Open Tree Research Articles

MODELAGEM DO ESPAÇO DE CRESCIMENTO PARA ARAUCÁRIA

Este estudo foi desenvolvido com objetivo de modelar o espaço de crescimento para árvores de Araucaria angustifolia (Bertol.) Kuntze. Um total de 869 araucárias foram amostradas em três municípios no sul do Brasil, sendo 175 árvores com crescimento livre de competição nos municípios de Canoinhas-SC e Lages-SC, e 694 sob influência da competição em floresta natural nos municípios de São Francisco de Paula-RS e Lages-SC. Em cada árvore, foi medido o diâmetro a altura do peito, altura total e raios de copa seguindo as direções dos pontos cardeais. O diâmetro de copa foi determinado dobrando o valor do raio médio da copa. Três modelos foram ajustados e avaliados quanto ao ajuste, à precisão e à análise gráfica dos resíduos, segundo o município e a condição de crescimento. Na comparação das equações, a análise de covariância não indicou diferença significativa entre nível e inclinação das equações de diâmetro de copa de árvores livres e sob competição nos diferentes locais em que os dados foram amostrados. Uma única equação foi definida para estimar o diâmetro de copa em função do diâmetro a altura do peito para a espécie.

Nurturing a sustainable Open Tree of Life

The Open Tree of Life project is a collaborative effort to synthesize, share and update a comprehensive tree of life Fig. 1. We have completed a draft synthesis of a tree summarizing digitally available taxonomic and phylogenetic knowledge for all 2.6 million named species, available at tree.opentreeoflife.org Hinchliff et al. 2015. . . This tree provides ready access to phylogenetic information which can link together biodiversity data on the basis of what we know about relevant evolutionary history. Both the unified reference taxonomy Rees and Cranston 2017 and the published phylogenetic statements underlying the tree McTavish et al. 2015 are available and accessible online. Taxa in the phylogenies are mapped to the the reference taxonomy, which aligns Open Tree taxon identifiers to those from NCBI and GBIF, among several other taxonomy resources. The synthesis tree is revised as new data become available, and captures conflict and consensus across different published phylogenetic estimates. This undertaking requires both development of novel infrastructure and analysis tools, as well as community engagement with the Open Tree of Life project. I will discuss the challenges in and the progress towards achieving these goals.

Phenomap - Challenges and Successes in Bringing Together Multiple Data Projects to Build New Visualizations of Phenotypic Information and Specimen Records

Connecting biodiversity data across databases is not as easy as one might think. Different databases use different identifiers and taxonomies and connecting these data often results in loss of information and precision. Here we present some of the challenges we faced with integrating multiple biodiversity data sets, including specimen data from the scientific collections, during a hackathon hosted by the Phenoscape project in December of 2017. The hackathon brought together a diverse group of participants, including biologists and software developers, to explore ways of using the computable phenotype data in the Phenoscape Knowledgebase (KB) (Edmunds et al. 2015). The KB contains ontology-annotated data that links evolutionary phenotypes from the comparative literature to model organism phenotypes enabling, e.g., the retrieval of candidate genes for evolutionary phenotypes and the generation of synthetic supermatrices of presence/absence characters. During this hackathon, our team explored how to link phenotype data in the KB to museum specimen data in iDigBio (Matsunaga et al. 2013) with the hope of creating visualizations including world maps showing species distributions with different character states and their phylogenetic relationships. We visualized lineage relationships by querying the Open Tree of Life (OT) (Hinchliff et al. 2015) website using data integrated by another group at the hackathon that linked KB and OT taxonomic identifiers. Phenoscape uses terms from anatomy, quality, and taxonomy ontologies to annotate characters and taxonomic information from the phylogenetic literature along with specimen information. When populating the KB, specimen identifiers such as occurrence identifiers, collector’s number, and catalog numbers were preserved if present in the literature. We found that these identifiers, although standard in the biodiversity domain, were mostly insufficient to uniquely identify the source specimen in iDigBio. As an alternative, we instead mapped all the occurrences of taxa using string matches of the genus and species from Vertebrate Taxonomy Ontology identifiers. Without specimen identifiers that are consistent across databases, we lost the ability to explore spatial and temporal variation of characters within genera and were only able to explore phenotypes and geographic distributions among genera. We look forward to discussing these issues with the collections community represented at this meeting by the Society for the Preservation of Natural History Collections (SPNHC). We developed an R Shiny application that integrates characters and taxa from Phenoscape with specimen records from iDigBio and phylogenies from OT, to visualize phenotypic characters and taxon distributions in three interactive panels. The app allows a user to visualize OT phylogenies and place presence/absence character data on the tree. Specifically, users can: select taxa or specific characters to visualize their geographic distributions, navigate a phylogeny browser which displays character and specimen data available for taxa under consideration, and view a heatmap of characters available for character and taxon combinations. Because of our challenges joining data, our distribution map leaves users with the impression that all individuals in a genus exhibit a character whereas the KB was populated with data describing individuals. We hope that with improved data standards and their use by more people, constructing applications like ours will become easier.

