The PD calculus and rapid biodiversity assessments using DNA barcoding

PD (phylogenetic diversity) analyses on DNA barcoding trees enable rapid biodiversity assessments.

Predictions of species richness using PD are well-established, but decision-makers and planners need other information, including measures of biodiversity gains/losses.

See a Commentary on "Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras" (Costion et al PLOS ONE, 2011)

It is nice to see case studies applying PD (Faith 1992) to DNA barcoding information. But I found it hard to understand the authors’ claimed “new perspectives and methods on biodiversity value and quantification”. Indeed, I wondered whether the paper reflects all the progress that already has been made in the exploration of PD analyses on DNA barcoding trees, for rapid biodiversity assessments that side-step the species problem.

Several years ago, Smith and Fisher (‘Invasions, DNA barcodes, and rapid biodiversity assessment using ants of Mauritius’. Frontiers in Zoology 2009, 6:31; http://www.frontiersinzoo... ) nicely demonstrated that PD applied to barcode data provides good estimates of species richness - but they also went further. They also documented how PD calculations can estimate species-level complementarity values (gains/losses in diversity):

“estimated incidences of diversity and complementarity were similar when measured by standard morphological alpha-taxonomy or phylogenetic diversity (PD)…. costs related to site loss (considered loss of evolutionary history measured as loss of barcode PD) were not significantly different from predictions made either a) using standard morphology-based taxonomy, or b) measured using a nuclear marker.”

They concluded:
“This work adds to the growing body literature demonstrating that PD in general provides a unique and important measure of biological diversity, and further that PD estimates based on standardized DNA barcodes will provide a critical scaffold for comparing those estimates between taxa and sites”

Use of the PD calculus to estimate complementarity and uniqueness (endemicity) values is critically important in practice, as the conservation value of a locality typically is its PD complementarity value, not its overall PD value.

See also: 

Zhou et al (2009) Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Frontiers in Zoology 2009, 6:30.

They concluded that “…rescaled phylogenetic diversity (PD) curves, a threshold-free concept of genetic diversity that is measured by total branch lengths in a tree .. followed a very similar shape to the species accumulation curves..”

For more of the early work on rapid biodiversity assessments based on PD calculations applied to DNA barcoding, see:

Faith, DP. and Baker, AM. (2006) Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online. 2006; 2: 121–128.

Faith, DP (2008) Phylogenetic diversity and conservation. 99–115 In (eds: SP Carroll and C Fox) Conservation Biology: Evolution in Action. Oxford University Press.

See also: powerpoint slides

A recent review on DNA barcoidng and biodiversity conservation includes discussion of the utility of PD:        Krishnamurthy PK Francis RA. (2012) A critical review on the utility of DNA barcoding in biodiversity conservation. Biodivers Conserv 21:1901–1919

Dan Faith

Dr Dan Faith , Senior Principal Research Scientist email:danfaith8[at]
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