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Research Article

Threatened Reef Corals of the World

  • Danwei Huang mail

    huangdanwei@nus.edu.sg

    Affiliations: Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America, Department of Biological Sciences, National University of Singapore, Singapore, Singapore

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  • Published: March 30, 2012
  • DOI: 10.1371/journal.pone.0034459

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The need for phylogenetic risk analyses for corals

Posted by DanFaith on 22 Apr 2012 at 08:46 GMT

Huang (2012) forcefully argues for a phylogenetic perspective for conservation assessment of reef-building corals, and supports that goal by providing an improved phylogenetic framework for the group. The combination of phylogenetic information and inferred extinction probabilities supports priority setting to conserve phylogenetic diversity (PD; Faith 1992). However, Huang’s analysis strategy for corals may represent a step backwards.

Huang does note that his method may not work as well as some existing alternatives:
“a probabilistic approach that accounts for future extinctions of related species may be more suitable than the static allocation of conservation value afforded by the ED measure…”
Faith (2008) described this “expected PD” approach, and provided an example for forest songbirds in the genus Myadestes: “Expected PD calculations therefore would justify a relatively high conservation priority for Myadestes obscures, reflecting not only its increased extinction risk but also its elevated importance, given the expected loss of sister species, in representing the unique PD of this genus”.

But Faith (2008) also argued that EDGE and expected-PD assessments are too focussed on finding good outcomes “on average”, and could increase the probability of worst-case losses of PD. Risk aversion, through phylogenetic risk analysis, would instead prioritise to avoid worst-case losses of PD.

Such an approach in fact has already been trialled for corals (Faith et al 2010), revealing some cases where priorities could focus on avoiding loss of deeper phylogenetic branches. Given the extensive threats to corals, we cannot afford to revert to priorities systems, such as EDGE, that ignore such dangers of worst case losses.

Faith DP (2008) Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conserv Biol 22: 1461–1470.

Faith DP, Magallon S, Hendry AP, Conti E, Yahara T, et al. (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. Curr Opin Environ Sustain 2: 66–74.

No competing interests declared.

RE: The need for phylogenetic risk analyses for corals

Danwei replied to DanFaith on 23 Apr 2012 at 20:05 GMT

Dr. Dan Faith brought up an excellent point that detailed phylogenetic risk analysis, rather than a priority system, more likely avoids worst-case PD losses. This is currently being explored for different reef regions based on the "expected PD" approach (Faith 2008, Conserv. Biol.) to choose the best sets of species that minimise the chance of maximum PD loss. The example used in Faith et al. (2010, Curr. Opin. Environ. Sustain.) of Catalaphyllia, Physogyra, and Euphyllia is a good proof of principle (note however that these three genera are not closely related [Fukami et al. 2008, PLoS ONE; Kitahara et al. 2010, PLoS ONE; Barbeitos et al. 2010, PNAS]).

On the issue of alternative methods, following are two sets of species with the highest EDGE and HEDGE scores. The latter is based on the algorithm by Steel et al. (2007, Evol. Bioinform.), which computes the expected contribution of a focal species to species subsets weighted by their extinction probability (A. Mooers, pers. comm.). This is also the "expected PD" measure expounded by Faith (2008, Conserv. Biol.: restricted case of the change in expected PD in equation 3).

Top 30 EDGE species (* denote species not in HEDGE list)
MEA Ctenella chagius (EN)
FAV Montastraea annularis (EN)
FAV Montastraea faveolata (EN)
SID Siderastrea glynni (CR) *
POC Stylophora madagascarensis (EN) *
POC Pocillopora fungiformis (EN) *
FUN Lithophyllon ranjithi (EN) *
ACR Acropora palmata (CR)
ACR Acropora cervicornis (CR)
FAV Parasimplastrea sheppardi (EN) *
FAV Goniastrea deformis (VU)
POR Alveopora excelsa (EN) *
POR Alveopora minuta (EN) *
SID Horastrea indica (VU)
MUS Lobophyllia serratus (EN) *
FUN Heliofungia actiniformis (VU)
AGA Pavona cactus (VU)
ACR Anacropora spinosa (EN) *
SID Anomastraea irregularis (VU)
ACR Isopora togianensis (EN)
FUN Halomitra clavator (VU) *
FUN Cantharellus noumeae (EN) *
MER Hydnophora bonsai (EN) *
PEC Pectinia maxima (EN) *
ACR Montipora dilatata (EN) *
ACR Isopora cuneata (VU)
EUP Physogyra lichtensteini (VU) *
EUP Plerogyra discus (VU) *
EUP Nemenzophyllia turbida (VU) *
FAV Moseleya latistellata (VU)

Top 30 HEDGE species (* denote species not in EDGE list)
MEA Ctenella chagius (EN)
ACR Acropora palmata (CR)
ACR Acropora cervicornis (CR)
FAV Goniastrea deformis (VU)
AGA Pavona cactus (VU)
FUN Heliofungia actiniformis (VU)
SID Horastrea indica (VU)
FAV Montastraea faveolata (EN)
FAV Montastraea annularis (EN)
ACR Isopora cuneata (VU)
FAV Moseleya latistellata (VU)
FAV Montastraea franksi (VU) *
DEN Turbinaria peltata (VU) *
ACR Acropora derawanensis (VU) *
ACR Acropora papillare (VU) *
ACR Acropora speciosa (VU)*
SID Anomastraea irregularis (VU)
ACR Acropora echinata (VU) *
ACR Isopora togianensis (EN)
ACR Montipora altasepta (VU) *
ACR Anacropora matthai (VU) *
ACR Acropora caroliniana (VU) *
EUP Catalaphyllia jardinei (VU) *
ACR Montipora gaimardi (VU) *
ACR Montipora angulata (VU) *
ACR Acropora walindii (VU) *
ACR Acropora hemprichii (VU) *
ACR Montipora capricornis (VU) *
ACR Montipora florida (VU) *
ACR Acropora batunai (VU) *

More species sets, based on different measures calculated in Tuatara 1.01 (Maddison & Mooers 2007) and various transformations of extinction probabilities (Mooers et al. 2008, PLoS ONE), are available upon request or already in Table S1. They would have been included in the paper, but over the course of the review process, I was persuaded to focus on the most widely-used EDGE metric. It is not the intention of the paper to advocate the use of any particular metric or transformation. It does support phylogenetically-informed assessments of risks as another strategy to protect the future of coral diversity.

No competing interests declared.

RE: RE: The need for phylogenetic risk analyses for corals

DanFaith replied to Danwei on 24 Apr 2012 at 03:45 GMT

A further clarification may be useful.
Huang now plans "detailed phylogenetic risk analysis....based on the "expected PD" approach"
But a caution is that simply optimising "expected PD" (or HEDGE, etc, which follow the basic methds of Witting and Loeschke 1995) does not minimise worst case PD losses.
The 2008 paper presents a simple example.

No competing interests declared.