Parasitism in Eukaryota - Reconstruction of Ancestral and Unavailable Extant States

Parasitism can be defined as an interaction between species in which one of the interaction partners, the parasite, lives in or on the other, the host. The parasite draws food from its host and harms it in the process. According to some estimates, over 40% of all eukaryotes are parasites. Nevertheless, it is difficult to obtain information about a particular taxon is a parasite computationally making it difficult to query large sets of taxa. Here we test to what extend it is possible to use the Open Tree of Life (OTL), a synthesis of phylogenetic trees on a backbone taxonomy (resulting in unresolved nodes), to expand available information via phylogenetic trait prediction. We use the Global Biotic Interactions (GloBI) database to categorise 25,992 and 34,879 species as parasites and free-living, respectively, and predict states for over ~2.3 million (97.34%) leaf nodes without state information. We estimate the accuracy of our maximum parsimony based predictions using cross-validation and simulation at roughly 60-80% overall, but strongly varying between clades. The cross-validation resulted in an accuracy of 98.17% which is explained by the fact that the data are not uniformly distributed. We describe this variation across taxa as associated with available state and topology information. We compare our results with several smaller scale studies, which used manual expert curation and conclude that computationally inferred state changes largely agree in number and placement with those. In clades in which available state information is biased (mostly towards parasites, e.g. in Nematodes) phylogenetic prediction is bound to provide results contradicting conventional wisdom. This represents, to our knowledge, the first comprehensive computational reconstruction of the emergence of parasitism in eukaryotes. We argue that such an approach is necessary to allow further incorporation of parasitism as an important trait in species interaction databases and in individual studies on eukaryotes, e.g. in the microbiome.

All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions

Taxonomic names are ambiguous as identifiers of biodiversity data, as they refer to a particular concept of a taxon in an expert’s mind (Kennedy et al. 2005). This ambiguity is particularly problematic when attempting to reconcile taxonomic names from disparate sources with clades on a phylogeny. Currently, such reconciliation requires expert interpretation, which is necessarily subjective, difficult to reproduce, and refractory to scaling. In contrast, phylogenetic clade definitions are a well-developed method for unambiguously defining the semantics of a clade concept in terms of shared evolutionary ancestry (Queiroz and Gauthier 1990, Queiroz and Gauthier 1994), and these semantics allow locating clades on any phylogeny. Although a few software tools have been created for resolving clade definitions, including for definitions expressed in the Mathematical Markup Language (e.g. Names on Nodes in Keesey 2007) and as lists of GenBank accession numbers (e.g. mor in Hibbett et al. 2005), these are application-specific representations that do not provide formal definitions with well-defined semantics for every component of a clade definition. Being able to create such machine-interpretable definitions would allow computers to store, compare, distribute and resolve semantically-rich clade definitions. To this end, the Phyloreferencing project (http://phyloref.org, Cellinese and Lapp 2015) is working on a specification for encoding phylogenetic clade definitions as ontologies using the Web Ontology Language (OWL in W3C OWL Working Group 2012). Our specification allows the semantics of these definitions, which we call phyloreferences, to be described in terms of shared ancestor and excluded lineage properties. The aim of this effort is to allow any OWL-DL reasoner to resolve phyloreferences on a phylogeny that has itself been translated into a compatible OWL representation. We have developed a workflow that allows us to curate phyloreferences from phylogenetic clade definitions published in natural language, and to resolve the curated phyloreference against the phylogeny upon which the definition was originally created, allowing us to validate that the phyloreference reflects the authors’ original intent. We have started work on curating dozens of phyloreferences from publications and the clade definition database RegNum (http://phyloregnum.org), which will provide an online catalog of all clade definitions that are part of the Phylonym Volume, to be published together with the PhyloCode (https://www.ohio.edu/phylocode/). We will comprehensively curate these definitions into a reusable and fully computable ontology of phyloreferences. In our presentation, we will provide an overview of phyloreferencing and will describe the model and workflow we use to encode clade definitions in OWL, based on concepts and terms taken from the Comparative Data Analysis Ontology (Prosdocimi et al. 2009), Darwin-SW (Baskauf and Webb 2016) and Darwin Core (Wieczorek et al. 2012). We will demonstrate how phyloreferences can be visualized, resolved and tested on the phylogeny that they were originally described on, and how they resolve on one of the largest synthetic phylogenies available, the Open Tree of Life (Hinchliff et al. 2015). We will conclude with a discussion of the problems we faced in referring to taxonomic units in phylogenies, which is one of the key challenges in enabling better integration of phylogenetic information into biodiversity analyses.

