of LNR populations estimated both in the dry and rainy seasons and the presence of legume <span class="hlt">tree</span> hosts. There were significant increases in Rhizobium spp. population densities in response to planting with Acacia spp., and high genetic diversities and richness of genotypes were fittest in these <span class="hlt">tree</span> plantations. This suggests that enrichment of soil Rhizobium spp. populations is host specific. The results indicated also that <span class="hlt">species</span> of genera Mesorhizobium and Sinorhizobium were lacking in plantations of non-host <span class="hlt">species</span>. By contrast, there was a widespread distribution of Bradyrhizobium spp. strains across the <span class="hlt">tree</span> plantations, with no evident specialization in regard to plantation type. Finally, the study provides information about the LNR communities associated with a range of old <span class="hlt">tree</span> plantations and some aspects of their relationships to soil factors, which may facilitate the management of man-made forest systems that target ecosystem rehabilitation and preservation of soil biota. PMID:22864803</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013EnMan..51..524M&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013EnMan..51..524M&link_type=ABSTRACT"><span id="translatedtitle">Certified and Uncertified Logging Concessions Compared in Gabon: Changes in Stand Structure, <span class="hlt">Tree</span> <span class="hlt">Species</span>, and Biomass</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Medjibe, V. P.; Putz, Francis E.; Romero, Claudia</p> <p>2013-03-01</p> <p>Forest management certification is assumed to promote sustainable forest management, but there is little field-based evidence to support this claim. To help fill this gap, we compared a Forest Stewardship Council (FSC)-certified with an adjacent uncertified, conventionally logged concession (CL) in Gabon on the basis of logging damage, above-ground biomass (AGB), and <span class="hlt">tree</span> <span class="hlt">species</span> diversity and composition. Before logging, we marked, mapped, and measured all <span class="hlt">trees</span> >10 cm dbh in 20 and twelve 1-ha permanent plots in the FSC and CL areas, respectively. Soil and <span class="hlt">tree</span> damage due to felling, skidding, and road-related activities was then assessed 2-3 months after the 508 ha FSC study area and the 200 ha CL study area were selectively logged at respective intensities of 5.7 m3/ha (0.39 <span class="hlt">trees</span>/ha) and 11.4 m3/ha (0.76 <span class="hlt">trees</span>/ha). For each <span class="hlt">tree</span> felled, averages of 9.1 and 20.9 other <span class="hlt">trees</span> were damaged in the FSC and CL plots, respectively; when expressed as the impacts per timber volume extracted, the values did not differ between the two treatments. Skid trails covered 2.9 % more of the CL surface, but skid trail length per unit timber volume extracted was not greater. Logging roads were wider in the CL than FSC site and disturbed 4.7 % more of the surface. Overall, logging caused declines in AGB of 7.1 and 13.4 % at the FSC and CL sites, respectively. Changes in <span class="hlt">tree</span> <span class="hlt">species</span> composition were small but greater for the CL site. Based on these findings and in light of the pseudoreplicated study design with less-than perfect counterfactual, we cautiously conclude that certification yields environmental benefits even after accounting for differences in logging intensities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23277438','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23277438"><span id="translatedtitle">Certified and uncertified logging concessions compared in Gabon: changes in stand structure, <span class="hlt">tree</span> <span class="hlt">species</span>, and biomass.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Medjibe, V P; Putz, Francis E; Romero, Claudia</p> <p>2013-03-01</p> <p>Forest management certification is assumed to promote sustainable forest management, but there is little field-based evidence to support this claim. To help fill this gap, we compared a Forest Stewardship Council (FSC)-certified with an adjacent uncertified, conventionally logged concession (CL) in Gabon on the basis of logging damage, above-ground biomass (AGB), and <span class="hlt">tree</span> <span class="hlt">species</span> diversity and composition. Before logging, we marked, mapped, and measured all <span class="hlt">trees</span> >10 cm dbh in 20 and twelve 1-ha permanent plots in the FSC and CL areas, respectively. Soil and <span class="hlt">tree</span> damage due to felling, skidding, and road-related activities was then assessed 2-3 months after the 508 ha FSC study area and the 200 ha CL study area were selectively logged at respective intensities of 5.7 m(3)/ha (0.39 <span class="hlt">trees</span>/ha) and 11.4 m(3)/ha (0.76 <span class="hlt">trees</span>/ha). For each <span class="hlt">tree</span> felled, averages of 9.1 and 20.9 other <span class="hlt">trees</span> were damaged in the FSC and CL plots, respectively; when expressed as the impacts per timber volume extracted, the values did not differ between the two treatments. Skid trails covered 2.9 % more of the CL surface, but skid trail length per unit timber volume extracted was not greater. Logging roads were wider in the CL than FSC site and disturbed 4.7 % more of the surface. Overall, logging caused declines in AGB of 7.1 and 13.4 % at the FSC and CL sites, respectively. Changes in <span class="hlt">tree</span> <span class="hlt">species</span> composition were small but greater for the CL site. Based on these findings and in light of the pseudoreplicated study design with less-than perfect counterfactual, we cautiously conclude that certification yields environmental benefits even after accounting for differences in logging intensities. PMID:23277438</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27490180','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27490180"><span id="translatedtitle">Direct vs. Microclimate-Driven Effects of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity on Litter Decomposition in Young Subtropical Forest Stands.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Seidelmann, Katrin N; Scherer-Lorenzen, Michael; Niklaus, Pascal A</p> <p>2016-01-01</p> <p>Effects of <span class="hlt">tree</span> <span class="hlt">species</span> diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy <span class="hlt">tree</span> <span class="hlt">species</span> richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with <span class="hlt">tree</span> communities ranging from monocultures to mixtures of 24 native subtropical <span class="hlt">tree</span> <span class="hlt">species</span>. Litter bags filled with senescent leaves of three native <span class="hlt">tree</span> <span class="hlt">species</span> were placed from Nov. 2011 to Oct. 2012 on 134 plots along the <span class="hlt">tree</span> <span class="hlt">species</span> diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand <span class="hlt">species</span> richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. <span class="hlt">Tree</span> stands were 2-3 years old, but nevertheless <span class="hlt">tree</span> <span class="hlt">species</span> diversity explained more variation (54.3%) in decomposition than topography (7.7%). <span class="hlt">Tree</span> <span class="hlt">species</span> richness slowed litter decomposition, an effect that slightly depended on litter <span class="hlt">species</span> identity. A large part of the variance in decomposition was explained by <span class="hlt">tree</span> <span class="hlt">species</span> composition, with the presence of three <span class="hlt">tree</span> <span class="hlt">species</span> playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, <span class="hlt">species</span> diversity (without composition) explained 8.9% and topography 34.4% of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973968','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973968"><span id="translatedtitle">Direct vs. Microclimate-Driven Effects of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity on Litter Decomposition in Young Subtropical Forest Stands</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Seidelmann, Katrin N.; Scherer-Lorenzen, Michael; Niklaus, Pascal A.</p> <p>2016-01-01</p> <p>Effects of <span class="hlt">tree</span> <span class="hlt">species</span> diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy <span class="hlt">tree</span> <span class="hlt">species</span> richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with <span class="hlt">tree</span> communities ranging from monocultures to mixtures of 24 native subtropical <span class="hlt">tree</span> <span class="hlt">species</span>. Litter bags filled with senescent leaves of three native <span class="hlt">tree</span> <span class="hlt">species</span> were placed from Nov. 2011 to Oct. 2012 on 134 plots along the <span class="hlt">tree</span> <span class="hlt">species</span> diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand <span class="hlt">species</span> richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. <span class="hlt">Tree</span> stands were 2–3 years old, but nevertheless <span class="hlt">tree</span> <span class="hlt">species</span> diversity explained more variation (54.3%) in decomposition than topography (7.7%). <span class="hlt">Tree</span> <span class="hlt">species</span> richness slowed litter decomposition, an effect that slightly depended on litter <span class="hlt">species</span> identity. A large part of the variance in decomposition was explained by <span class="hlt">tree</span> <span class="hlt">species</span> composition, with the presence of three <span class="hlt">tree</span> <span class="hlt">species</span> playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, <span class="hlt">species</span> diversity (without composition) explained 8.9% and topography 34.4% of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4134238','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4134238"><span id="translatedtitle">Patterns of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian</p> <p>2014-01-01</p> <p>Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within <span class="hlt">species</span>, between <span class="hlt">species</span>, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different <span class="hlt">species</span> of Pinus (ca. 22% on the whole), 54 <span class="hlt">species</span> of Quercus (ca. 9–14%), 7 <span class="hlt">species</span> of Arbutus (ca. 50%) and many other <span class="hlt">trees</span> <span class="hlt">species</span>. The objectives of this study were to model how <span class="hlt">tree</span> <span class="hlt">species</span> diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum <span class="hlt">tree</span> <span class="hlt">species</span> diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of <span class="hlt">tree</span> <span class="hlt">species</span> are generally higher in cold</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25127455','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25127455"><span id="translatedtitle">Patterns of <span class="hlt">tree</span> <span class="hlt">species</span> diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian</p> <p>2014-01-01</p> <p>Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within <span class="hlt">species</span>, between <span class="hlt">species</span>, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different <span class="hlt">species</span> of Pinus (ca. 22% on the whole), 54 <span class="hlt">species</span> of Quercus (ca. 9-14%), 7 <span class="hlt">species</span> of Arbutus (ca. 50%) and many other <span class="hlt">trees</span> <span class="hlt">species</span>. The objectives of this study were to model how <span class="hlt">tree</span> <span class="hlt">species</span> diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum <span class="hlt">tree</span> <span class="hlt">species</span> diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of <span class="hlt">tree</span> <span class="hlt">species</span> are generally higher in cold</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li class="active"><span>10</span></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_10 --> <div id="page_11" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li class="active"><span>11</span></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="201"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21691855','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21691855"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> identity and interactions with neighbors determine nutrient leaching in model tropical forests.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ewel, John J; Bigelow, Seth W</p> <p>2011-12-01</p> <p>An ecosystem containing a mixture of <span class="hlt">species</span> that differ in phenology, morphology, and physiology might be expected to resist leaching of soil nutrients to a greater extent than one composed of a single <span class="hlt">species</span>. We tested the effects of <span class="hlt">species</span> identity and plant-life-form richness on nutrient leaching at a lowland tropical site where deep infiltration averages >2 m year(-1). Three indigenous <span class="hlt">tree</span> <span class="hlt">species</span> with contrasting leafing phenologies (evergreen, dry-season deciduous, and wet-season deciduous) were grown in monoculture and together with two other life-forms with which they commonly occur in tropical forests: a palm and a giant, perennial herb. To calculate nutrient leaching over an 11-year period, concentrations of nutrients in soil water were multiplied by drainage rates estimated from a water balance. The effect of plant-life-form richness on retention differed according to <span class="hlt">tree</span> <span class="hlt">species</span> identity and nutrient. Nitrate retention was greater in polycultures of the dry-season deciduous <span class="hlt">tree</span> <span class="hlt">species</span> (mean of 7.4 kg ha(-1) year(-1) of NO(3)-N lost compared to 12.7 in monoculture), and calcium and magnesium retention were greater in polycultures of the evergreen and wet-season deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. Complementary use of light led to intensification of soil exploitation by roots, the main agent responsible for enhanced nutrient retention in some polycultures. Other mechanisms included differences in nutrient demand among <span class="hlt">species</span>, and avoidance of catastrophic failure due to episodic weather events or pest outbreaks. Even unrealistically simple multi-life-form mimics of tropical forest can safeguard a site's nutrient capital if careful attention is paid to <span class="hlt">species</span>' characteristics and temporal changes in interspecific interactions. PMID:21691855</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4206468','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4206468"><span id="translatedtitle">Data Concatenation, Bayesian Concordance and Coalescent-Based Analyses of the <span class="hlt">Species</span> <span class="hlt">Tree</span> for the Rapid Radiation of Triturus Newts</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wielstra, Ben; Arntzen, Jan W.; van der Gaag, Kristiaan J.; Pabijan, Maciej; Babik, Wieslaw</p> <p>2014-01-01</p> <p>The phylogenetic relationships for rapid <span class="hlt">species</span> radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine <span class="hlt">species</span>. Bayesian analysis of population structure allocates all individuals to their respective <span class="hlt">species</span>. