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Tropical forests occupy small coral atolls to the vast Amazon basin. They occur across bioregions with different geological and climatic history. Differences in area and bioregional history shape species immigration, extinction and diversification. How this effects local diversity is unclear. The Indonesian archipelago hosts thousands of tree species whose coexistence should depend upon these factors. Using a novel dataset of 215 Indonesian forest plots, across fifteen islands ranging in area from 120 to 785 000 km2, we apply Gaussian mixed effects models to examine the simultaneous effects of environment, earthquake proximity, island area and bioregion upon tree diversity for trees ≥ 10 cm diameter at breast height. We find that tree diversity declines with precipitation seasonality and increases with island area. Accounting for the effects of environment and island area we show that the westernmost bioregion Sunda has greater local diversity than Wallacea, which in turn has greater local diversity than easternmost Sahul. However, when the model includes geological activity (here proximity to major earthquakes), bioregion differences are reduced. Overall, results indicate that multi‐scale, current and historic effects dictate tree diversity. These multi‐scale drivers should not be ignored when studying biodiversity gradients and their impacts upon ecosystem function. [ABSTRACT FROM AUTHOR]

Plant species composition and structural attributes are related to physiographic factors such as slope orientation and topographic position. This relationship is accentuated with increasing seasonality in temperature and precipitation. We quantified the relationship between topography and the taxonomic, functional and phylogenetic community composition of woody species at the northernmost distribution of seasonally dry tropical forests (STDF) in the Americas. We related slope orientation (north-facing vs. south-facing) and position (upper slope vs. lower slope) to the distribution of species, assessed their habitat preference by life stage (juvenile vs. adult) and compared the observed phylogenetic distance of species against random species assemblages. Our results showed the segregation of two species groups in both life stages is related to slope orientation, but not to topographic position. We found a strong habitat association for 68% of the species with both juveniles and adults similarly associated with the same habitat. Slope orientation was related to taxonomic, functional and phylogenetic structure, but it differed in the two life stages. The functional and evolutionary segregation of species between north-facing vs. south-facing habitats indicates that species are non-randomly distributed; suggesting that deterministic mechanisms (e.g. topographic habitat specialisation) are operating at a local scale. Slope orientation drives the species-habitat association, and functional/phylogenetic structure of the northernmost tropical dry forests on the American continent. Juveniles and adults of tree species share similar habitat association patterns, conserving habitat preference. In both life stages, the functional and phylogenetic structure of trees was clearly differentiated between north-facing and south-facing slopes, but similar within each slope. Dry forest tree species are non-randomly distributed among topographic habitats. The contrasting periods of water availability in the soil and solar radiation between slopes have revealed emerging patterns of topographic habitat specialisation. [ABSTRACT FROM AUTHOR]

Mastwatch is a community of observers who share information about mass flowering and mast fruiting events in Sundaland using an online mailing list. The project was started in 2002. Members have contributed observations of 98 independent masting events in Sabah, Kalimantan, Sarawak, Brunei, Sumatra, Peninsular Malaysia, and Singapore. [ABSTRACT FROM AUTHOR]

Abstract: This is the first comprehensive analysis of vascular plant diversity patterns in the Aleutian Islands to identify and quantify the impact of Aleutian Island distance dispersal barriers, geographical, ecological and anthropogenic factors. Data from public Open Access databases, printed floristic accounts, and from collections made by the primary author were used to develop an Aleutian floristic database. The most common plant distribution pattern was “an eastern origin community”, though it compared similarly to the “Western” and “Widespread” distribution pattern. We established an ecological plant community composition class for each island, based on clustering species assemblage dissimilarity measurements (Jaccard Index), and a measurement of phylogenetic dissimilarity (UniFrac). We modelled these composition classes and species richness values in non‐parametric algorithmic models and concepts (data cloning using machine learning, stochastic boosting‐ TreeNet) based on classic and Aleutians‐specific island biogeography hypotheses. Plant species richness is strongly associated with the equilibrium model variables of area and island isolation, as well as distance to the Alaska Peninsula, and island total stream length. Species composition is strongly associated with the landmass groups during the last glacial maximum, maximum island elevation, island isolation and island area. Phylogenetic composition is associated with island area, distance from the islands to the Chukotka Peninsula, maximum island elevation, island geologic age, and island isolation. This study extends the equilibrium theory of island biogeography by including additional drivers of diversity during the Anthropocene, such as the landmass during the LGM, as well as factors that may be related to anthropogenic extinction rate. [ABSTRACT FROM AUTHOR]

