spacodiR: structuring of phylogenetic diversity in ecological communities

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spacodiR: structuring of phylogenetic diversity in ecological communities

MOTIVATION spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities. AVAILABILITY Integrated with other sof...

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Diversity spurs diversification in ecological communities

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that eve...

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Optimizing Phylogenetic Diversity with Ecological Constraints

Given an edge-weighted tree T with leaf set X, define the weight of a subset S of X as the sum of the edge-weights of the minimal subtree of T connecting the elements in S. It is known that the problem of selecting subsets of X of a given size to maximize this weight can be solved using a greedy algorithm. This optimization problem arises in conservation biology where the weight is referred to ...

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Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history.

Phylogenetic information is increasingly being used to understand the assembly of biological communities and ecological processes. However, commonly used metrics of phylogenetic diversity (PD) do not incorporate information on the relative abundances of individuals within a community. In this study, we develop three indices of PD that explicitly consider species abundances. First, we present a ...

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Using ecological diversity measures with bacterial communities.

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2011

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btr403