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the <span class="hlt">species</span> <span class="hlt">tree</span> differ from one another. The data concatenation based <span class="hlt">species</span> <span class="hlt">tree</span> shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene <span class="hlt">trees</span> for part of the Triturus <span class="hlt">species</span> <span class="hlt">tree</span> as low concordance factors. The coalescent-based <span class="hlt">species</span> <span class="hlt">tree</span> is relatively similar to a previously published <span class="hlt">species</span> <span class="hlt">tree</span> based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene <span class="hlt">tree</span> discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent <span class="hlt">species</span> radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus <span class="hlt">species</span> <span class="hlt">tree</span> even more genes will have to be consulted. PMID:25337997</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016EGUGA..1810323K&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016EGUGA..1810323K&link_type=ABSTRACT"><span id="translatedtitle">Investigating the limitations of <span class="hlt">tree</span> <span class="hlt">species</span> classification using the Combined Cluster and Discriminant Analysis method for low density ALS data from a dense forest region in Aggtelek (Hungary)</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Koma, Zsófia; Deák, Márton; Kovács, József; Székely, Balázs; Kelemen, Kristóf; Standovár, Tibor</p> <p>2016-04-01</p> <p>Airborne Laser Scanning (ALS) is a widely used technology for forestry classification applications. However, single <span class="hlt">tree</span> detection and <span class="hlt">species</span> classification from low density ALS point cloud is limited in a dense forest region. In this study we investigate the division of a forest into homogenous groups at stand level. The study area is located in the Aggtelek karst region (Northeast Hungary) with a complex relief topography. The ALS dataset contained only 4 discrete echoes (at 2-4 pt/m2 density) from the study area during leaf-on season. Ground-truth measurements about canopy closure and proportion of <span class="hlt">tree</span> <span class="hlt">species</span> cover are available for every 70 meter in 500 square meter circular plots. In the first step, ALS data were processed and geometrical and intensity based features were calculated into a 5×5 meter raster based grid. The derived features contained: basic statistics of relative height, canopy RMS, echo ratio, openness, pulse penetration ratio, basic statistics of radiometric feature. In the second step the data were investigated using Combined Cluster and Discriminant Analysis (CCDA, Kovács et al., 2014). The CCDA method first determines a basic grouping for the multiple circle shaped sampling locations using hierarchical clustering and then for the arising grouping possibilities a core cycle is executed comparing the goodness of the investigated groupings with random ones. Out of these comparisons difference values arise, yielding information about the optimal grouping out of the investigated ones. If sub-groups are then further investigated, one might even find homogeneous groups. We found that low density ALS data classification into homogeneous groups are highly dependent on canopy closure, and the proportion of the dominant <span class="hlt">tree</span> <span class="hlt">species</span>. The presented results show high potential using CCDA for determination of homogenous separable groups in LiDAR based <span class="hlt">tree</span> <span class="hlt">species</span> classification. Aggtelek Karst/Slovakian Karst Caves" (HUSK/1101/221/0180, Aggtelek NP</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015EGUGA..1712942H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015EGUGA..1712942H"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> specific soil moisture patterns and dynamics through the seasons</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Heidbüchel, Ingo; Dreibrodt, Janek; Simard, Sonia; Güntner, Andreas; Blume, Theresa</p> <p>2015-04-01</p> <p>Soil moisture patterns in the landscape are largely controlled by soil types (pore size distributions) and landscape position. But how strong is the influence of vegetation on patterns within a single soil type? While we would envision a clear difference in soil moisture patterns and responses between for example bare soil, a pasture and a forest, our conceptual images start to become less clear when we move on to different forest stands. Do different <span class="hlt">tree</span> <span class="hlt">species</span> cause different moisture patterns to emerge? Could it be possible to identify the dominant <span class="hlt">tree</span> <span class="hlt">species</span> of a site by classifying its soil moisture pattern? To investigate this question we analyzed data from 15 sensor clusters in the lowlands of north-eastern Germany (within the TERENO observatory) which were instrumented with soil moisture sensors (5 profiles per site), tensiometers, sap flow sensors, throughfall and stemflow gages. Data has been collected at these sites since May 2014. While the summer data has already been analyzed, the analysis of the winter data and thus the possible seasonal shifts in patterns will be carried out in the coming months. Throughout the last summer we found different dynamics of soil moisture patterns under pine <span class="hlt">trees</span> compared to beech <span class="hlt">trees</span>. While the soils under beech <span class="hlt">trees</span> were more often relatively wet and more often relatively dry, the soils under pine <span class="hlt">trees</span> showed less variability and more often average soil moisture. These differences are most likely due to differences in both throughfall patterns as well as root water uptake. Further analysis includes the use of throughfall and stemflow data as well as stable water isotope samples that were taken at different depths in the soil, in the groundwater and from the sapwood. The manifestation of <span class="hlt">tree</span> <span class="hlt">species</span> differences in soil moisture patterns and dynamics is likely to have implications for groundwater recharge, transit times and hydrologic partitioning.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70031880','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70031880"><span id="translatedtitle">Influences of calcium availability and <span class="hlt">tree</span> <span class="hlt">species</span> on Ca isotope fractionation in soil and vegetation</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Page, B.D.; Bullen, T.D.; Mitchell, M.J.</p> <p>2008-01-01</p> <p>The calcium (Ca) isotope system is potentially of great use for understanding biogeochemical processes at multiple scales in forest ecosystems, yet remains largely unexplored for this purpose. In order to further our understanding of Ca behavior in forests, we examined two nearly adjacent hardwood-dominated catchments with differing soil Ca concentrations, developed from crystalline bedrock, to determine the variability of 44Ca/ 40Ca ratios (expressed as ??44Ca) within soil and vegetation pools. For both sugar maple and American beech, the Ca isotope compositions of the measured roots and calculated bulk <span class="hlt">trees</span> were considerably lighter than those of soil pools at these sites, suggesting that the <span class="hlt">trees</span> were able to preferentially take up light Ca at the root-soil interface. The Ca isotope compositions of three of four root samples were among the lightest values yet reported for terrestrial materials (??44Ca ???-3.95???). Our results further indicate that Ca isotopes were fractionated along the transpiration streams of both <span class="hlt">tree</span> <span class="hlt">species</span> with roots having the least ??44Ca values and leaf litter the greatest. An approximately 2??? difference in ??44Ca values between roots and leaf litter of both <span class="hlt">tree</span> <span class="hlt">species</span> suggests a persistent fractionation mechanism along the transpiration stream, likely related to Ca binding in wood tissue coupled with internal ion exchange. Finally, our data indicate that differing <span class="hlt">tree</span> <span class="hlt">species</span> demand for Ca and soil Ca concentrations together may influence Ca isotope distribution within the <span class="hlt">trees</span>. Inter-catchment differences in Ca isotope distributions in soils and <span class="hlt">trees</span> were minor, indicating that the results of our study may have broad transferability to studies of forest ecosystems in catchments developed on crystalline substrates elsewhere. ?? 2008 Springer Science+Business Media B.V.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17204076','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17204076"><span id="translatedtitle">Large variation in whole-plant water-use efficiency among tropical <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cernusak, Lucas A; Aranda, Jorge; Marshall, John D; Winter, Klaus</p> <p>2007-01-01</p> <p>It is well known that whole-plant water-use efficiency (transpiration efficiency of carbon gain, TE(C)) varies among plant <span class="hlt">species</span> with different photosynthetic pathways. However, less is known of such variation among <span class="hlt">tree</span> <span class="hlt">species</span> within the C(3) group. Here we measured the TE(C) of seven C(3) tropical <span class="hlt">tree</span> <span class="hlt">species</span>. Isotopic analyses (delta(13)C, delta(18)O, and delta(15)N) and elemental analyses (carbon and nitrogen) were undertaken to provide insight into sources of variation in TE(C). Plants were grown over several months in approx. 80% full sunlight in individual 38-l containers in the Republic of Panama. Soil moisture content was nonlimiting. Significant variation was observed in TE(C) among the C(3) <span class="hlt">tree</span> <span class="hlt">species</span>. Values ranged from 1.6 mmol C mol(-1) H(2)O for teak (Tectona grandis) to 4.0 mmol C mol(-1) H(2)O for a legume, Platymiscium pinnatum. Variation in TE(C) was correlated with both leaf N concentration, a proxy for photosynthetic capacity, and oxygen-isotope enrichment, a proxy for stomatal conductance. The TE(C) varied with C-isotope discrimination within <span class="hlt">species</span>, but the relationship broke down among <span class="hlt">species</span>, reflecting the existence of <span class="hlt">species</span>-specific offsets. PMID:17204076</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2009AGUFM.B23A0359M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2009AGUFM.B23A0359M"><span id="translatedtitle">Leaf gas exchange traits of domestic and exotic <span class="hlt">tree</span> <span class="hlt">species</span> in Cambodia</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Miyazawa, Y.; Tateishi, M.; Kumagai, T.; Otsuki, K.</p> <p>2009-12-01</p> <p>In forests under the management by community villagers, exotic <span class="hlt">tree</span> <span class="hlt">species</span> with rapid growth rate are introduced in wide range of Cambodia. To evaluate the influence of the introduction on the forest gas exchange and water budget, we investigated the leaf gas exchange traits of two domestic (Dipterocarpus obtusifolius and Shorea roxburghii) and exotic <span class="hlt">tree</span> <span class="hlt">species</span> (Acasia auriculiformis and Eucalyptus camadilansis). We sampled shoots of each <span class="hlt">species</span> and measured the leaf gas exchange traits (photosynthetic rates under different CO2 concentrations, transpiration rate and stomatal conductance) (6 leaves x 3 <span class="hlt">trees</span> x 4 <span class="hlt">species</span>). We carried out this measurement at 2 months intervals for a year from the beginning of rainy season and compared the obtained traits among <span class="hlt">species</span>. Light saturated rate of net photosynthesis was higher in E. camadilansis but did not differ among other <span class="hlt">species</span> both in rainy and dry seasons. Seasonal patter in photosynthetic traits was not obvious. Each <span class="hlt">species</span> changed stomatal conductance in response to changes in environmental conditions. The response was more sensitive than reported values. In this presentation, we show details about the basic information about the leaf-level gas exchange traits, which are required to run soil- vegetation - atmosphere transfer model.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20010004211','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20010004211"><span id="translatedtitle">BOREAS TE-4 Gas Exchange Data from Boreal <span class="hlt">Tree</span> <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Collatz, G. James; Berry, Joseph A.; Gamon, John; Fredeen, Art; Fu, Wei</p> <p>2000-01-01</p> <p>The BOREAS TE-4 team collected steady-state gas exchange and reflectance data from several <span class="hlt">species</span> in the BOREAS SSA during 1994 and in the NSA during 1996. Measurements of light, CO2, temperature, and humidity response curves were made by the BOREAS TE-4 team during the summers of 1994 and 1996 using intact attached leaves of boreal forest <span class="hlt">species</span> located in the BOREAS SSA and NSA. These measurements were conducted to calibrate models used to predict photosynthesis, stomatal conductance, and leaf respiration. The 1994 and 1996 data can be used to construct plots of response functions or for parameterizing models. Parameter values are suitable for application in SiB2 (Sellers et al., 1996) or the leaf model of Collatz et al. (1991), and programs can be obtained from the investigators. