Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses

Abstract

The phylogenetic diversity measure, ('PD'), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas.

Keywords: breed diversity; expected phylogenetic diversity; functional trait diversity; key biodiversity areas; phylogenetic risk analysis; tipping point.

Figure 1.

(a) A functional space for species of Anseriformes, shown as dots. D, diving; S, surface feeding; G, grazing. Multiple loops represent one of the convergently derived traits (a femur trait) revealed on the Anseriformes phylogenetic tree; each loop is a different derivation of the trait on the tree. The ordination explains these convergently derived traits when all species having the trait are found close together in the functional space. For further analysis details, see [25]. (b) The same functional space with the 49 species numbered. Larger hollow dots are those species that are red-listed threatened species.

Figure 2.

A portion of the phylogenetic tree from Batista et al., for the genus Lynchius, with branches labelled a–e. Branch a is one of the long branches on the anuran tree (see complete tree in Appendix S1 in Batista et al. [29]).

Figure 3.

A portion of the phylogenetic tree among cattle breeds, from Simianer et al. [31]. Abbreviations of cattle breed names follow [31]: a, Butana; b, Nuba; c, Iringared; d, Malazebu. Estimated probabilities of extinction are a, 0.43; b, 0.57; c, 0.60; d, 0.50. For further information, see text.

Figure 4.

(a) A hypothetical tree for four species, a–d. Numbers represent branch lengths. (b) The distribution of PD outcomes for different scenarios of extinction probabilities for the four species. The distribution categorizes outcomes as ‘good case’ versus ‘worst case’. Black bars: all four species have probabilities of extinction of 0.5; light grey bars: species a changes to probability of extinction of 0.1; dark grey bars: species b changes to probability of extinction of 0.1.

Figure 5.

A schematic drawing of the phylogenetic relationships among Pseudophilautus hoipolloi and its relatives (re-drawn from Onezoom (www.onezoom.org)). Pseudophilautus hoipolloi is shown as light grey leaf, indicating Least Concern status. Other species shown in black are endangered. This shows one possible resolution of a polytomy for these six species, at the end of a branch of approximately 15 Myr.

Figure 6.

A portion of the phylogeny from Beenaerts et al. study [35] of Sri Lanka's freshwater crab species. Numbers refer to four of the long branches. Branch 1 is ancestral to Perbrinckia cracens. Branch 3 is ancestral to Pastilla ruhuna. Both Branch 2 and 4 are ancestral to several Ceylonthelphua species. Red-list category assignments are: cr, critically endangered; en, endangered; vu, vulnerable; nt, near-threatened. Multiple labels at the end of a branch designate status of multiple descendants.

Figure 7.

The distribution of PD outcomes for different scenarios of extinction probabilities for the four species in the tree of figure 4a. The distribution categorizes outcomes as ‘good case’ versus ‘worst case’. Dark grey bars: species a and species b have low probabilities of extinction of 0.1, and c and d have probabilities of extinction of 0.5.; black bars: expectations given the loss of the site with species b, changing its probability of extinction to 0.5; light grey bars: expectations given the loss of the site with species a, changing its probability of extinction to 0.5.