The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost‐effective generation of high‐quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia. [ABSTRACT FROM AUTHOR]

The Darwin Core vocabulary is widely used to transmit biodiversity data in the form of simple text files. In order to support expression of biodiversity data in the Resource Description Framework (RDF), a guide was created as a non-normative addition to the Darwin Core standard. This paper describes the major issues that were addressed in the creation of the guide, particularly problems related to adapting terms designed to have literal values for use with IRI references. By making it possible to express millions of existing records as RDF, the guide is an important step towards enabling the biodiversity informatics community to participate in broader Linked Data and Semantic Web efforts. [ABSTRACT FROM AUTHOR]

Darwin-SW (DSW) is an RDF vocabulary designed to complement the Biodiversity Information Standards (TDWG) Darwin Core Standard. DSW is based on a model derived from a community discussion about the relationships among the main Darwin Core classes. DSW creates a new class to accommodate an important aspect of its model that is not currently part of Darwin Core: a class of Tokens, which are forms of evidence. DSW uses Web Ontology Language (OWL) to make assertions about the classes in its model and to define object properties that are used to link instances of those classes. A goal in the creation of DSW was to facilitate consistent markup of biodiversity data so that RDF graphs created by different providers could be easily merged. Accordingly, DSW provides a mechanism for testing whether its terms are being used in a manner consistent with its model. Two transitive object properties enable the creation of simple SPARQL queries that can be used to discover new information about linked resources whose metadata are generated by different providers. The Organism class enables semantic linking of biodiversity resources to vocabularies outside of TDWG that deal with observations and ecological phenomena. [ABSTRACT FROM AUTHOR]

The article discusses the significant role of biodiversity in the evolution. Topics discussed include importance of applying evolutionary principles in conservation and human well-being, fundamental relevance of evolution in the production, maintenance, and future of biodiversity and biodiversity arises from the approach that treats groups of taxa with similar traits as a significant functional unit.

Background: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proofof- concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment. [ABSTRACT FROM AUTHOR]

Assessing risk from a novel pest or pathogen requires knowing which local plant species are susceptible. Empirical data on the local host range of novel pests are usually lacking, but we know that some pests are more likely to attack closely related plant species than species separated by greater evolutionary distance. We use the Global Pest and Disease Database, an internal database maintained by the United States Department of Agriculture Animal and Plant Health Inspection Service - Plant Protection and Quarantine Division (USDA APHIS-PPQ), to evaluate the strength of the phylogenetic signal in host range for nine major groups of plant pests and pathogens. Eight of nine groups showed significant phylogenetic signal in host range. Additionally, pests and pathogens with more known hosts attacked a phylogenetically broader range of hosts. This suggests that easily obtained data - the number of known hosts and the phylogenetic distance between known hosts and other species of interest - can be used to predict which plant species are likely to be susceptible to a particular pest. This can facilitate rapid assessment of risk from novel pests and pathogens when empirical host range data are not yet available and guide efficient collection of empirical data for risk evaluation. [ABSTRACT FROM AUTHOR]

Understanding the causes of spatial variation in species richness is a major research focus of biogeography and macroecology. Gridded environmental data and species richness maps have been used in increasingly sophisticated curve-fitting analyses, but these methods have not brought us much closer to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non-linearity. However, curve-fitting approaches are problematic because most theoretical models in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species’ geographical ranges in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell of the domain. In contrast to curve-fitting analysis, simulation modelling explicitly incorporates the processes believed to be affecting the geographical ranges of species and generates a number of quantitative predictions that can be compared to empirical patterns. We describe three of the ‘control knobs’ for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include the predicted species richness per grid cell, the range size frequency distribution, the simulated phylogeny and simulated geographical ranges of the component species, all of which can be compared to empirical patterns. Challenges to the development of the GSM include the measurement of goodness of fit (GOF) between observed data and model predictions, as well as the estimation, optimization and interpretation of the model parameters. The simulation approach offers new insights into the origin and maintenance of species richness patterns, and may provide a common framework for investigating the effects of contemporary climate, evolutionary history and geometric constraints on global biodiversity gradients. With further development, the GSM has the potential to provide a conceptual bridge between macroecology and historical biogeography. [ABSTRACT FROM AUTHOR]