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3892915','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3892915"><span id="translatedtitle">Eco-physiological adaptation of dominant <span class="hlt">tree</span> <span class="hlt">species</span> at two contrasting karst habitats in southwestern China</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wu, Qian; Yan, Hui; Xu, Xinwu</p> <p>2013-01-01</p> <p>The purpose of this study was to investigate the eco-physiological adaptation of indigenous woody <span class="hlt">species</span> to their habitats in karst areas of southwestern China. Two contrasting forest habitats were studied: a degraded habitat in Daxiagu and a well-developed habitat in Tianlongshan, and the eco-physiological characteristics of the <span class="hlt">trees</span> were measured for three growth seasons. Photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr) of the <span class="hlt">tree</span> <span class="hlt">species</span> in Daxiagu were 2-3 times higher than those in Tianlongshan under ambient conditions. However, this habitat effect was not significant when measurements were taken under controlled conditions. Under controlled conditions, Pn, gs, and Tr of the deciduous <span class="hlt">species</span> were markedly higher than those for the evergreen <span class="hlt">species</span>. Habitat had no significant effect on water use efficiency (WUE) or photochemical characteristics of PSII. The stomatal sensitivity of woody <span class="hlt">species</span> in the degraded habitat was much higher than that in the well-developed habitat. Similarly, the leaf total nitrogen (N) and phosphorus (P) contents expressed on the basis of either dry mass or leaf area were also much higher in Daxiagu than they were in Tianlongshan. The mass-based leaf total N content of deciduous <span class="hlt">species</span> was much higher than that of evergreen <span class="hlt">species</span>, while leaf area-based total N and P contents of evergreens were significantly higher than those of deciduous <span class="hlt">species</span>. The photosynthetic nitrogen- and phosphorus-use efficiencies (PNUE and PPUE) of deciduous <span class="hlt">species</span> were much higher than those of evergreens. Further, the PPUE of the woody <span class="hlt">species</span> in Tianlongshan was much higher than that  of the woody <span class="hlt">species</span> in Daxiagu. The results from three growth seasons imply that the <span class="hlt">tree</span> <span class="hlt">species</span> were able to adapt well to their growth habitats. Furthermore, it seems that so-called “temporary drought stress” may not occur, or may not be severe for most woody plants in karst areas of southwestern China. PMID:24555059</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3586649','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3586649"><span id="translatedtitle">Epigenetic regulation of adaptive responses of forest <span class="hlt">tree</span> <span class="hlt">species</span> to the environment</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Bräutigam, Katharina; Vining, Kelly J; Lafon-Placette, Clément; Fossdal, Carl G; Mirouze, Marie; Marcos, José Gutiérrez; Fluch, Silvia; Fraga, Mario Fernández; Guevara, M Ángeles; Abarca, Dolores; Johnsen, Øystein; Maury, Stéphane; Strauss, Steven H; Campbell, Malcolm M; Rohde, Antje; Díaz-Sala, Carmen; Cervera, María-Teresa</p> <p>2013-01-01</p> <p>Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant <span class="hlt">species</span>, and may be especially important for long-lived organisms with complex life cycles, including forest <span class="hlt">trees</span>. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest <span class="hlt">tree</span> <span class="hlt">species</span>. We consider the possible role of forest <span class="hlt">tree</span> epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change. PMID:23467802</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25775797','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25775797"><span id="translatedtitle">[Effects of <span class="hlt">tree</span> <span class="hlt">species</span> on polysaccharides content of epiphytic Dendrobium officinale].</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Guo, Ying-Ying; Zhu, Yan; Si, Jin-Ping; Liu, Jing-Jing; Wu, Cheng-Yong; Li, Hui</p> <p>2014-11-01</p> <p>To reveals the effects of <span class="hlt">tree</span> <span class="hlt">species</span> on polysaccharides content of epiphytic Dendrobium officinale. The polysaccharides content of D. officinale attached to living tress in wild or stumps in bionic-facility was determined by phenol-sulfuric acid method. There were extremely significant differences of polysaccharides content of D. officinale attached to different <span class="hlt">tree</span> <span class="hlt">species</span>, but the differences had no relationship with the form and nutrition of barks. The polysaccharides content of D. officinale mainly affected by the light intensity of environment, so reasonable illumination favored the accumulation of polysaccharides. Various polysaccharides content of D. officinal from different attached <span class="hlt">trees</span> is due to the difference of light regulation, but not the form and nutrition of barks. PMID:25775797</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014AGUFM.B51B0028L&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014AGUFM.B51B0028L&link_type=ABSTRACT"><span id="translatedtitle">Dynamics of <span class="hlt">Tree</span> <span class="hlt">Species</span> Composition in Temperate Mountains of South Korea over Fourteen Years using 880 Permanent Plots</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lee, B.; Kim, H. S.; Park, J.; Moon, M.; Cho, S.; Ryu, D.; Wynn, K. Z.; Park, J.</p> <p>2014-12-01</p> <p>The structure of forest and diversity of <span class="hlt">tree</span> <span class="hlt">species</span> in temperate mountains have been influenced by changing climate conditions as well as successional changes. To understand how <span class="hlt">tree</span> <span class="hlt">species</span> composition and stand structure change across temperate mountains, the <span class="hlt">species</span> composition, size, and environmental information were collected over the past fourteen years in 880 quadrats of 20 m x 50 m of woodland communities distributed across Jiri and Baekoon Mountains, South Korea. The preliminary investigation on variations of <span class="hlt">tree</span> <span class="hlt">species</span> revealed that overall composition of <span class="hlt">tree</span> <span class="hlt">species</span> increased in terms of both diversity and biomass growth of <span class="hlt">tree</span> <span class="hlt">species</span>, reflecting fast and wide changes in temperate forests of Korea. Among dominant <span class="hlt">trees</span>, the Quercus mongolica, Styrax japonicu, and Acer pseudosieboldianum recorded the highest increase in stand density, implying the most prosperous <span class="hlt">species</span> under current conditions, while the <span class="hlt">species</span> of Quercus variabilis and Fraxinus mandshurica appeared as fast declining <span class="hlt">species</span> in the number. In terms of biomass growth of dominant <span class="hlt">species</span>, the Stewartia pseudocamellia showed the largest increase of biomass, followed by Quercus serrata and Quercus mongolica., while the Fraxinus mandshurica appeared to have a rapid decline, followed by Alnus japonica and Quercus dentata. Overall, the fast change of composition in <span class="hlt">tree</span> <span class="hlt">species</span> is clear and further analysis to clarify the reasons for such fast and <span class="hlt">species</span>-specific changes is underway especially to separate the effect of successional change and climate change.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25555688','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25555688"><span id="translatedtitle">Characterization of mariner-like transposons of the mauritiana Subfamily in seven <span class="hlt">tree</span> aphid <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kharrat, Imen; Mezghani, Maha; Casse, Nathalie; Denis, Françoise; Caruso, Aurore; Makni, Hanem; Capy, Pierre; Rouault, Jacques-Deric; Chénais, Benoît; Makni, Mohamed</p> <p>2015-02-01</p> <p>Mariner-like elements (MLEs) are Class II transposons present in all eukaryotic genomes in which MLEs have been searched for. This article reports the detection of MLEs in seven of the main fruit <span class="hlt">tree</span> aphid <span class="hlt">species</span> out of eight <span class="hlt">species</span> studied. Deleted MLE sequences of 916-919 bp were characterized, using the terminal-inverted repeats (TIRs) of mariner elements belonging to the mauritiana Subfamily as primers. All the sequences detected were deleted copies of full-length elements that included the 3'- and 5'-TIRs but displayed internal deletions affecting Mos1 activity. Networks based on the mtDNA cytochrome oxidase subunit-I (CO-I) and MLE sequences were incongruent, suggesting that mutations in transposon sequences had accumulated before speciation of <span class="hlt">tree</span> aphid <span class="hlt">species</span> occurred, and that they have been maintained in this <span class="hlt">species</span> via vertical transmissions. This is the first evidence of the widespread occurrence of MLEs in aphids. PMID:25555688</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/11737299','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/11737299"><span id="translatedtitle">Fine-scale spatial genetic structure of eight tropical <span class="hlt">tree</span> <span class="hlt">species</span> as analysed by RAPDs.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Degen, B; Caron, H; Bandou, E; Maggia, L; Chevallier, M H; Leveau, A; Kremer, A</p> <p>2001-10-01</p> <p>The fine-scale spatial genetic structure of eight tropical <span class="hlt">tree</span> <span class="hlt">species</span> (Chrysophyllum sanguinolentum, Carapa procera, Dicorynia guianensis, Eperua grandiflora, Moronobea coccinea, Symphonia globulifera, Virola michelii, Vouacapoua americana) was studied in populations that were part of a silvicultural trial in French Guiana. The <span class="hlt">species</span> analysed have different spatial distribution, sexual system, pollen and seed dispersal agents, flowering phenology and environmental demands. The spatial position of <span class="hlt">trees</span> and a RAPD data set for each <span class="hlt">species</span> were combined using a multivariate genetic distance method to estimate spatial genetic structure. A significant spatial genetic structure was found for four of the eight <span class="hlt">species</span>. In contrast to most observations in temperate forests, where spatial structure is not usually detected at distances greater than 50 m, significant genetic structure was found at distances up to 300 m. The relationships between spatial genetic structure and life history characteristics are discussed. PMID:11737299</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=89709','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=89709"><span id="translatedtitle">In Vitro Activities of Ketoconazole, Econazole, Miconazole, and Melaleuca alternifolia (Tea <span class="hlt">Tree</span>) Oil against Malassezia <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hammer, K. A.; Carson, C. F.; Riley, T. V.</p> <p>2000-01-01</p> <p>The in vitro activities of ketoconazole, econazole, miconazole, and tea <span class="hlt">tree</span> oil against 54 Malassezia isolates were determined by agar and broth dilution methods. Ketoconazole was more active than both econazole and miconazole, which showed very similar activities. M. furfur was the least susceptible <span class="hlt">species</span>. M. sympodialis, M. slooffiae, M. globosa, and M. obtusa showed similar susceptibilities to the four agents. PMID:10639388</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19256435','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19256435"><span id="translatedtitle">[Reproductive phenology of <span class="hlt">tree</span> <span class="hlt">species</span> in the Tenosique tropical forest, Tabasco, Mexico].</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ochoa-Gaona, Susana; Hernández, Isidro Pérez; de Jong, Bernardus H J</p> <p>2008-06-01</p> <p>Between August 2003 and August 2005 we registered the flowering and fruiting of 75 <span class="hlt">tree</span> <span class="hlt">species</span> (341 individual <span class="hlt">trees</span>) in a tropical rain forest at Tenosique, Tabasco, Mexico. Monthly we checked five transects (500 m long; 5 m wide). To test the homogeneity of flowering and fruiting during the year, and between adjacent months, we applied a chi2 test. The flowering was bimodal, with a highest peak in March and April, coinciding with the dry season, and a second lower peak in July when precipitation is relatively low. The highest number of fruiting <span class="hlt">tree</span> <span class="hlt">species</span> occur between May and July, with its peak in May. Each of the most common botanical families showed a particular phenological pattern. Monthly rainfall and the number of <span class="hlt">species</span> flowering or fruiting were not significantly correlated. This means that <span class="hlt">trees</span> are flowering and fruiting all year long, with seasonal increases of both phenological phenomena in the dryer periods. We conclude that phenological patterns vary between individuals and between years and are not seasonally correlated. The data we generated are relevant to program the best periods of seed collections according to individual or groups of <span class="hlt">species</span>, as part of forest management and conservation practices. PMID:19256435</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26164201','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26164201"><span id="translatedtitle">New flux based dose-response relationships for ozone for European forest <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Büker, P; Feng, Z; Uddling, J; Briolat, A; Alonso, R; Braun, S; Elvira, S; Gerosa, G; Karlsson, P E; Le Thiec, D; Marzuoli, R; Mills, G; Oksanen, E; Wieser, G; Wilkinson, M; Emberson, L D</p> <p>2015-11-01</p> <p>To derive O3 dose-response relationships (DRR) for five European forest <span class="hlt">trees</span> <span class="hlt">species</span> and broadleaf deciduous and needleleaf <span class="hlt">tree</span> plant functional types (PFTs), phytotoxic O3 doses (PODy) were related to biomass reductions. PODy was calculated using a stomatal flux model with a range of cut-off thresholds (y) indicative of varying detoxification capacities. Linear regression analysis showed that DRR for PFT and individual <span class="hlt">tree</span> <span class="hlt">species</span> differed in their robustness. A simplified parameterisation of the flux model was tested and showed that for most non-Mediterranean <span class="hlt">tree</span> <span class="hlt">species</span>, this simplified model led to similarly robust DRR as compared to a <span class="hlt">species</span>- and climate region-specific parameterisation. Experimentally induced soil water stress was not found to substantially reduce PODy, mainly due to the short duration of soil water stress periods. This study validates the stomatal O3 flux concept and represents a step forward in predicting O3 damage to forests in a spatially and temporally varying climate. PMID:26164201</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=276289','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=276289"><span id="translatedtitle">Conspecific plant-soil feedbacks of temperate <span class="hlt">tree</span> <span class="hlt">species</span> in the southern Appalachians, USA</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Many <span class="hlt">tree</span> <span class="hlt">species</span> have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify cases of negative distance-dependence effects and whether variation in these e...