Recommendations of an International Multidisciplinary Committee on standards for reporting outcomes of treating biliary injuries

Background: A standard way of reporting outcomes of treatment of biliary injury is needed. The method should permit evaluation and comparison of surgical, endoscopic, and interventional radiologic treatments. A 19 person international multidisciplinary group has addressed this problem. Methods: The method is based on the concept of “Patency”, derived partly from reporting standards for arteriovenous hemodialysis access. Patency means an open functional biliary tree without devices, interventions, or episodes of infection, obstruction, or fistula. “Primary Patency” is achieved when patency exists at the end of the index treatment period, which is 3 months from surgical reconstruction and 12 months from initiation of treatment for non-surgical interventions. Primary patency is lost if subsequent interventions are needed or infection, obstruction or fistula occur. Attainment of patency after the index treatment period or restoration of patency after primary patency is lost is called “Secondary Patency”. Biliary injuries are graded according to severity (3 grades) and results according to patency (4 grades) The latter includes primary patency (Grade A), 2 levels of secondary patency (Grades B,C) and lack of patency (Grade D). The key metrics are Per Cent of Patients Attaining Primary Patency and the Actuarial Primary Patency Rate (APPR). Results: APPR is calculated like a Kaplan-Meier cancer survival curve with primary patency equivalent to survival (Figure). APPR has the advantages of having time as a continuous variable and the ability to account for variable follow-up periods. Conclusion: This method provides a rational approach to reporting outcomes of treatment of bile duct injuries in future studies.

Constructing a broadly inclusive seed plant phylogeny.

Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade. The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants. This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.

Factors Influencing the Regional Dynamics of Butternut Canker.

Butternut (Juglans cinerea) is an important component of native biodiversity in eastern North America. Of urgent concern is the survival of butternut, whose populations are declining rapidly, in large part due to an exotic pathogen, Ophiognomonia clavigignenti-juglandacearum, that causes butternut canker. The disease presently occurs throughout the range of butternut in North America, causing branch and stem cankers, dieback, and tree mortality. Despite the existential threat posed by O. clavigignenti-juglandacearum to butternut, a detailed understanding of the factors that drive cross-scale disease patterns is lacking. Therefore, we investigated the association of a range of factors, including tree attributes, topography, and weather, with butternut canker spatial dynamics at different scales using data collected in the province of Quebec, Canada. Trunk canker damage and dieback showed distinct geographic patterns. Bark phenotype was not significantly associated with trunk canker damage. Results suggest that open or dominant trees may show less dieback than intermediate or suppressed trees. Probability of the presence of trunk canker and percent dieback were proportional to the tree diameter at breast height. Temperature was positively associated with disease severity at a 1-km2 scale. Our results provide strong evidence that multiple factors, notably weather, influence butternut canker epidemiology.

Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes.

Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the presence and absence of pectoral and pelvic fins of 12,582 species. To do this, we integrated a synthetic morphological supermatrix of phenotypic data for the pectoral and pelvic fins for teleost fishes from the Phenoscape Knowledgebase (two presence/absence characters for 3047 taxa) with a species-level tree for teleost fishes from the Open Tree of Life project (38,419 species). The integration method detailed herein harnessed a new combined approach by utilizing data based on ontological inference, as well as phylogenetic propagation, to reduce overall data loss. Using inference enabled by ontology-based annotations, missing data were reduced from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data propagation. These methods allowed us to extend the data to an additional 11,293 species for a total of 12,582 species with trait data. The pectoral fin appears to have been independently lost in a minimum of 19 lineages and the pelvic fin in 48. Though interpretation is limited by lack of phylogenetic resolution at the species level, it appears that following loss, both pectoral and pelvic fins were regained several (3) to many (14) times respectively. Focused investigation into putative regains of the pectoral fin, all within one clade (Anguilliformes), showed that the pectoral fin was regained at least twice following loss. Overall, this study points to specific teleost clades where strategic phylogenetic resolution and genetic investigation will be necessary to understand the pattern and frequency of pectoral fin reversals.

Spatio-Temporal Dynamic of Land Use and Land Cover in the Classified Forest of Djoli-Kera, South-Eastern, Chad

This study was carried out in the classified forest of Djoli-Kera found in the South-Eastern part of Chad. It aimed to analyze the spatial and temporal dy-namics of land cover between 1972 and 2013 and to determine the drivers of vegetation degradation. The databases used were made up of 4 Landsat satellite images (1MSS of 1972, 5TM of 1984, 7ETM+ of 1990 and 2010) and a spot 6 image of 2013, supplemented by field studies. Satellite images were processed using ENVI and ArcGIS software. Interview was used to identify the activities carried out by the local population. In 1972, the classified forest consisted of four types of land cover, the most important of which was open forest (51%), followed by wooded savannah (26%), tree savannah (21%) and sparse vegetation consisting of farms and fallows (2%). Gradually open forest and tree savannah disappeared. In 2013, the main types of land cover were shrub savannah (40%), sparse vegetation (28%), wooded savannah (12%), bare soil (12%) and dwellings (8%). Livestock, agriculture, wood collection and bushfires are perceived by local population as main drivers of forest cover change. Awareness-raising, monitoring and regulation of access to resources must be pursued, but also managers of the classified forest must accompany the local populations in the planting of trees and the setting up of more efficient farming systems to reduce pressure on the forest’s resources.

Human-biometeorological significance of shading in urban public spaces—Summertime measurements in Pécs, Hungary

Shading is shown to be one of the most effective strategies to mitigate urban heat stress, especially on a small scale. This paper presents an empirical study investigating the effectiveness of different means of shading—by sun sails and trees—to improve the local thermal environment during the summer. Three different urban settings were investigated through detailed human-biometeorological measurements in the Hungarian city of Pécs. Our study employed the accurate six-directional radiation measurement technique, and calculated Physiological Equivalent Temperature (PET) from the obtained data to assess outdoor thermal conditions. Our results indicate that in open urban squares trees can mitigate heat stress more effectively than low-hanging sun sails, installed right above the head of pedestrians. In the period of 9:00–16:00, the average PET reduction by trees and low sun sails was 9.0°C and 5.8°C, respectively. Sun sails, installed at higher elevation to shade an entire street canyon, and mature trees with dense canopy had more pronounced heat stress reduction ability, and were able to reduce the local PET by over 10°C. Our study demonstrates the importance of detailed small-scale field measurements, the outcomes of which can be incorporated into climate-responsive urban design strategies with ease.