The taxonomic foundation of a new regional flora or monograph is the reconciliation of preexisting names and taxonomic concepts (i.e., variation in usage of those names). This reconciliation is traditionally done manually, but the availability of taxonomic resources online and of text manipulation software means that some of the work can now be automated, speeding up the development of new taxonomic products. As a contribution to developing a new Flora of Alaska (floraofalaska.org), we have digitized the main preexisting flora (Hultén 1968) and combined it with key online taxonomic name sources (Pan arctic Flora, Flora of North America, International Plant Names Index - IPNI, Tropicos, Kew's World Checklist of Selected Plant Families), to build a canonical list of names anchored to external Globally Unique Identifiers (GUIDs) (e.g., IPNI URLs). We developed taxonomically-aware fuzzy-matching software (matchnames, Webb 2020) to identify cognates in different lists. The taxa for which there are variations between different sources in accepted names and synonyms are then flagged for review by taxonomic experts. However, even though names may be consistent across previous monographs and floras, the taxonomic concept (or circumscription) of a name may differ among authors, meaning that the way an accepted name in the flora is applied may be unfamiliar to the users of previous floras. We therefore have begun to manually align taxonomic concepts across five existing floras: Panarctic Flora, Flora of North America, Cody's Flora of the Yukon (Cody 2000), Welsh's Flora (Welsh 1974) and Hultén's Flora (Hultén 1968), analysing usage and recording the Region Connection Calculus (RCC-5) relationships between taxonomic concepts common to each source. So far, we have mapped taxa in 13 genera, containing 557 taxonomic concepts and 482 taxonomic concept relationships. To facilitate this alignment process we developed software (tcm, Webb 2021) to record publications, names, taxonomic concepts and relationships, and to visualize the taxonomic concept relationships as graphs. These relationship graphs have proved to be accessible and valuable in discussing the frequently complex shifts in circumscription with the taxonomic experts who have reviewed the work. The taxonomic concept data are being integrated into the larger dataset to permit users of the new flora to instantly see both the chain of synonymy and concept map for any name. We have also worked with the developer of the Arctos Collection Management Solution (a database used for the majority of Alaskan collections) on new data tables for storage and display of taxonomic concept data. In this presentation, we will describe some of the ideas and workflows that may be of value to others working to connect across taxonomic resources. [ABSTRACT FROM AUTHOR]

Some species introduced into new geographical areas from their native ranges wreak ecological and economic havoc in their new environment. Although many studies have searched for either species or habitat characteristics that predict invasiveness of exotic species, the match between characteristics of the invader and those of members of the existing native community may be essential to understanding invasiveness. Here, we find that one metric, the phylogenetic relatedness of an invader to the native community, provides a predictive tool for invasiveness. Using a phylogenetic supertree of all grass species in California, we show that highly invasive grass species are, on average, significantly less related to native grasses than are introduced but noninvasive grasses. The match between the invader and the existing native community may explain why exotic pest species are not uniformly noxious in all novel habitats. Relatedness of invaders to the native biota may be one useful criterion for prioritizing management efforts of exotic species. [ABSTRACT FROM AUTHOR]

Dispersal limitation may promote high tree-species diversity in rain forest by slowing local competitive exclusion, but evidence is scarce. By comparing the species lists of tree plots with those of nested seedling plots in rain forest at Gunung Palung, we found that the proportion of local seedlings arising from active dispersal events (via wind or animals, but not simply dropped from parent trees) was high: 68% of species and 46% of the individual seedlings. Local seedling species richness was not limited by the local richness of adults. Using these data, a spatially explicit simulation model indicated that dispersal limitation may not contribute substantially to the maintenance of tree diversity in this forest. We predict that the loss of animal seed dispersers would reduce local species richness of seedlings by 60%. While this reduction could possibly increase the influence of dispersal limitation, it would interfere with other mechanisms maintaining diversity. [ABSTRACT FROM AUTHOR]

Phylomatic ( ) is an online phylogenetic query tool where users submit a list of taxa (e.g. from an ecological community), with modern family and genus names, and which returns a phylogenetic hypothesis for the relationships among taxa. Any set of stored phylogenies, or a user-supplied one, can be chosen as the basis for the returned phylogeny, and several output formats for the tree can be selected. Currently, the source databases cover seed plants. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editors discuss various reports within the issue on topics including the local community of species, phylogenetic community structure of trees, and the evolution of organism's niche.

An introduction is presented in which the editors discuss various reports within the issue on topics including the local community of species, phylogenetic community structure of trees, and the evolution of organism's niche.