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25065257','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25065257"><span id="translatedtitle">Responses of <span class="hlt">tree</span> <span class="hlt">species</span> to heat waves and extreme heat events.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Teskey, Robert; Wertin, Timothy; Bauweraerts, Ingvar; Ameye, Maarten; McGuire, Mary Anne; Steppe, Kathy</p> <p>2015-09-01</p> <p>The number and intensity of heat waves has increased, and this trend is likely to continue throughout the 21st century. Often, heat waves are accompanied by drought conditions. It is projected that the global land area experiencing heat waves will double by 2020, and quadruple by 2040. Extreme heat events can impact a wide variety of <span class="hlt">tree</span> functions. At the leaf level, photosynthesis is reduced, photooxidative stress increases, leaves abscise and the growth rate of remaining leaves decreases. In some <span class="hlt">species</span>, stomatal conductance increases at high temperatures, which may be a mechanism for leaf cooling. At the whole plant level, heat stress can decrease growth and shift biomass allocation. When drought stress accompanies heat waves, the negative effects of heat stress are exacerbated and can lead to <span class="hlt">tree</span> mortality. However, some <span class="hlt">species</span> exhibit remarkable tolerance to thermal stress. Responses include changes that minimize stress on photosynthesis and reductions in dark respiration. Although there have been few studies to date, there is evidence of within-<span class="hlt">species</span> genetic variation in thermal tolerance, which could be important to exploit in production forestry systems. Understanding the mechanisms of differing <span class="hlt">tree</span> responses to extreme temperature events may be critically important for understanding how <span class="hlt">tree</span> <span class="hlt">species</span> will be affected by climate change. PMID:25065257</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=541764','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=541764"><span id="translatedtitle">C4 Photosynthesis in <span class="hlt">Tree</span> Form Euphorbia <span class="hlt">Species</span> from Hawaiian Rainforest Sites 1</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Pearcy, Robert W.; Troughton, John</p> <p>1975-01-01</p> <p>The 13C 12C isotope ratios and the leaf anatomy of 18 <span class="hlt">species</span> and varieties of Euphorbia native to the Hawaian Islands indicated that all possess C4 photosynthesis. These <span class="hlt">species</span> range from small prostrate coastal strand shrubs to shrubs and <span class="hlt">trees</span> in rainforest and bog habitats. The results show that C4 photosynthesis occurs in plants from a much wider range of habitats and life-forms than has been previously reported. PMID:16659208</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li class="active"><span>11</span></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_11 --> <div id="page_12" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li class="active"><span>12</span></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="221"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70045618','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70045618"><span id="translatedtitle">Effects of canopy <span class="hlt">tree</span> <span class="hlt">species</span> on belowground biogeochemistry in a lowland wet tropical forest</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Keller, Adrienne B.; Reed, Sasha C.; Townsend, Alan R.; Cleveland, Cory C.</p> <p>2013-01-01</p> <p>Tropical rain forests are known for their high biological diversity, but the effects of plant diversity on important ecosystem processes in this biome remain unclear. Interspecies differences in both the demand for nutrients and in foliar and litter nutrient concentrations could drive variations in both the pool sizes and fluxes of important belowground resources, yet our understanding of the effects and importance of aboveground heterogeneity on belowground biogeochemistry is poor, especially in the <span class="hlt">species</span>-rich forests of the wet tropics. To investigate the effects of individual <span class="hlt">tree</span> <span class="hlt">species</span> on belowground biogeochemical processes, we used both field and laboratory studies to examine how carbon (C), nitrogen (N), and phosphorus (P) cycles vary under nine different canopy <span class="hlt">tree</span> <span class="hlt">species</span> – including three legume and six non-legume <span class="hlt">species</span> – that vary in foliar nutrient concentrations in a wet tropical forest in southwestern Costa Rica. We found significant differences in belowground C, N and P cycling under different canopy <span class="hlt">tree</span> <span class="hlt">species</span>: total C, N and P pools in standing litter varied by <span class="hlt">species</span>, as did total soil and microbial C and N pools. Rates of soil extracellular acid phosphatase activity also varied significantly among <span class="hlt">species</span> and functional groups, with higher rates of phosphatase activity under legumes. In addition, across all <span class="hlt">tree</span> <span class="hlt">species</span>, phosphatase activity was significantly positively correlated with litter N/P ratios, suggesting a tight coupling between relative N and P inputs and resource allocation to P acquisition. Overall, our results suggest the importance of aboveground plant community composition in promoting belowground biogeochemical heterogeneity at relatively small spatial scales.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011AGUFM.B52C..06K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011AGUFM.B52C..06K"><span id="translatedtitle">Leaf nitrate assimilation during leaf expansion period: comparison of temperate and boreal <span class="hlt">tree</span> <span class="hlt">species</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Koyama, L.; Tokuchi, N.; Kielland, K.</p> <p>2011-12-01</p> <p>We examined nitrate assimilation in several <span class="hlt">tree</span> <span class="hlt">species</span> to test the hypothesis that plant N acquisition is highest in early spring due to the N demands of leaf growth and the seasonal availability of soil N. Specifically, we advance the idea that <span class="hlt">trees</span> acquire N most actively during the leaf expansion period, which serves to offset growth-dilution of foliar N. However, it has been observed that boreal <span class="hlt">species</span> expand their leaves more rapidly than do temperate <span class="hlt">species</span>, suggesting that they exhibit a different seasonal pattern of N acquisition than do temperate <span class="hlt">species</span>. To examine these relationships we measured leaf nitrate reductase activity (NRA) as a proxy for nitrate assimilation, leaf expansion rates, and foliar N concentrations on three boreal <span class="hlt">tree</span> <span class="hlt">species</span> and three temperate <span class="hlt">tree</span> <span class="hlt">species</span> throughout their leaf expansion period. An evergreen <span class="hlt">species</span> (Quercus glauca) and two deciduous <span class="hlt">species</span> (Acer palmatum and Zelkova serrata) were investigated in temperate Japan, and three deciduous <span class="hlt">species</span> Alnus crispa, Betula papyrifera and Populus tremuloides were chosen in a boreal forest in interior Alaska, US. The patterns of foliar N concentrations were very similar across all six <span class="hlt">species</span>, but the mean leaf expansion period was shorter in the boreal <span class="hlt">species</span> (about 25 days) than in temperate <span class="hlt">species</span> (about 29 days). All temperate <span class="hlt">species</span> showed clear peaks of leaf NRA in the middle of leaf expansion period, suggesting that leaves partly compensate for the N dilution during expansion via foliar nitrate assimilation, and that plant nitrate acquisition was effectively timed to coincide with soil N availability generally increased in early spring. By contrast, peak NRA in the boreal <span class="hlt">species</span> were observed in different stage of leaf expansion, but as in the temperate <span class="hlt">species</span> declined to very low levels after the leaves were fully expanded. Our results demonstrate that plant nitrate assimilation is concentrated during leaf expansion in spring and early summer, but declines to</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/5224196','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/5224196"><span id="translatedtitle">Narrowing historical uncertainty: probabilistic classification of ambiguously identified <span class="hlt">tree</span> <span class="hlt">species</span> in historical forest survey data</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Mladenoff, D.J.; Dahir, S.E.; Nordheim, E.V.; Schulte, L.A.; Guntenspergen, G.R.</p> <p>2002-01-01</p> <p>Historical data have increasingly become appreciated for insight into the past conditions of ecosystems. Uses of such data include assessing the extent of ecosystem change; deriving ecological baselines for management, restoration, and modeling; and assessing the importance of past conditions on the composition and function of current systems. One historical data set of this type is the Public Land Survey (PLS) of the United States General Land Office, which contains data on multiple <span class="hlt">tree</span> <span class="hlt">species</span>, sizes, and distances recorded at each survey point, located at half-mile (0.8 km) intervals on a 1-mi (1.6 km) grid. This survey method was begun in the 1790s on US federal lands extending westward from Ohio. Thus, the data have the potential of providing a view of much of the US landscape from the mid-1800s, and they have been used extensively for this purpose. However, historical data sources, such as those describing the <span class="hlt">species</span> composition of forests, can often be limited in the detail recorded and the reliability of the data, since the information was often not originally recorded for ecological purposes. Forest <span class="hlt">trees</span> are sometimes recorded ambiguously, using generic or obscure common names. For the PLS data of northern Wisconsin, USA, we developed a method to classify ambiguously identified <span class="hlt">tree</span> <span class="hlt">species</span> using logistic regression analysis, using data on <span class="hlt">trees</span> that were clearly identified to <span class="hlt">species</span> and a set of independent predictor variables to build the models. The models were first created on partial data sets for each <span class="hlt">species</span> and then tested for fit against the remaining data. Validations were conducted using repeated, random subsets of the data. Model prediction accuracy ranged from 81% to 96% in differentiating congeneric <span class="hlt">species</span> among oak, pine, ash, maple, birch, and elm. Major predictor variables were <span class="hlt">tree</span> size, associated <span class="hlt">species</span>, landscape classes indicative of soil type, and spatial location within the study region. Results help to clarify ambiguities</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27481793','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27481793"><span id="translatedtitle">The Trichoptera barcode initiative: a strategy for generating a <span class="hlt">species</span>-level <span class="hlt">Tree</span> of Life.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhou, Xin; Frandsen, Paul B; Holzenthal, Ralph W; Beet, Clare R; Bennett, Kristi R; Blahnik, Roger J; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V; Collins, Gemma E; deWaard, Jeremy; Dean, John; Flint, Oliver S; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D; Kondratieff, Boris C; Malicky, Hans; Milton, Megan A; Morinière, Jérôme; Morse, John C; Mwangi, François Ngera; Pauls, Steffen U; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A; Zamora-Muñoz, Carmen; Ziesmann, Tanja; Kjer, Karl M</p> <p>2016-09-01</p> <p>DNA barcoding was intended as a means to provide <span class="hlt">species</span>-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the <span class="hlt">Tree</span> of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described <span class="hlt">species</span>. Most Trichoptera, as with most of life's <span class="hlt">species</span>, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained <span class="hlt">tree</span> searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the <span class="hlt">tree</span>. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous <span class="hlt">species</span> boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and '<span class="hlt">species</span>' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for <span class="hlt">species</span> description.