Phylogenetics and Biodiversity Philadelphia Pennsylvania 17 18 April

Phylogenetics and Biodiversity Philadelphia, Pennsylvania, 17 -18 April 2015 “Can phylogenetic diversity be the basis for a planetary boundary for biodiversity? ” Daniel P. Faith The Australian Museum GEO BON

Bio. GENESIS Providing an evolutionary framework for biodiversity science Future Earth Faith et al (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST

Steffen et al. The trajectory of the Anthropocene: The Great Acceleration (Anthropocene Review) 16 January 2015. Design: Globaia

Biodiversity loss Mathematically calculated rate of extinction. Source: Wilson (1992) The diversity of life, the Penguin Press. IGBP synthesis: Global Change and the Earth System, Steffen et al 2004

Planetary Boundaries Rockström et al. 2009 A safe operating space for humanity, Nature Steffen et al. 2015. Planetary Boundaries: Guiding human development on a changing planet. Science

Planetary Boundaries and biodiversity From a recent Georgina Mace talk - Various proposals for biodiversity • Rockström et al. 2009 A safe operating space for humanity, Nature • Faith et al 2010 Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST • Mace GM, et al 2014. Approaches to defining a planetary boundary for biodiversity. Global Environmental Change • Steffen et al. 2015. Planetary Boundaries: Guiding human development on a changing planet. Science

Mace et al 2014 Approaches to defining a planetary boundary for biodiversity. Global Environmental Change • “…human wellbeing will depend on the biota’s continued ability to support desired ecosystem services and processes in the face of often rapidlychanging selective pressures. Because it is not possible to predict which functional trait combinations will be most needed, it is not possible to identify the most important species a priori with any certainty. Instead, we should aim to manage the risks…

Mace et al 2014 Approaches to defining a planetary boundary for biodiversity. Global Environmental Change • “…human wellbeing will depend on the biota’s continued ability to support desired ecosystem services and processes in the face of often rapidlychanging selective pressures. Because it is not possible to predict which functional trait combinations will be most needed, it is not possible to identify the most important species a priori with any certainty. Instead, we should aim to manage the risks…” • “a species’ future importance depends on how much it adds to the overall diversity of unspecified functional traits, ultimately reflected in the extent of phylogenetic diversity (Faith, 1992) representing future option values of biodiversity (sensu Faith 1994)”

From a recent Georgina Mace talk -

Another interesting alternative is Helmus’ phylogenetic species variability PSV Note difference from PD – species can be lost and PSV can go up Lose a species

bio. GENESIS (Faith et al 2010) proposed a planetary boundary for biodiversity, based on PD Phylogenetic tipping points - successive species extinctions each may imply only a moderate loss of PD, until, abruptly, the last species goes extinct — and the long branch, representing a large amount of PD, is lost Faith et al (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST

bio. GENESIS (Faith et al 2010) proposed a planetary boundary for biodiversity, based on PD Phylogenetic tipping points - successive species extinctions each may imply only a moderate loss of PD, until, abruptly, the last species goes extinct — and the long branch, representing a large amount of PD, is lost Faith et al (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST

bio. GENESIS (Faith et al 2010) proposed a planetary boundary for biodiversity, based on PD Phylogenetic tipping points - successive species extinctions each may imply only a moderate loss of PD, until, abruptly, the last species goes extinct — and the long branch, representing a large amount of PD, is lost Faith et al (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST

bio. GENESIS (Faith et al 2010) proposed a planetary boundary for biodiversity, based on PD Phylogenetic tipping points - successive species extinctions each may imply only a moderate loss of PD, until, abruptly, the last species goes extinct — and the long branch, representing a large amount of PD, is lost “A nominated ‘boundary’ could reflect the degree of acceptable risk to evosystem services relative to this tipping point. An approach called ‘phylogenetic risk analysis’ [Faith 2008] provides exactly this kind of risk assessment. “ Faith et al (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. COSUST