White picket fences & other features of the suburban physical environment: Correlates of neighbourhood attachment in 3 australian low-density suburbs

This study examines the relationship between neighbourhood attachment and five groups of physical characteristics of low-density suburbs: (1) street layout, (2) pedestrian environment, (3) neighbourhood connectivity, (4) public space provision, and (5) dwelling form. Although much research has investigated whether neighbourhood attachment is influenced by the urban design characteristics of high density contexts, there is little evidence of the impact of such characteristics in suburban environments with lower population densities, such as the types of low-density suburbs that ring Australian cities. Surveys were conducted in Victoria, Australia, to examine how these five groups of characteristics might impact residents’ neighbourhood attachment in three suburbs with equivalent socioeconomic profiles. Questionnaires were delivered to eight streets of different layout in each suburb, and via on-street face-to-face surveys in public spaces adjacent to neighbourhood libraries. The results of five separate regression models indicated that all five groups of physical neighbourhood characteristics significantly predicted neighbourhood attachment. Home ownership, length of residence and age were also found to have strong correlation with neighbourhood attachment. When length of residency is controlled for, it was found that five physical variables were the best predictors of neighbourhood attachment: provision of open spaces, street type, trees coverage, sidewalk provision and number of community spaces. Only the provision of open spaces had greater impact on attachment than length of residency. Hence, the study findings suggest that both social and physical factors should be considered in the planning of suburban neighbourhoods.

Shrub Encroachment Under the Trees Diversifies the Herb Layer in a Romanian Silvopastoral System

Rangelands with scattered trees are complex and dynamic systems with a long history in Europe. Generally referred to as “wood-pastures,” they are considered to have outstanding conservation value. Thorny shrubs are important for supporting the biodiversity of these wooded rangelands, as well as facilitating the regeneration of trees by acting as nurse species. We assess the direct effects of temporary shrub encroachment under the cover of mature sparse trees on overall plant and habitat diversity. We surveyed the herb layer of the main landscape features of a wood-pasture: open pasture, trees with a grass understory, trees with shrubs, and adjacent forest edges. The herb layer under trees with shrubs resembled that of forest edges more than open pastures and trees with grass. Trees with grass had a higher cover of ruderal species than trees with shrubs, while forest edges and open pastures had a lower cover of them. Forest species were absent from open pastures but were well represented in the other sites. The herb layer of trees with shrubs and forest edges had similar cover values, while trees with grass had a significantly lower cover of herbs than the other types. Trees with shrubs had higher species richness than any of the other three landscape features and had a much higher proportion of diagnostic species. We conclude that the scattered trees and shrubs of the studied silvopastoral system have additive facilitative effects on their understory, probably through modifying the microenvironment and grazing pressure, leading to the formation of temporary diversity hot spots with distinct vegetation. Thus maintaining a moderate level of shrub-encroachment under sparse trees is recommended for not only creating safe havens for tree recruitment but also increasing the overall species and habitat diversity of wood-pastures.

How and Why to Build a Unified Tree of Life.

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

Plant community composition and structural characteristics of an invaded forest in the Galápagos

Non-native species have invaded habitats worldwide, greatly impacting the structure and function of native communities and ecosystems. To better understand mechanisms of invasion impacts and how to restore highly impacted and transformed ecosystems, studies are needed that evaluate invader effects on both biotic communities and structural characteristics. On Santa Cruz Island in Galapagos we compared biotic (plant species richness, diversity, and community composition) and structural (canopy openness, forest height, and leaf litter) characteristics of a relic forest dominated by an endemic and highly threatened tree and a forest dominated by an invasive tree. The forests are located within the historical distribution of the endemic tree, which now occupies only 1% of its original extent. We found that the invaded forest had 42% lower native plant species richness and 17% less plant diversity than the endemic tree dominated forest. Additionally, with the invader there was 36% greater non-native plant species richness, 37% higher non-native plant diversity, and highly dissimilar plant composition when compared to the endemic-dominated forest. Additionally, the invaded forest had a more open and taller tree canopy and greater leaf litter cover than native forest. The presence of the invasive tree and the associated forest structural changes were the primary factors in models that best explained higher non-native diversity in the invaded forest. Our correlational results suggest that an invasive tree has significantly altered plant assemblage and forest structural characteristics in this unique ecosystem. Experiments that remove the invader and evaluate native plant community responses are needed to identify thresholds for practical restoration of this threatened and biologically unique native forest.