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481793</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4406680','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4406680"><span id="translatedtitle">Mapping and Characterizing Selected Canopy <span class="hlt">Tree</span> <span class="hlt">Species</span> at the Angkor World Heritage Site in Cambodia Using Aerial Data</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean</p> <p>2015-01-01</p> <p>At present, there is very limited information on the ecology, distribution, and structure of Cambodia’s <span class="hlt">tree</span> <span class="hlt">species</span> to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., <span class="hlt">tree</span> height and crown width) of selected <span class="hlt">tree</span> <span class="hlt">species</span> found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual <span class="hlt">tree</span> crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and <span class="hlt">tree</span> height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the <span class="hlt">trees</span> (Spearman’s rho 0.782 and 0.589, respectively). Individual <span class="hlt">tree</span> crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas <span class="hlt">tree</span> crowns delineated using watershed segmentation underestimated the field-measured <span class="hlt">tree</span> crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected <span class="hlt">tree</span> <span class="hlt">species</span>. The latter was found to be more suitable for <span class="hlt">tree</span> <span class="hlt">species</span> classification. Individual <span class="hlt">tree</span> <span class="hlt">species</span> were identified with high accuracy. Inclusion of textural information further improved <span class="hlt">species</span> identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for <span class="hlt">tree</span> <span class="hlt">species</span> mapping and for studies of the forest mensuration variables. PMID:25902148</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25902148','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25902148"><span id="translatedtitle">Mapping and characterizing selected canopy <span class="hlt">tree</span> <span class="hlt">species</span> at the Angkor World Heritage site in Cambodia using aerial data.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean</p> <p>2015-01-01</p> <p>At present, there is very limited information on the ecology, distribution, and structure of Cambodia's <span class="hlt">tree</span> <span class="hlt">species</span> to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., <span class="hlt">tree</span> height and crown width) of selected <span class="hlt">tree</span> <span class="hlt">species</span> found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual <span class="hlt">tree</span> crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and <span class="hlt">tree</span> height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the <span class="hlt">trees</span> (Spearman's rho 0.782 and 0.589, respectively). Individual <span class="hlt">tree</span> crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas <span class="hlt">tree</span> crowns delineated using watershed segmentation underestimated the field-measured <span class="hlt">tree</span> crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected <span class="hlt">tree</span> <span class="hlt">species</span>. The latter was found to be more suitable for <span class="hlt">tree</span> <span class="hlt">species</span> classification. Individual <span class="hlt">tree</span> <span class="hlt">species</span> were identified with high accuracy. Inclusion of textural information further improved <span class="hlt">species</span> identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for <span class="hlt">tree</span> <span class="hlt">species</span> mapping and for studies of the forest mensuration variables. PMID:25902148</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/18608895','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/18608895"><span id="translatedtitle">The expanding host <span class="hlt">tree</span> <span class="hlt">species</span> spectrum of Cryptococcus gattii and Cryptococcus neoformans and their isolations from surrounding soil in India.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Randhawa, H S; Kowshik, T; Chowdhary, Anuradha; Preeti Sinha, K; Khan, Z U; Sun, Sheng; Xu, Jianping</p> <p>2008-12-01</p> <p>This study reports the widespread prevalence of Cryptococcus neoformans and Cryptococcus gattii in decayed wood inside trunk hollows of 14 <span class="hlt">species</span> representing 12 families of <span class="hlt">trees</span> and from soil near the base of various host <span class="hlt">trees</span> from Delhi and several places in the Indian states of Uttar Pradesh, Haryana, Tamil Nadu and Chandigarh Union Territory. Of the 311 <span class="hlt">trees</span> from which samples were obtained, 64 (20.5%) were found to contain strains of the C. neoformans <span class="hlt">species</span> complex. The number of <span class="hlt">trees</span> positive for C. neoformans var grubii (serotypeA) was 51 (16.3%), for C. gattii (serotype B) 24 (7.7%) and for both C. neoformans and C. gattii 11 (3.5%). The overall prevalence of C. neoformans <span class="hlt">species</span> complex in decayed wood samples was 19.9% (111/556). There was no obvious correlation between the prevalence of these two yeast <span class="hlt">species</span> and the <span class="hlt">species</span> of host <span class="hlt">trees</span>. The data on prevalence of C. gattii (24%) and C. neoformans (26%) in soil around the base of some host <span class="hlt">trees</span> indicated that soil is another important ecologic niche for these two Cryptococcus <span class="hlt">species</span> in India. Among our sampled <span class="hlt">tree</span> <span class="hlt">species</span>, eight and six were recorded for the first time as hosts for C. neoformans var grubii and C. gattii, respectively. A longitudinal surveillance of 8 host <span class="hlt">tree</span> <span class="hlt">species</span> over 0.7 to 2.5 years indicated long term colonization of Polyalthia longifolia, Mimusops elengi and Manilkara hexandra <span class="hlt">trees</span> by C. gattii and/or C. neoformans. The mating type was determined for 153 of the isolates, including 98 strains of serotype A and 55 of serotype B and all proved to be mating type alpha (MAT alpha). Our observations document the rapidly expanding spectrum of host <span class="hlt">tree</span> <span class="hlt">species</span> for C. gattii and C. neoformans and indicate that decayed woods of many <span class="hlt">tree</span> <span class="hlt">species</span> are potentially suitable ecological niches for both pathogens. PMID:18608895</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20140009601','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20140009601"><span id="translatedtitle"><span class="hlt">Tree</span> Density and <span class="hlt">Species</span> Decline in the African Sahel Attributable to Climate</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Gonzalez, Patrick; Tucker, Compton J.; Sy, H.</p> <p>2012-01-01</p> <p>Increased aridity and human population have reduced <span class="hlt">tree</span> cover in parts of the African Sahel and degraded resources for local people. Yet, <span class="hlt">tree</span> cover trends and the relative importance of climate and population remain unresolved. From field measurements, aerial photos, and Ikonos satellite images, we detected significant 1954-2002 <span class="hlt">tree</span> density declines in the western Sahel of 18 +/- 14% (P = 0.014, n = 204) and 17 +/- 13% (P = 0.0009, n = 187). From field observations, we detected a significant 1960-2000 <span class="hlt">species</span> richness decline of 21 +/- 11% (P = 0.0028, n = 14) across the Sahel and a southward shift of the Sahel, Sudan, and Guinea zones. Multivariate analyses of climate, soil, and population showed that temperature most significantly (P < 0.001) explained <span class="hlt">tree</span> cover changes. Multivariate and bivariate tests and field observations indicated the dominance of temperature and precipitation, supporting attribution of <span class="hlt">tree</span> cover changes to climate variability. Climate change forcing of Sahel climate variability, particularly the significant (P < 0.05) 1901-2002 temperature increases and precipitation decreases in the research areas, connects Sahel <span class="hlt">tree</span> cover changes to global climate change. This suggests roles for global action and local adaptation to address ecological change in the Sahel.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25526843','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25526843"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> diversity mitigates disturbance impacts on the forest carbon cycle.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pedro, Mariana Silva; Rammer, Werner; Seidl, Rupert</p> <p>2015-03-01</p> <p>Biodiversity fosters the functioning and stability of forest ecosystems and, consequently, the provision of crucial ecosystem services that support human well-being and quality of life. In particular, it has been suggested that <span class="hlt">tree</span> <span class="hlt">species</span> diversity buffers ecosystems against the impacts of disturbances, a relationship known as the "insurance hypothesis". Natural disturbances have increased across Europe in recent decades and climate change is expected to amplify the frequency and severity of disturbance events. In this context, mitigating disturbance impacts and increasing the resilience of forest ecosystems is of growing importance. We have tested how <span class="hlt">tree</span> <span class="hlt">species</span> diversity modulates the impact of disturbance on net primary production and the total carbon stored in living biomass for a temperate forest landscape in Central Europe. Using the simulation model iLand to study the effect of different disturbance regimes on landscapes with varying levels of <span class="hlt">tree</span> <span class="hlt">species</span> richness, we found that increasing diversity generally reduces the disturbance impact on carbon storage and uptake, but that this effect weakens or even reverses with successional development. Our simulations indicate a clear positive relationship between diversity and resilience, with more diverse systems experiencing lower disturbance-induced variability in their trajectories of ecosystem functioning. We found that positive effects of <span class="hlt">tree</span> <span class="hlt">species</span> diversity are mainly driven by an increase in functional diversity and a modulation of traits related to recolonization and resource usage. The results of our study suggest that increasing <span class="hlt">tree</span> <span class="hlt">species</span> diversity could mitigate the effects of intensifying disturbance regimes on ecosystem functioning and improve the robustness of forest carbon storage and the role of forests in climate change mitigation. PMID:25526843</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2714761','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2714761"><span id="translatedtitle">Temperature dependence, spatial scale, and <span class="hlt">tree</span> <span class="hlt">species</span> diversity in eastern Asia and North America</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wang, Zhiheng; Brown, James H.; Tang, Zhiyao; Fang, Jingyun</p> <p>2009-01-01</p> <p>The increase of biodiversity from poles to equator is one of the most pervasive features of nature. For 2 centuries since von Humboldt, Wallace, and Darwin, biogeographers and ecologists have investigated the environmental and historical factors that determine the latitudinal gradient of <span class="hlt">species</span> diversity, but the underlying mechanisms remain poorly understood. The recently proposed metabolic theory of ecology (MTE) aims to explain ecological patterns and processes, including geographical patterns of <span class="hlt">species</span> richness, in terms of the effects of temperature and body size on the metabolism of organisms. Here we use 2 comparable databases of <span class="hlt">tree</span> distributions in eastern Asia and North America to investigate the roles of environmental temperature and spatial scale in shaping geographical patterns of <span class="hlt">species</span> diversity. We find that number of <span class="hlt">species</span> increases exponentially with environmental temperature as predicted by the MTE, and so does the rate of spatial turnover in <span class="hlt">species</span> composition (slope of the <span class="hlt">species</span>-area relationship). The magnitude of temperature dependence of <span class="hlt">species</span> richness increases with spatial scale. Moreover, the relationship between <span class="hlt">species</span> richness and temperature is much steeper in eastern Asia than in North America: in cold climates at high latitudes there are more <span class="hlt">tree</span> <span class="hlt">species</span> in North America, but the reverse is true in warmer climates at lower latitudes. These patterns provide evidence that the kinetics of ecological and evolutionary processes play a major role in the latitudinal pattern of biodiversity. PMID:19628692</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3626689','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3626689"><span id="translatedtitle">Winning and Losing <span class="hlt">Tree</span> <span class="hlt">Species</span> of Reassembly in Minnesota’s Mixed and Broadleaf Forests</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hanberry, Brice B.; Palik, Brian J.; He, Hong S.</p> <p>2013-01-01</p> <p>We examined reassembly of winning and losing <span class="hlt">tree</span> <span class="hlt">species</span>, <span class="hlt">species</span> traits including shade and fire tolerance, and associated disturbance filters and forest ecosystem types due to rapid forest change in the Great Lakes region since 1850. We identified winning and losing <span class="hlt">species</span> by changes in composition, distribution, and site factors between historical and current surveys in Minnesota’s mixed and broadleaf forests. In the Laurentian Mixed Forest, shade-intolerant aspen replaced shade-intolerant tamarack as the most dominant <span class="hlt">tree</span> <span class="hlt">species</span>. Fire-tolerant white pine and jack pine decreased, whereas shade-tolerant ashes, maples, and white cedar increased. In the Eastern Broadleaf Forest, fire-tolerant white oaks and red oaks decreased, while shade-tolerant ashes, American basswood, and maples increased. Tamarack, pines, and oaks have become restricted to sites with either wetter or sandier and drier soils due to increases in aspen and shade-tolerant, fire-sensitive <span class="hlt">species</span> on mesic sites. The proportion of shade-tolerant <span class="hlt">species</span> increased in both regions, but selective harvest reduced the applicability of functional groups alone to specify winners and losers. Harvest and existing forestry practices supported aspen dominance in mixed forests, although without aspen forestry and with fire suppression, mixed forests will transition to a greater composition of shade-tolerant <span class="hlt">species</span>, converging to forests similar to broadleaf forests. A functional group framework provided a perspective of winning and losing <span class="hlt">species</span> and traits, selective filters, and forest ecosystems that can be generalized to other regions, regardless of <span class="hlt">species</span> identity. PMID:23613911</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/16995629','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/16995629"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> effects on decomposition and forest floor dynamics in a common garden.