Biodiverse, a tool for the spatial analysis of biological and related diversity

Laffan, Shawn W.; Lubarsky, Eugene; Rosauer, Dan F.

doi:10.1111/j.1600-0587.2010.06237.x

Cited by 277 publications

(266 citation statements)

References 14 publications

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“…We used BIODIVERSE [22] to map phylogeographic endemism across the Atlantic forest based on new and published mitochondrial sequence-level data from 25 vertebrate species or closely related species groups (electronic supplementary material, methods, tables S1 and S2). As we are interested in the distribution of genetic lineage diversity and it is somewhat arbitrary whether lineages are recognized taxonomically (typically depending on whether divergence is morphologically cryptic or diagnosable), we include phylogeographic data both within-species (n ¼ 19) and across very closely related species (n ¼ 06).…”

Section: Methodsmentioning

confidence: 99%

“…Because BIODIVERSE [22] requires species presence data for all grid cells to estimate endemism, we used geo-referenced information from each species to generate correlative models of species distribution (electronic supplementary material, methods and dataset S1). Lineage-specific ranges were defined by superimposing the geo-referenced haplotype data on the genealogical trees.…”

Section: Methodsmentioning

confidence: 99%

“…Lineage-specific ranges were defined by superimposing the geo-referenced haplotype data on the genealogical trees. The molecular data were represented in BIODIVERSE [22] as a single, composite phylogeny that includes the withinspecies genetic information for all species in the study. To focus on recent evolutionary history, we incorporated only those well-supported clades identified within each species (more than 80% maximum-likelihood bootstrap support) and removed all other (higher level) phylogenetic information from our analyses (electronic supplementary material, figure S1).…”

Section: Methodsmentioning

confidence: 99%

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Prediction of phylogeographic endemism in an environmentally complex biome

et al. 2014

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Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Prediction of phylogeographic endemism in an environmentally complex biome

et al. 2014

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“…We investigated the relationship between fruit type and size, range size, and the distribution of tree and vine species across the Australian rainforests and within regional areas (figure 1) using the BIODIVERSE software, v. 1.0 (http://purl.org/biodiverse; [25]). The continent-wide distribution and trait data used were described by Kooyman et al [7] and aggregated to square 50 Â 50 km grid cells.…”

Section: (B) Fruit Size and Species' Distributionsmentioning

confidence: 99%

From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly

et al. 2015

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ResearchCite this article: Rossetto M, Kooyman R, Yap J-YS, Laffan SW. 2015 From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly. Seed dispersal is a key process in plant spatial dynamics. However, consistently applicable generalizations about dispersal across scales are mostly absent because of the constraints on measuring propagule dispersal distances for many species. Here, we focus on fleshy-fruited taxa, specifically taxa with large fleshy fruits and their dispersers across an entire continental rainforest biome. We compare species-level results of whole-chloroplast DNA analyses in sister taxa with large and small fruits, to regional plot-based samples (310 plots), and whole-continent patterns for the distribution of woody species with either large (more than 30 mm) or smaller fleshy fruits (1093 taxa). The pairwise genomic comparison found higher genetic distances between populations and between regions in the large-fruited species (Endiandra globosa), but higher overall diversity within the small-fruited species (Endiandra discolor). Floristic comparisons among plots confirmed lower numbers of large-fruited species in areas where more extreme rainforest contraction occurred, and recolonization by small-fruited species readily dispersed by the available fauna. Species' distribution patterns showed that larger-fruited species had smaller geographical ranges than smaller-fruited species and locations with stable refugia (and high endemism) aligned with concentrations of large fleshy-fruited taxa, making them a potentially valuable conservation-planning indicator.

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“…Several programs provide visualizations of 2D or 3D geophylogenies, along with functionality to explore the temporal structure of this data (Kidd and Liu 2008;Janies et al 2011) or the geographic uncertainty associated with Bayesian techniques for phylogeographic inference (Bielejec et al 2011). Other programs have focused on displaying the spatial distribution and diversity of taxa using pie charts or geographic heat maps, and incorporate phylogenetic information by focusing on specific lineages or assigning molecular sequences to haplotypes (Hijmans et al 2001;Laffan et al 2010;Tsai 2011). We developed GenGIS (Beiko et al 2008;Parks et al 2009a) as a tool to merge geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment which supports a wider range of visualization and analysis options than existing software packages.…”

Section: Introductionmentioning

confidence: 99%

GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework

Beiko

Parks

Mankowski

et al. 2013

Preprint

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Abstract. GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted.The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada.GenGIS release versions, tutorials and documentation are freely available at

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Biodiverse, a tool for the spatial analysis of biological and related diversity

Cited by 277 publications

References 14 publications

Prediction of phylogeographic endemism in an environmentally complex biome

Prediction of phylogeographic endemism in an environmentally complex biome

From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly

GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework

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