The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies

Recent developments in phylogenetic methods and data acquisition have allowed for the construction of large and comprehensive phylogenetic relationships. Published phylogenies represent an enormous resource that not only facilitates the resolution of questions related to comparative biology, but also provides a resource on which to gauge the development of concordance across the tree of life. From the Open Tree of Life, we gathered 290 avian phylogenies representing all major groups that have been published over the last few decades and analyzed how concordance and conflict develop among these trees through time. Nine large scale phylogenetic hypotheses (including a new synthetic tree from this study) were used for comparisons. We found that conflicts were over-represented both along the backbone (higher-level neoavian relationships) and within the oscine Passeriformes. Importantly, although we have made major strides in the resolution of major clades, recent published comprehensive trees, as well as trees of individual clades, continue to contribute significantly to the resolution of relationships throughout the avian phylogeny. Our analyses highlight the need for continued research into the resolution of avian relationships.

Ecological indicators of Tuber aestivum habitats in temperate European beech forests

Abstract Although Tuber aestivum is widely distributed across Europe, little is known about its biology and ecology. We assess the vegetation composition of wild T. aestivum sites and use this information to characterise suitable habitats in Fagus sylvatica , Carpinus betulus and Ostrya carpinifolia (FCO) forests. Plant species composition at 16 naturally colonised T. aestivum sites in southwestern Germany and Switzerland was compared with that of 232 reference sites in Swiss FCO forest communities. The vegetation composition of truffle sites exhibits a high proportion of herb and shrub species that are indicators of a warm and dry climate, alkaline soil, and open tree canopy and thus typically occur in thermophilous FCO communities on calcareous bedrock. We conclude that T. aestivum is associated with a set of key species in addition to known host species. Based on their floristic composition, we identified FCO forest communities with high and low suitability for T. aestivum .

Effects of flood irrigation on the risk of selected zoonotic pathogens in an arid and semi-arid area in the eastern Kenya.

To investigate the effects of irrigation on land cover changes and the risk of selected zoonotic pathogens, we carried out a study in irrigated, pastoral and riverine areas in the eastern Kenya. Activities implemented included secondary data analyses to determine land use and land cover (LULC) changes as well as human, livestock and wildlife population trends; entomological surveys to characterize mosquitoes population densities and species distribution by habitat and season; and serological surveys in people to determine the risk of Rift Valley fever virus (RVFV), West Nile fever virus (WNV), dengue fever virus (DFV), Leptospira spp. and Brucella spp. Results demonstrate a drastic decline in vegetation cover over ≈25 years particularly in the irrigated areas where cropland increased by about 1,400% and non-farm land (under closed trees, open to closed herbaceous vegetation, bushlands and open trees) reduced by 30–100%. The irrigated areas had high densities of Aedes mcintoshi, Culex spp. and Mansonia spp. (important vectors for multiple arboviruses) during the wet and dry season while pastoral areas had high densities of Ae. tricholabis specifically in the wet season. The seroprevalences of RVFV, WNV and DFV were higher in the irrigated compared to the pastoral areas while those for Leptospira spp and Brucella spp. were higher in the pastoral compared to the irrigated areas. It is likely that people in the pastoral areas get exposed to Leptospira spp by using water fetched from reservoirs that are shared with livestock and wildlife, and to Brucella spp. by consuming raw or partially cooked animal-source foods such as milk and meat. This study suggests that irrigation increases the risk of mosquito-borne infections while at the same time providing a protective effect against zoonotic pathogens that thrive in areas with high livestock population densities.

Automated assembly of a reference taxonomy for phylogenetic data synthesis.

Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive supertrees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.

Development of a Parallel Version of PhyML 3.0 Using Shared Memory

This work presents the main steps towards a parallel version of the open source phylogenetic tree reconstruction software PhyML 3.0, which uses the method of maximum likelihood in phylogenetic reconstruction process. The PhyML was parallelized by a shared memory approach (using OpenMP) and at the same time using the version already consolidated in PhyML 3.0, the version passing messages with distributed memory (using MPI), was also constructed a version hybrid (MPI and OpenMP) of PhyML. The tests for the efficiency and speedup were carried out in a cluster of two ways, the first only by analyzing the performance version with OpenMP (DNA and proteins) and the second making a comparative analysis of the performance of three parallel versions (OpenMP, MPI and Hybrid) using DNA data only. The results obtained show speedup of approximately six to 8 cores on 1 server, which allows the use of this code problems that require a lot of time in the serial version, front the need or urgent of the fast processing of data.