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hobbie, Sarah E; Reich, Peter B; Oleksyn, Jacek; Ogdahl, Megan; Zytkowiak, Roma; Hale, Cynthia; Karolewski, Piotr</p> <p>2006-09-01</p> <p>We studied the effects of <span class="hlt">tree</span> <span class="hlt">species</span> on leaf litter decomposition and forest floor dynamics in a common garden experiment of 14 <span class="hlt">tree</span> <span class="hlt">species</span> (Abies alba, Acer platanoides, Acer pseudoplatanus, Betula pendula, Carpinus betulus, Fagus sylvatica, Larix decidua, Picea abies, Pinus nigra, Pinus sylvestris, Pseudotsuga menziesii, Quercus robur, Quercus rubra, and Tilia cordata) in southwestern Poland. We used three simultaneous litter bag experiments to tease apart <span class="hlt">species</span> effects on decomposition via leaf litter chemistry vs. effects on the decomposition environment. Decomposition rates of litter in its plot of origin were negatively correlated with litter lignin and positively correlated with mean annual soil temperature (MAT(soil)) across <span class="hlt">species</span>. Likewise, decomposition of a common litter type across all plots was positively associated with MAT(soil), and decomposition of litter from all plots in a common plot was negatively related to litter lignin but positively related to litter Ca. Taken together, these results indicate that <span class="hlt">tree</span> <span class="hlt">species</span> influenced microbial decomposition primarily via differences in litter lignin (and secondarily, via differences in litter Ca), with high-lignin (and low-Ca) <span class="hlt">species</span> decomposing most slowly, and by affecting MAT(soil), with warmer plots exhibiting more rapid decomposition. In addition to litter bag experiments, we examined forest floor dynamics in each plot by mass balance, since earthworms were a known component of these forest stands and their access to litter in litter bags was limited. Forest floor removal rates estimated from mass balance were positively related to leaf litter Ca (and unrelated to decay rates obtained using litter bags). Litter Ca, in turn, was positively related to the abundance of earthworms, particularly Lumbricus terrestris. Thus, while <span class="hlt">species</span> influence microbially mediated decomposition primarily through differences in litter lignin, differences among <span class="hlt">species</span> in litter Ca are most important in</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012JGRG..117.0N16Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012JGRG..117.0N16Z"><span id="translatedtitle">Large difference of inhibitive effect of nitrogen deposition on soil methane oxidation between plantations with N-fixing <span class="hlt">tree</span> <span class="hlt">species</span> and non-N-fixing <span class="hlt">tree</span> <span class="hlt">species</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zhang, Wei; Zhu, Xiaomin; Liu, Lei; Fu, Shenglei; Chen, Hao; Huang, Juan; Lu, Xiankai; Liu, Zhanfeng; Mo, Jiangming</p> <p>2012-12-01</p> <p>The responses of soil methane (CH4) net fluxes to nitrogen (N) addition in a N-fixing <span class="hlt">tree</span> <span class="hlt">species</span> (Acacia auriculiformis (AA)) and a non-N-fixing <span class="hlt">tree</span> <span class="hlt">species</span> (Eucalyptus citriodora (EU)) plantation were studied in southern China. Treatments were conducted at each plantation with three N levels (0, 50, and 100 kg N ha-1 yr-1 for control, medium-N, and high-N treatment, respectively, abbreviated as C, MN, and HN). From August 2010 to July 2011, CH4 flux was measured biweekly using a static chamber and gas chromatography technique. The soils of both sites acted as sink of atmospheric CH4. The CH4 uptake rate in control of the AA site (36.3 ± 3.2 μg CH4-C m-2 h-1) was greater than that of the EU plantation (29.9 ± 0.9 μg CH4-C m-2 h-1). In the AA plantation, the averaged rates of CH4 uptake for the MN (28.6 ± 2.3 μg CH4-C m-2 h-1) and HN treatment (23.8 ± 2.8 μg CH4-C m-2 h-1) were decreased by 21% and 35%, respectively, compared to the control. However, there was no change of soil CH4 uptake between N-treated plots and the controls in the EU site. Our results indicated that there might be large difference of inhibitive effect of N deposition on soil CH4 oxidation between the AA and EU plantations. The projected increase of N deposition would weaken the capability of N-fixing <span class="hlt">tree</span> <span class="hlt">species</span> plantations for atmospheric CH4 sink in tropical and subtropical regions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/20472645','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/20472645"><span id="translatedtitle">The influence of mixed <span class="hlt">tree</span> plantations on the nutrition of individual <span class="hlt">species</span>: a review.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Richards, Anna E; Forrester, David I; Bauhus, Jürgen; Scherer-Lorenzen, Michael</p> <p>2010-09-01</p> <p>Productivity of <span class="hlt">tree</span> plantations is a function of the supply, capture and efficiency of use of resources, as outlined in the Production Ecology Equation. <span class="hlt">Species</span> interactions in mixed-<span class="hlt">species</span> stands can influence each of these variables. The importance of resource-use efficiency in determining forest productivity has been clearly demonstrated in monocultures; however, substantial knowledge gaps remain for mixtures. This review examines how the physiology and morphology of a given <span class="hlt">species</span> can vary depending on whether it grows in a mixture or monoculture. We outline how physiological and morphological shifts within <span class="hlt">species</span>, resulting from interactions in mixtures, may influence the three variables of the Production Ecology Equation, with an emphasis on nutrient resources [nitrogen (N) and phosphorus (P)]. These include (i) resource availability, including soil nutrient mineralization, N₂ fixation and litter decomposition; (ii) proportion of resources captured, resulting from shifts in spatial, temporal and chemical patterns of root dynamics; (iii) resource-use efficiency. We found that more than 50% of mixed-<span class="hlt">species</span> studies report a shift to greater above-ground nutrient content of <span class="hlt">species</span> grown in mixtures compared to monocultures, indicating an increase in the proportion of resources captured from a site. Secondly, a meta-analysis showed that foliar N concentrations significantly increased for a given <span class="hlt">species</span> in a mixture containing N₂-fixing <span class="hlt">species</span>, compared to a monoculture, suggesting higher rates of photosynthesis and greater resource-use efficiency. Significant shifts in N- and P-use efficiencies of a given <span class="hlt">species</span>, when grown in a mixture compared to a monoculture, occurred in over 65% of studies where resource-use efficiency could be calculated. Such shifts can result from changes in canopy photosynthetic capacities, changes in carbon allocation or changes to foliar nutrient residence times of <span class="hlt">species</span> in a mixture. We recommend that future research</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70025565','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70025565"><span id="translatedtitle">Impacts of the Brown <span class="hlt">Tree</span> Snake: Patterns of Decline and <span class="hlt">Species</span> Persistence in Guam's Avifauna</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Wiles, G.J.; Bart, J.; Beck, R.E., Jr.; Aguon, C.F.</p> <p>2003-01-01</p> <p>Predation by brown <span class="hlt">tree</span> snakes (Boiga irregularis) devastated the avifauna of Guam in the Mariana Islands during the last half of the twentieth century, causing the extirpation or serious reduction of most of the island's 25 resident bird <span class="hlt">species</span>. Past studies have provided qualitative descriptions of the decline of native forest birds but have not considered all <span class="hlt">species</span> or presented quantitative analyses. We analyzed two sets of survey data gathered in northern Guam between 1976 and 1998 and reviewed unpublished sources to provide a comprehensive account of the impact of brown <span class="hlt">tree</span> snakes on the island's birds. Our results indicate that 22 <span class="hlt">species</span>, including 17 of 18 native <span class="hlt">species</span>, were severely affected by snakes. Twelve <span class="hlt">species</span> were likely extirpated as breeding residents on the main island, 8 others experienced declines of ???90% throughout the island or at least in the north, and 2 were kept at reduced population levels during all or much of the study. Declines of ???90% occurred rapidly, averaging just 8.9 years along three roadside survey routes combined and 1.6 years at a 100-ha forested study site. Declines in northern Guam were also relatively synchronous and occurred from about 1976 to 1986 for most <span class="hlt">species</span>. The most important factor predisposing a <span class="hlt">species</span> to coexistence with brown <span class="hlt">tree</span> snakes was its ability to nest and roost at locations where snakes were uncommon. Large clutch size and large body size were also related to longer persistence times, although large body size appeared to delay, but not prevent, extirpation. Our results draw attention to the enormous detrimental impact that brown <span class="hlt">tree</span> snakes are likely to have upon invading new areas. Increased containment efforts on Guam are needed to prevent further colonizations, but a variety of additional management efforts would also benefit the island's remaining bird populations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/283030','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/283030"><span id="translatedtitle">Anatomical, chemical, and ecological factors affecting <span class="hlt">tree</span> <span class="hlt">species</span> choice in dendrochemistry studies</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Cutter, B.E.; Guyette, R.P.</p> <p>1993-07-01</p> <p>Recently, element concentrations in <span class="hlt">tree</span> rings have been used to monitor metal contamination, fertilization, and the effects of acid precipitation on soils. This has stimulated interest in which <span class="hlt">tree</span> <span class="hlt">species</span> may be suitable for use in studies of long-term trends in environmental chemistry. Potential radial translocation of elements across living boundaries can be a confounding factor in assessing environmental change. The selection of <span class="hlt">species</span> which minimizes radial translocation of elements can be critical to the success of dendrochemical research. Criteria for selection of <span class="hlt">species</span> with characteristics favorable for dendrochemical analysis are categorized into (1) habitat-based factors, (2) xylem-based factors, and (3) element-based factors. A wide geographic range and ecological amplitude provide an advantage in calibration and better controls on the effects of soil chemistry. The most important xylem-based criteria are heartwood moisture content, permeability, and the nature of the sapwood-heartwood transition. The element of interest is important in determining suitable <span class="hlt">tree</span> <span class="hlt">species</span> because all elements are not equally mobile or detectable in the xylem. Ideally, the <span class="hlt">tree</span> <span class="hlt">species</span> selected for dendrochemical study will be long-lived, grow on a wide range of sites over a large geographic distribution, have a distinct heartwood with a low number of rings in the sapwood, a low heartwood moisture content, and have low radial permeability. Recommended temperate zone North American <span class="hlt">species</span> include white oak (Quercus alba L.), post oak (Q. stellate Wangenh.), eastern redcedar (funiperus virginiana L.), old-growth Douglas-fir [Pseudoaugu menziesii (Mirb.) Franco] and big sagebrush (Artemisia tridentata Nutt.). In addition, <span class="hlt">species</span> such as bristlecone pine (Pinus aristata Engelm. syn. longaeva), old-growth redwood [Sequoia sempervirens (D. Don) Endl.], and giant sequoia [S. gigantea (Lindl.) Deene] may be suitable for local purposes. 118 refs., 2 tabs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21302839','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21302839"><span id="translatedtitle">The trait contribution to wood decomposition rates of 15 Neotropical <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>van Geffen, Koert G; Poorter, Lourens; Sass-Klaassen, Ute; van Logtestijn, Richard S P; Cornelissen, Johannes H C</p> <p>2010-12-01</p> <p>The decomposition of dead wood is a critical uncertainty in models of the global carbon cycle. Despite this, relatively few studies have focused on dead wood decomposition, with a strong bias to higher latitudes. Especially the effect of interspecific variation in <span class="hlt">species</span> traits on differences in wood decomposition rates remains unknown. In order to fill these gaps, we applied a novel method to study long-term wood decomposition of 15 <span class="hlt">tree</span> <span class="hlt">species</span> in a Bolivian semi-evergreen tropical moist forest. We hypothesized that interspecific differences in <span class="hlt">species</span> traits are important drivers of variation in wood decomposition rates. Wood decomposition rates (fractional mass loss) varied between 0.01 and 0.31 yr(-1). We measured 10 different chemical, anatomical, and morphological traits for all <span class="hlt">species</span>. The <span class="hlt">species</span>' average traits were useful predictors of wood decomposition rates, particularly the average diameter (dbh) of the <span class="hlt">tree</span> <span class="hlt">species</span> (R2 = 0.41). Lignin concentration further increased the proportion of explained inter-specific variation in wood decomposition (both negative relations, cumulative R2 = 0.55), although it did not significantly explain variation in wood decomposition rates if considered alone. When dbh values of the actual dead <span class="hlt">trees</span> sampled for decomposition rate determination were used as a predictor variable, the final model (including dead <span class="hlt">tree</span> dbh and lignin concentration) explained even more variation in wood decomposition rates (R2 = 0.71), underlining the importance of dbh in wood decomposition. Other traits, including wood density, wood anatomical traits, macronutrient concentrations, and the amount of phenolic extractives could not significantly explain the variation in wood decomposition rates. The surprising results of this multi-<span class="hlt">species</span> study, in which for the first time a large set of traits is explicitly linked to wood decomposition rates, merits further testing in other forest ecosystems. PMID:21302839</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015GPC...133..298B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015GPC...133..298B"><span id="translatedtitle">Oxygen isotopes in <span class="hlt">tree</span> rings show good coherence between <span class="hlt">species</span> and sites in Bolivia</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Baker, Jessica C. A.; Hunt, Sarah F. P.; Clerici, Santiago J.; Newton, Robert J.; Bottrell, Simon H.; Leng, Melanie J.; Heaton, Timothy H. E.; Helle, Gerhard; Argollo, Jaime; Gloor, Manuel; Brienen, Roel J. W.