Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges - PubMed (original) (raw)

Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges

Daniel P Faith et al. Evol Bioinform Online. 2007.

Abstract

Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, "PD", has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, "cryptic", taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based "species" designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

Keywords: phylogenetic; DNA barcoding; PD; biodiversity; invertebrates; species problem.

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Figures

Figure 1

Figure 1

A hypothetical phylogenetic tree, redrawn from Faith 1992a. The path connecting those four taxa (2, 6, 8, and 10) having maximum expected feature diversity, is shown by the thickened lines. The number of tick marks traversed by this spanning path is 28, indicating the relative feature diversity for the set.

Figure 2

Figure 2

A phylogenetic tree example, redrawn from Faith and Williams, 2006, for taxa a through h. Taxa are found in localities p1 through p4. Taxa f, g, and h are endemic to locality p1. The PDendemism of p1 reflects the potential loss not only of the proximal connecting branches, but also the loss of the deeper branch z.

Figure 3

Figure 3

A figure re-drawn from Crozier et al (2005; figure 1), with species labeled 1 through 4. Crozier et al claim that the PD of species 1 and 2 is only 2 units, in counting branch lengths only back to node t. However, correct PD calculations in this comparative context would record the PD based on branches extending back to the shared root R, yielding a PD of 4 units for this set of two species.

Figure 4

Figure 4

Phylogenetic and geographic distribution information for the “spiny crayfish” (Euastacus), as reported in Baker et al (2004) within the Sydney water supply catchment region of south-east NSW. a) The lineages labeled as A through E on the Euastacus phylogenetic tree shown in (b), are each represented only in a small number of places within the region. b) The phylogenetic pattern from Baker et al derived using the gene sequence, cytochrome c oxidase I gene (COI). Lineage A is a phylogenetic “sister” to lineage B. Given expected loss of biodiversity at localities containing lineage B, PD analysis assigns the localities containing lineage A higher priority, because the overall PD losses if both lineages were to be lost now would be high in reflecting also the loss of a shared, deeper, branch (marked X).

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References

    1. Andreasen K. Implications of molecular systematic analyses on the conservation of rare and threatened taxa: Contrasting examples from Malvaceae. Conserv Gen. 2005;6:399–412.
    1. Baker AM, Hughes JM, Dean JC, et al. Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages. Mar Freshw Res. 2004;55:629–40.
    1. Barker GM. Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biol J Linn Soc. 2002;76:165–94.
    1. Bininda-Emonds ORP, editor. Computational Biology. XIV. Vol. 4. Springer; 2004. Phylogenetic supertrees: Combining information to reveal the Tree of Life Series; p. 550.
    1. Blaxter M, Mann J, Chapman T, et al. Defining operational taxonomic units using DNA barcode data. Phil Trans R Soc B 2005 - PMC - PubMed

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