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

By Daniel P. Faith, A. Baker. Evolutionary bioinformatics online, 2006

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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. Bioinformatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socioeconomic data.

Subfields: Ecological Modeling, Ecology, Genetics

View Paper: https://www.semanticscholar.org/paper/984bb8680c30bbe8d2979486259efb373d108e62

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Citations in the corpus

Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales (2010, background): “However, because conservation tends to work at the margins, even small gains can impact prioritization schemes (Faith, 1992; Faith & Baker, 2006).”
From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome (2012, background): “Although ecologists are increasingly describing alpha diversity patterns using metrics that incorporate phylogenetic (Faith & Baker 2006) and functional or trait-based information (Petchey & Gaston 2007), we focus here on the taxonomic diversity of human-associated microbial communities as this is…”
Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long‐term fertilization management (2018, methodology): “A phylogenetic tree was then constructed using FastTree, and the phylogenetic diversity was calculated from this tree using Faith’s metric (Faith & Baker, 2006), which is based on the total branch length of the tree.”
DNA Barcodes for Marine Biodiversity: Moving Fast Forward? (2010, methodology): “Clusters of DNA barcodes might be used in biodiversity surveys by using a phylogenetic diversity analysis [105,106].”
Diversity, ecology and evolution of groundwater copepods (2009, background): “…species and pattern of species abundances but differing in the phylogenetic relatedness of the constituent species may be considered different in their conservation priorities, if higher-level taxonomic diversity is assigned greater value (Faith, 1992; Clarke & Warwick, 1999; Faith & Baker, 2006).”
Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent (2013, background): “Perez-Losada et al. (2002) found little difference in conservation priorities for Chilean freshwater crabs, regardless of whether SR or PD was considered (although Faith & Baker, 2006 raise doubts about these results).”
Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice (2017, methodology): “Alpha diversity was calculated using the phylogenetic diversity index method (37).”
Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity (2011, background): “As well, there is some evidence of phylogenetic clumping (Faith and Baker 2006), whereby the loss of species from certain locales would result in disproportionately greater December 2011 3009RIVERINE CONSERVATION IN ARID SYSTEMS losses in phylogenetic diversity compared to taxonomic diversity…”
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer (2016, unknown): “Alpha diversity on rarefied tables was estimated using Faith’s phylogenetic diversity 23 , and beta diversity using unweighted UniFrac 24 .”
Conservation biogeography of freshwater fishes: recent progress and future challenges (2010, background): “Alternative extinction scenarios can be expressed as potential losses in ‘feature diversity’ in regard to the evolutionary history of the studied region and may hence guide conservation priorities (Faith & Baker, 2006).”