The EDGE approach identifies the species representing most evolutionary history from among those in imminent danger of extinction. Our methods extend the application of PD-based conservation to a wider range of taxa and situations than previous approaches [4], [5], [13], [22], [24], [25]. Future work might incorporate socioeconomic considerations [5], [14] and the fact that a species' value depends also on the extinction risk of its close relatives [53]. However, our results suggest that large numbers of evolutionarily distinct species are inadequately served by existing conservation measures, and that more work is carried out to prevent the imminent loss of large quantities of our evolutionary heritage. It is hoped that this approach will serve to highlight their importance to biodiversity and emphasize the need for urgent conservation action.
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Materials and Methods
Implementing ED scores for mammals
We used a composite ‘supertree’ phylogeny [31] to calculate ED scores for mammals. The supertree presents several challenges to the estimation of ED when compared with the (unknown) true phylogeny: poor resolution, missing species and uncertainty in node ages. Accordingly, we modified the basic procedure to control for these problems.
Phylogenetic information is poor in many mammalian clades (especially bats and rodents, which together make up >60% of species) and the whole supertree contains only 47% of all possible nodes, many of which are polytomies (nodes with more than two daughter branches). Across the whole phylogeny, ∼40% of species are immediately descended from bifurcations, ∼20% from small polytomies (3–5 daughters), ∼15% from medium-sized polytomies (6–10 daughters) and the remainder from large polytomies with >10 daughters. Polytomies in supertrees result from poor or conflicting data rather than a true representation of the speciation process, so the distinctiveness of branches subtending them is overestimated [54], thus leading to biased ED scores. For example, the common ancestor of species X, Y and Z is believed to be 1 MY old, but the branching pattern within the clade is unknown. The polytomy appears to show that each species represents 1 MY of unique evolutionary history. In reality, the phylogeny is bifurcating, with one species aged 1 MY and the others sharing a more recent common ancestor. The bias induced by polytomies can be corrected by estimating the expected ED of descendant species under an appropriate null model of diversification. We achieved this by applying a scaling factor based on the empirical distribution of ED scores in a randomly generated phylogeny of 5000 species grown under constant rates of speciation (0.1) and extinction (0.08). The mean ED score of species in 819 clades of three species was 0.81 of the clade age; ED scores for nodes of 2–20 species scale according to (branch length) * (1.081–0.267 * ln{d}), where d is the number of descendent branches (n = 2873 clades, r2 = 0.69). Quantitatively similar values were obtained in bifurcating clades of primates [1.117–0.246 * ln{d}, n = 78, ref 55] and carnivores [1.139–0.269 * ln{d}, n = 101, ref 56].
The mammal supertree contains 4510 of the 4548 (>99%) extant species listed in Wilson & Reeder [35]. Although few in number, the missing species need to be taken into account because their absence will tend to inflate the ED scores of close relatives. For example, omitting species A from the phylogeny in figure 1 would elevate B from the joint lowest ranking species (with A) to the joint highest-ranking (with C), with an ED score of (2/1+1/2+2/4) = 3.5 MY. The problem is acute in real datasets since missing species tend not to be a random sample: 22 of the 38 missing mammals are from the genus Sorex. We account for this problem using a simple correction factor that allocates the missing species among their presumed closest relatives. For example, we correct for the omission of the bare-bellied hedgehog (Hemiechinus nudiventris) by treating the other five Hemiechinus spp. as 6/5 = 1.2 species, and we correct for the omission of both Cryptochloris species by spreading the two missing species evenly between other Chrysochloridae.
Variation among morphological and molecular estimates of divergence times (node ages) can lead to considerable uncertainty in ED scores. To reduce the effects of this uncertainty, we estimated ED using three sets of branch lengths. One set was based on the best (i.e. mean) estimates of node age; the others were derived from the upper and lower 95% confidence intervals around these dates. Species values of ED were calculated as the geometric mean of scores under the three sets of branch lengths. The geometric mean was preferred since it down-weights species whose scores are based on nodes with symmetrical but wide confidence intervals in estimate age, and is therefore more conservative than the arithmetic mean.
Extract only the main points for the information given above mentioned information
- The EDGE approach identifies species that have the most evolutionary history and are in imminent danger of extinction.
- The approach extends the application of PD-based conservation to a wider range of taxa and situations.
- Future work could incorporate socioeconomic considerations and the extinction risk of a species' close relatives.
- Existing conservation measures inadequately serve large numbers of evolutionarily distinct species.
- A composite 'supertree' phylogeny was used to calculate ED scores for mammals.
- The phylogeny presents challenges due to poor resolution, missing species, and uncertainty in node ages.
- A scaling factor based on the empirical distribution of ED scores in a randomly generated phylogeny was applied to correct for the bias induced by polytomies.
- Missing species were taken into account and a correction factor was used to allocate them among their closest relatives.
- Variation in divergence times led to uncertainty in ED scores, so three sets of branch lengths were used to estimate ED.
- The geometric mean was used to calculate species values of ED to account for uncertainty.
- The EDGE approach aims to identify species that represent a significant amount of evolutionary history and are at risk of extinction.
- The methods used in this approach are an extension of previous conservation approaches, allowing for a wider range of taxa and situations.
- Future work may include incorporating socioeconomic factors and considering the extinction risk of a species' close relatives.
- The results suggest that current conservation measures are inadequate for a large number of evolutionarily distinct species, emphasizing the need for urgent action to protect our evolutionary heritage.
- The ED scores for mammals were calculated using a composite 'supertree' phylogeny.
- The supertree presented challenges due to poor resolution, missing species, and uncertainty in node ages.
- A scaling factor was applied to correct for the bias induced by polytomies (nodes with more than two daughter branches), which overestimates the distinctiveness of branches.
- Missing species were taken into account by allocating them to their closest relatives using a correction factor.
- Variation in divergence time estimates led to uncertainty in ED scores, which was reduced by using three sets of branch lengths based on mean estimates and upper and lower confidence intervals.
- The geometric mean of scores under the three sets of branch lengths was used to calculate species values of ED, giving more weight to conservative estimates.
The main points from the information given are as follows:
1. The EDGE approach is used to identify species that have the most evolutionary history and are in imminent danger of extinction.
2. This approach extends the application of Phylogenetic Diversity (PD) based conservation to a wider range of taxa and situations than previous approaches.
3. Future work could incorporate socioeconomic considerations and the extinction risk of closely related species in determining a species' value.
4. The results suggest that existing conservation measures are inadequate for protecting a large number of evolutionarily distinct species.
5. The methods used to calculate Evolutionary Distinctiveness (ED) scores for mammals involve using a composite 'supertree' phylogeny and controlling for challenges such as poor resolution, missing species, and uncertainty in node ages.
6. Polytomies (nodes with more than two daughter branches) in the supertree can lead to biased ED scores, which can be corrected by estimating the expected ED of descendant species under a null model of diversification.
7. The missing species in the supertree need to be taken into account, and a correction factor is applied to allocate missing species among their closest relatives.
8. Variation in estimates of node ages can lead to uncertainty in ED scores, so three sets of branch lengths are used to calculate the scores, with the geometric mean preferred over the arithmetic mean.