</p> <p>2015-10-01</p> <p>A <span class="hlt">tree</span> ring oxygen isotope (δ18OTR) chronology developed from one <span class="hlt">species</span> (Cedrela odorata) growing in a single site has been shown to be a sensitive proxy for rainfall over the Amazon Basin, thus allowing reconstructions of precipitation in a region where meteorological records are short and scarce. Although these results suggest that there should be large-scale (> 100 km) spatial coherence of δ18OTR records in the Amazon, this has not been tested. Furthermore, it is of interest to investigate whether other, possibly longer-lived, <span class="hlt">species</span> similarly record interannual variation of Amazon precipitation, and can be used to develop climate sensitive isotope chronologies. In this study, we measured δ18O in <span class="hlt">tree</span> rings from seven lowland and one highland <span class="hlt">tree</span> <span class="hlt">species</span> from Bolivia. We found that cross-dating with δ18OTR gave more accurate <span class="hlt">tree</span> ring dates than using ring width. Our "isotope cross-dating approach" is confirmed with radiocarbon "bomb-peak" dates, and has the potential to greatly facilitate development of δ18OTR records in the tropics, identify dating errors, and check annual ring formation in tropical <span class="hlt">trees</span>. Six of the seven lowland <span class="hlt">species</span> correlated significantly with C. odorata, showing that variation in δ18OTR has a coherent imprint across very different <span class="hlt">species</span>, most likely arising from a dominant influence of source water δ18O on δ18OTR. In addition we show that δ18OTR series cohere over large distances, within and between <span class="hlt">species</span>. Comparison of two C. odorata δ18OTR chronologies from sites several hundreds of kilometres apart showed a very strong correlation (r = 0.80, p < 0.001, 1901-2001), and a significant (but weaker) relationship was found between lowland C. odorata <span class="hlt">trees</span> and a Polylepis tarapacana <span class="hlt">tree</span> growing in the distant Altiplano (r = 0.39, p < 0.01, 1931-2001). This large-scale coherence of δ18OTR records is probably triggered by a strong spatial coherence in precipitation δ18O due to large-scale controls. These results</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26663665','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26663665"><span id="translatedtitle">Drought stress limits the geographic ranges of two <span class="hlt">tree</span> <span class="hlt">species</span> via different physiological mechanisms.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Anderegg, Leander D L; HilleRisLambers, Janneke</p> <p>2016-03-01</p> <p>Range shifts are among the most ubiquitous ecological responses to anthropogenic climate change and have large consequences for ecosystems. Unfortunately, the ecophysiological forces that constrain range boundaries are poorly understood, making it difficult to mechanistically project range shifts. To explore the physiological mechanisms by which drought stress controls dry range boundaries in <span class="hlt">trees</span>, we quantified elevational variation in drought tolerance and in drought avoidance-related functional traits of a widespread gymnosperm (ponderosa pine - Pinus ponderosa) and angiosperm (trembling aspen - Populus tremuloides) <span class="hlt">tree</span> <span class="hlt">species</span> in the southwestern USA. Specifically, we quantified <span class="hlt">tree-to-tree</span> variation in growth, water stress (predawn and midday xylem tension), drought avoidance traits (branch conductivity, leaf/needle size, <span class="hlt">tree</span> height, leaf area-to-sapwood area ratio), and drought tolerance traits (xylem resistance to embolism, hydraulic safety margin, wood density) at the range margins and range center of each <span class="hlt">species</span>. Although water stress increased and growth declined strongly at lower range margins of both <span class="hlt">species</span>, ponderosa pine and aspen showed contrasting patterns of clinal trait variation. Trembling aspen increased its drought tolerance at its dry range edge by growing stronger but more carbon dense branch and leaf tissues, implying an increased cost of growth at its range boundary. By contrast, ponderosa pine showed little elevational variation in drought-related traits but avoided drought stress at low elevations by limiting transpiration through stomatal closure, such that its dry range boundary is associated with limited carbon assimilation even in average climatic conditions. Thus, the same climatic factor (drought) may drive range boundaries through different physiological mechanisms - a result that has important implications for process-based modeling approaches to <span class="hlt">tree</span> biogeography. Further, we show that comparing intraspecific patterns of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014EGUGA..16.2533C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014EGUGA..16.2533C"><span id="translatedtitle">Different <span class="hlt">tree</span> <span class="hlt">species</span> affect soil respiration spatial distribution in a subtropical forest of southern Taiwan</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chiang, Po-Neng; Yu, Jui-Chu; Wang, Ya-nan; Lai, Yen-Jen</p> <p>2014-05-01</p> <p>Global forests contain 69% of total carbon stored in forest soil and litter. But the carbon storage ability and release rate of warming gases of forest soil also affect global climate change. Soil carbon cycling processes are paid much attention by ecological scientists and policy makers because of the possibility of carbon being stored in soil via land use management. Soil respiration contributed large part of terrestrial carbon flux, but the relationship of soil respiration and climate change was still obscurity. Most of soil respiration researches focus on template and tropical area, little was known that in subtropical area. Afforestation is one of solutions to mitigate CO2 increase and to sequestrate CO2 in <span class="hlt">tree</span> and soil. Therefore, the objective of this study is to clarify the relationship of <span class="hlt">tree</span> <span class="hlt">species</span> and soil respiration distribution in subtropical broad-leaves plantation in southern Taiwan. The research site located on southern Taiwan was sugarcane farm before 2002. The sugarcane was removed and fourteen broadleaved <span class="hlt">tree</span> <span class="hlt">species</span> were planted in 2002-2005. Sixteen plots (250m*250m) were set on 1 km2 area, each plot contained 4 subplots (170m2). The forest biomass (i.e. <span class="hlt">tree</span> height, DBH) understory biomass, litter, and soil C were measured and analyzed at 2011 to 2012. Soil respiration measurement was sampled in each subplot in each month. The soil belongs to Entisol with over 60% of sandstone. The soil pH is 5.5 with low base cations because of high sand percentage. Soil carbon storage showed significantly negative relationship with soil bulk density (p<0.001) in research site. The differences of distribution of live <span class="hlt">tree</span> C pool among 16 plots were affected by growth characteristic of <span class="hlt">tree</span> <span class="hlt">species</span>. Data showed that the accumulation amount of litterfall was highest in December to February and lowest in June. Different <span class="hlt">tree</span> <span class="hlt">species</span> planted in 16 plots, resulting in high spatial variation of litterfall amount. It also affected total amount of litterfall</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li class="active"><span>12</span></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_12 --> <div id="page_13" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li class="active"><span>13</span></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="241"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4748750','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4748750"><span id="translatedtitle">SimPhy: Phylogenomic Simulation of Gene, Locus, and <span class="hlt">Species</span> <span class="hlt">Trees</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David</p> <p>2016-01-01</p> <p>We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to <span class="hlt">species</span> <span class="hlt">tree</span>/gene <span class="hlt">tree</span> discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of <span class="hlt">species</span>, locus, and gene <span class="hlt">trees</span> is governed by global and local parameters (e.g., genome-wide, <span class="hlt">species</span>-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large <span class="hlt">trees</span>, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27028757','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27028757"><span id="translatedtitle">Mechanism Underlying the Spatial Pattern Formation of Dominant <span class="hlt">Tree</span> <span class="hlt">Species</span> in a Natural Secondary Forest.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Jia, Guodong; Yu, Xinxiao; Fan, Dengxing; Jia, Jianbo</p> <p>2016-01-01</p> <p>Studying the spatial pattern of plant <span class="hlt">species</span> may provide significant insights into processes and mechanisms that maintain stand stability. To better understand the dynamics of naturally regenerated secondary forests, univariate and bivariate Ripley's L(r) functions were employed to evaluate intra-/interspecific relationships of four dominant <span class="hlt">tree</span> <span class="hlt">species</span> (Populus davidiana, Betula platyphylla, Larix gmelinii and Acer mono) and to distinguish the underlying mechanism of spatial distribution. The results showed that the distribution of soil, water and nutrients was not fragmented but presented clear gradients. An overall aggregated distribution existed at most distances. No correlation was found between the spatial pattern of soil conditions and that of <span class="hlt">trees</span>. Both positive and negative intra- and interspecific relationships were found between different DBH classes at various distances. Large <span class="hlt">trees</span> did not show systematic inhibition of the saplings. By contrast, the inhibition intensified as the height differences increased between the compared pairs. Except for Larix, universal inhibition of saplings by upper layer <span class="hlt">trees</span> occurred among other <span class="hlt">species</span>, and this reflected the vertical competition for light. Therefore, we believe that competition for light rather than soil nutrients underlies the mechanism driving the formation of stand spatial pattern in the rocky mountainous areas examined. PMID:27028757</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26526427','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26526427"><span id="translatedtitle">SimPhy: Phylogenomic Simulation of Gene, Locus, and <span class="hlt">Species</span> <span class="hlt">Trees</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David</p> <p>2016-03-01</p> <p>We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to <span class="hlt">species</span> <span class="hlt">tree</span>/gene <span class="hlt">tree</span> discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of <span class="hlt">species</span>, locus, and gene <span class="hlt">trees</span> is governed by global and local parameters (e.g., genome-wide, <span class="hlt">species</span>-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large <span class="hlt">trees</span>, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4814042','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4814042"><span id="translatedtitle">Mechanism Underlying the Spatial Pattern Formation of Dominant <span class="hlt">Tree</span> <span class="hlt">Species</span> in a Natural Secondary Forest</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jia, Guodong; Yu, Xinxiao; Fan, Dengxing; Jia, Jianbo</p> <p>2016-01-01</p> <p>Studying the spatial pattern of plant <span class="hlt">species</span> may provide significant insights into processes and mechanisms that maintain stand stability. To better understand the dynamics of naturally regenerated secondary forests, univariate and bivariate Ripley’s L(r) functions were employed to evaluate intra-/interspecific relationships of four dominant <span class="hlt">tree</span> <span class="hlt">species</span> (Populus davidiana, Betula platyphylla, Larix gmelinii and Acer mono) and to distinguish the underlying mechanism of spatial distribution. The results showed that the distribution of soil, water and nutrients was not fragmented but presented clear gradients. An overall aggregated distribution existed at most distances. No correlation was found between the spatial pattern of soil conditions and that of <span class="hlt">trees</span>. Both positive and negative intra- and interspecific relationships were found between different DBH classes at various distances. Large <span class="hlt">trees</span> did not show systematic inhibition of the saplings. By contrast, the inhibition intensified as the height differences increased between the compared pairs. Except for Larix, universal inhibition of saplings by upper layer <span class="hlt">trees</span> occurred among other <span class="hlt">species</span>, and this reflected the vertical competition for light. Therefore, we believe that competition for light rather than soil nutrients underlies the mechanism driving the formation of stand spatial pattern in the rocky mountainous areas examined. PMID:27028757</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23360009','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23360009"><span id="translatedtitle">Floristic diversity of regenerated <span class="hlt">tree</span> <span class="hlt">species</span> in Dipterocarp forests in Western Ghats of Karnataka, India.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Prasad, A G Devi; Al-Sagheer, Nageeb A</p> <p>2012-07-01</p> <p>The research was focused on exploring the structure, diversity and form of regeneration process of the Dipterocarp forests in Western Ghats in relation to environmental factors. Eight populations in the distribution range of Dipterocarp forests were selected. In each population 32 plots of 2mx2m were laid down randomly. Atotal of 1243 seedlings < or = 10 cm dbh (diameter at breast height) belonging to 99 <span class="hlt">species</span> and 48 families were recorded. The number of regenerated <span class="hlt">tree</span> <span class="hlt">species</span> was found to be high in the populations of Mudigere (40), Sakleshpura (40) and Makuta (39), which are characterized by favorable locality factors and lower disturbances. The highest similarity index in <span class="hlt">species</span> composition was recorded between the populations of Sampaje in Kodagu district and Gundya in Dakshina Kannada (60%) whereas the lowest similarity index was observed between the population of Sringeri in Chikmagalore and Sampaje (53%) and Gundya and Makuta (35%) in Kodagu district. Dipterocarpus indicus was found to be dominant among the regenerated <span class="hlt">tree</span> <span class="hlt">species</span> in all the sites studied except Gundy and Sampaje. The frequencies of regeneration classes (seedlings, saplings, poles and adult <span class="hlt">trees</span>) were shaped as inverse J curve indicating the normal regeneration pattern under the present disturbance. The average disturbance of litter collection, grazing, fire, weeds and canopy opening were significant among different populations (p < or = 0.05). Negative correlation was observed between disturbance and <span class="hlt">species</span> richness, number of individuals and density. PMID:23360009</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26702442','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26702442"><span id="translatedtitle">Estimating the global conservation status of more than 15,000 Amazonian <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ter Steege, Hans; Pitman, Nigel C A; Killeen, Timothy J; Laurance, William F; Peres, Carlos A; Guevara, Juan Ernesto; Salomão, Rafael P; Castilho, Carolina V; Amaral, Iêda Leão; de Almeida Matos, Francisca Dionízia; de Souza Coelho, Luiz; Magnusson, William E; Phillips, Oliver L; de Andrade Lima Filho, Diogenes; de Jesus Veiga Carim, Marcelo; Irume, Mariana Victória; Martins, Maria Pires; Molino, Jean-François; Sabatier, Daniel; Wittmann, Florian; López, Dairon Cárdenas; da Silva Guimarães, José Renan; Mendoza, Abel Monteagudo; Vargas, Percy Núñez; Manzatto, Angelo Gilberto; Reis, Neidiane Farias Costa; Terborgh, John; Casula, Katia Regina; Montero, Juan Carlos; Feldpausch, Ted R; Honorio Coronado, Euridice N; Montoya, Alvaro Javier Duque; Zartman, Charles Eugene; Mostacedo, Bonifacio; Vasquez, Rodolfo; Assis, Rafael L; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Camargo, José Luís; Laurance, Susan G W; Nascimento, Henrique Eduardo Mendonça; Marimon, Beatriz S; Marimon, Ben-Hur; Costa, Flávia; Targhetta, Natalia; Vieira, Ima Célia Guimarães; Brienen, Roel; Castellanos, Hernán; Duivenvoorden, Joost F; Mogollón, Hugo F; Piedade, Maria Teresa Fernandez; Aymard C, Gerardo A; Comiskey, James A; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Diaz, Pablo Roberto Stevenson; Vincentini, Alberto; Emilio, Thaise; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Alonso, Alfonso; Dallmeier, Francisco; Ferreira, Leandro Valle; Neill, David; Araujo-Murakami, Alejandro; Arroyo, Luzmila; Carvalho, Fernanda Antunes; Souza, Fernanda Coelho; do Amaral, Dário Dantas; Gribel, Rogerio; Luize, Bruno Garcia; Pansonato, Marcelo Petrati; Venticinque, Eduardo; Fine, Paul; Toledo, Marisol; Baraloto, Chris; Cerón, Carlos; Engel, Julien; Henkel, Terry W; Jimenez, Eliana M; Maas, Paul; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Revilla, Juan David Cardenas; Silveira, Marcos; Stropp, Juliana; Thomas-Caesar, Raquel; Baker, Tim R; Daly, Doug; Paredes, Marcos Ríos; da Silva, Naara Ferreira; Fuentes, Alfredo; Jørgensen, Peter Møller; Schöngart, Jochen; Silman, Miles R; Arboleda, Nicolás Castaño; Cintra, Bruno Barçante Ladvocat; Valverde, Fernando Cornejo; Di Fiore, Anthony; Phillips, Juan Fernando; van Andel, Tinde R; von Hildebrand, Patricio; Barbosa, Edelcilio Marques; de Matos Bonates, Luiz Carlos; de Castro, Deborah; de Sousa Farias, Emanuelle; Gonzales, Therany; Guillaumet, Jean-Louis; Hoffman, Bruce; Malhi, Yadvinder; de Andrade Miranda, Ires Paula; Prieto, Adriana; Rudas, Agustín; Ruschell, Ademir R; Silva, Natalino; Vela, César I A; Vos, Vincent A; Zent, Eglée L; Zent, Stanford; Cano, Angela; Nascimento, Marcelo Trindade; Oliveira, Alexandre A; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Sierra, Rodrigo; Tirado, Milton; Medina, Maria Natalia Umaña; van der Heijden, Geertje; Torre, Emilio Vilanova; Vriesendorp, Corine; Wang, Ophelia; Young, Kenneth R; Baider, Claudia; Balslev, Henrik; de Castro, Natalia; Farfan-Rios, William; Ferreira, Cid; Mendoza, Casimiro; Mesones, Italo; Torres-Lezama, Armando; Giraldo, Ligia Estela Urrego; Villarroel, Daniel; Zagt, Roderick; Alexiades, Miguel N; Garcia-Cabrera, Karina; Hernandez, Lionel; Huamantupa-Chuquimaco, Isau; Milliken, William; Cuenca, Walter Palacios; Pansini, Susamar; Pauletto, Daniela; Arevalo, Freddy Ramirez; Sampaio, Adeilza Felipe; Valderrama Sandoval, Elvis H; Gamarra, Luis Valenzuela</p> <p>2015-11-01</p> <p>Estimates of extinction risk for Amazonian plant and animal <span class="hlt">species</span> are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian <span class="hlt">tree</span> <span class="hlt">species</span> are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant <span class="hlt">species</span> on Earth by 22%. We show that the trends observed in Amazonia apply to <span class="hlt">trees</span> throughout the tropics, and we predict that most of the world's >40,000 tropical <span class="hlt">tree</span> <span class="hlt">species</span> now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened <span class="hlt">species</span> if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century. PMID:26702442</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4681336','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4681336"><span id="translatedtitle">Estimating the global conservation status of more than 15,000 Amazonian <span class="hlt">tree</span> <span class="hlt">species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>ter Steege, Hans; Pitman, Nigel C. A.; Killeen, Timothy J.; Laurance, William F.; Peres, Carlos A.; Guevara, Juan Ernesto; Salomão, Rafael P.; Castilho, Carolina V.; Amaral, Iêda Leão; de Almeida Matos, Francisca Dionízia; de Souza Coelho, Luiz; Magnusson, William E.; Phillips, Oliver L.; de Andrade Lima Filho, Diogenes; de Jesus Veiga Carim, Marcelo; Irume, Mariana Victória; Martins, Maria Pires; Molino, Jean-François; Sabatier, Daniel; Wittmann, Florian; López, Dairon Cárdenas; da Silva Guimarães, José Renan; Mendoza, Abel Monteagudo; Vargas, Percy Núñez; Manzatto, Angelo Gilberto; Reis, Neidiane Farias Costa; Terborgh, John; Casula, Katia Regina; Montero, Juan Carlos; Feldpausch, Ted R.; Honorio Coronado, Euridice N.; Montoya, Alvaro Javier Duque; Zartman, Charles Eugene; Mostacedo, Bonifacio; Vasquez, Rodolfo; Assis, Rafael L.; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Camargo, José Luís; Laurance, Susan G. W.; Nascimento, Henrique Eduardo Mendonça; Marimon, Beatriz S.; Marimon, Ben-Hur; Costa, Flávia; Targhetta, Natalia; Vieira, Ima Célia Guimarães; Brienen, Roel; Castellanos, Hernán; Duivenvoorden, Joost F.; Mogollón, Hugo F.; Piedade, Maria Teresa Fernandez; Aymard C., Gerardo A.; Comiskey, James A.; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Diaz, Pablo Roberto Stevenson; Vincentini, Alberto; Emilio, Thaise; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Alonso, Alfonso; Dallmeier, Francisco; Ferreira, Leandro Valle; Neill, David; Araujo-Murakami, Alejandro; Arroyo, Luzmila; Carvalho, Fernanda Antunes; Souza, Fernanda Coelho; do Amaral, Dário Dantas; Gribel, Rogerio; Luize, Bruno Garcia; Pansonato, Marcelo Petrati; Venticinque, Eduardo; Fine, Paul; Toledo, Marisol; Baraloto, Chris; Cerón, Carlos; Engel, Julien; Henkel, Terry W.; Jimenez, Eliana M.; Maas, Paul; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Revilla, Juan David Cardenas; Silveira, Marcos; Stropp, Juliana; Thomas-Caesar, Raquel; Baker, Tim R.; Daly, Doug; Paredes, Marcos Ríos; da Silva, Naara Ferreira; Fuentes, Alfredo; Jørgensen, Peter Møller; Schöngart, Jochen; Silman, Miles R.; Arboleda, Nicolás Castaño; Cintra, Bruno Barçante Ladvocat; Valverde, Fernando Cornejo; Di Fiore, Anthony; Phillips, Juan Fernando; van Andel, Tinde R.; von Hildebrand, Patricio; Barbosa, Edelcilio Marques; de Matos Bonates, Luiz Carlos; de Castro, Deborah; de Sousa Farias, Emanuelle; Gonzales, Therany; Guillaumet, Jean-Louis; Hoffman, Bruce; Malhi, Yadvinder; de Andrade Miranda, Ires Paula; Prieto, Adriana; Rudas, Agustín; Ruschell, Ademir R.; Silva, Natalino; Vela, César I. A.; Vos, Vincent A.; Zent, Eglée L.; Zent, Stanford; Cano, Angela; Nascimento, Marcelo Trindade; Oliveira, Alexandre A.; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Sierra, Rodrigo; Tirado, Milton; Medina, Maria Natalia Umaña; van der Heijden, Geertje; Torre, Emilio Vilanova; Vriesendorp, Corine; Wang, Ophelia; Young, Kenneth R.; Baider, Claudia; Balslev, Henrik; de Castro, Natalia; Farfan-Rios, William; Ferreira, Cid; Mendoza, Casimiro; Mesones, Italo; Torres-Lezama, Armando; Giraldo, Ligia Estela Urrego; Villarroel, Daniel; Zagt, Roderick; Alexiades, Miguel N.; Garcia-Cabrera, Karina; Hernandez, Lionel; Huamantupa-Chuquimaco, Isau; Milliken, William; Cuenca, Walter Palacios; Pansini, Susamar; Pauletto, Daniela; Arevalo, Freddy Ramirez; Sampaio, Adeilza Felipe; Valderrama Sandoval, Elvis H.; Gamarra, Luis Valenzuela</p> <p>2015-01-01</p> <p>Estimates of extinction risk for Amazonian plant and animal <span class="hlt">species</span> are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian <span class="hlt">tree</span> <span class="hlt">species</span> are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant <span class="hlt">species</span> on Earth by 22%. We show that the trends observed in Amazonia apply to <span class="hlt">trees</span> throughout the tropics, and we predict that most of the world’s >40,000 tropical <span class="hlt">tree</span> <span class="hlt">species</span> now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened <span class="hlt">species</span> if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century. PMID:26702442</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4971193','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4971193"><span id="translatedtitle">The Trichoptera barcode initiative: a strategy for generating a <span class="hlt">species</span>-level <span class="hlt">Tree</span> of Life</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Frandsen, Paul B.; Holzenthal, Ralph W.; Beet, Clare R.; Bennett, Kristi R.; Blahnik, Roger J.; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V.; Collins, Gemma E.; deWaard, Jeremy; Dean, John; Flint, Oliver S.; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D.; Kondratieff, Boris C.; Malicky, Hans; Milton, Megan A.; Morinière, Jérôme; Morse, John C.; Mwangi, François Ngera; Pauls, Steffen U.; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L.; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A.; Zamora-Muñoz, Carmen; Ziesmann, Tanja</p> <p>2016-01-01</p> <p>DNA barcoding was intended as a means to provide <span class="hlt">species</span>-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the <span class="hlt">Tree</span> of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described <span class="hlt">species</span>. Most Trichoptera, as with most of life's <span class="hlt">species</span>, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained <span class="hlt">tree</span> searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the <span class="hlt">tree</span>. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous <span class="hlt">species</span> boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for <span class="hlt">species</span> description. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481793</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/927777','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/927777"><span id="translatedtitle">Managing Commercial <span class="hlt">Tree</span> <span class="hlt">Species</span> for Timber Production and Carbon Sequestration: Management Guidelines and Financial Returns</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Gary D. Kronrad</p> <p>2006-09-19</p> <p>A carbon credit market is developing in the United States. Information is needed by buyers and sellers of carbon credits so that the market functions equitably and efficiently. Analyses have been conducted to determine the optimal forest management regime to employ for each of the major commercial <span class="hlt">tree</span> <span class="hlt">species</span> so that profitability of timber production only or the combination of timber production and carbon sequestration is maximized. Because the potential of a forest ecosystem to sequester carbon depends on the <span class="hlt">tree</span> <span class="hlt">species</span>, site quality and management regimes utilized, analyses have determined how to optimize carbon sequestration by determining how to optimally manage each <span class="hlt">species</span>, given a range of site qualities, discount rates, prices of carbon credits and other economic variables. The effects of a carbon credit market on the method and profitability of forest management, the cost of sequestering carbon, the amount of carbon that can be sequestered, and the amount of timber products produced has been determined.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4255775','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4255775"><span id="translatedtitle">Multispecies Coalescent Analysis of the Early Diversification of Neotropical Primates: Phylogenetic Inference under Strong Gene <span class="hlt">Trees/Species</span> <span class="hlt">Tree</span> Conflict</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Schrago, Carlos G.; Menezes, Albert N.; Furtado, Carolina; Bonvicino, Cibele R.; Seuanez, Hector N.</p> <p>2014-01-01</p> <p>Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene <span class="hlt">trees</span> within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene <span class="hlt">trees</span> within proposed phylogenies is crucial for distinguishing the mean genetic divergence between <span class="hlt">species</span> (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms. 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