Loss of the world’s corals • “the proportion of corals (57. 8%) exceeds that of all terrestrial animal groups assessed to date. . ” • Carpenter et al (2008) Science sometimes entire clades fall into IUCN threatened classes - Faith DP and ZT Richards (2013) Implications of climate change for the tree of life. Biology

Will the impacts of climate change on PD be large or small? Yesson, C. and A. Culham. 2006. • small loss of PD or evolutionary potential for given species loss red = surviving PD • large loss of PD or • large loss of PDpotential or evolutionary for evolutionary potential given species loss

Expected PD calculations may be useful Convert IUCN red list categories to probabilities of extinction (see Mooers et al) Forest F, Crandall KA, Chase MW, Faith DP. 2015 Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency. Phil. Trans. R. Soc. B 37:

Beyond expected PD “phylogenetic risk analysis” (PRA) outcomes are classed according to their PD values. e. g. “c 1” for PD values in the lower 10% of all values. ∑q(c)∗PD(c) = ∑q(c 1)∗PD(c 1) + ∑q(c 2)∗PD(c 2)… Have the probability, P, that we fall in that worst-case class, based on the probabilities of extinction of species. PRA prefers conservation actions that reduce the probability, P, of the “worst-case” PD outcomes. PRA may select different conservation actions compared to expected PD.

Phylogenetic tree for species a, b, c, d Each has current probability of extinction of 0. 5 Expected PD = 4. 0 with possible worst case outcomes Expected PD

Suppose one species can shift from 0. 5 to 0. 1 probability of extinction. Choose species a Expected PD = 4. 4 - still with possible worst case outcomes Expected PD

if instead choose species b, expected diversity is the same, but probability of worst case outcomes is now near-zero PD risk analysis

if instead choose species b, expected diversity is the same, but probability of worst case outcomes is now near-zero PD risk analysis Low probability of worst case outcomes

Talk about whole clades -

or note the high probability of a worst case loss

LEDGE species • These species are the secure, distinctive, species whose loss would mean a big reduction in expected PD (or whose loss would mean a big increase in probability of a worst case outcome) – ‘Loss-significant evolutionarily distinctive globally enduring’ (LEDGE) species.

Phylogenetic relationships among Pseudophilautus hoipolloi (green leaf) and its relatives (re-drawn from ONEZOOM www. onezoom. org). Faith (2015) Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses

Pseudophilautus hoipolloi a good example of a LEDGE species • ‘hoi polloi’ means ‘the majority’, … the working class, the commoners…. a bit derogatory • resonates with our conventional conservation biases, focussing on threatened species, including evolutionarily distinctive, as special • common secure species like P. hoipolloi are under -appreciated. – secure species whose loss would imply a very large loss in expected PD deserve acknowledgement as key PD species because they safe-guard a large amount of our evolutionary heritage. • part of a strategy for addressing PD tipping points

“key biodiversity species” • key biodiversity areas are sites contributing significantly to the persistence of biodiversity features which they hold • “key biodiversity species” are species contributing significantly to the persistence of biodiversity features which they represent – perhaps any LEDGE species is a KBS – but by nature their ancestral lineages are secure – perhaps any critically endangered species is a KBS • thresholds (analogous to those for KBAs) could consider a species’ share of threatened branches or features distribution among species

Species, clades and tipping points • Monitor clades where have high probability of worst case PD losses • Monitor clades with LEDGE species • Continue to set conservation priorities within a phylogenetic systematic conservation planning e. g. using ADEPT criterion

Looking at areas/regions to address planetary boundaries, phylogenetic tipping points • consider dependencies among the probabilities of extinction of the descendant species • frog example - three threatened Lynchius species are largely restricted to the Huancabamba region in Peru. – threatened by land use changes – abandon individual independent probabilities, and conclude that the current probability of reaching a phylogenetic tipping point is even greater. Faith (2015)

For mammals “At regional scales, losses differ dramatically: several biodiversity hotspots in southern Asia and Amazonia will lose an unexpectedly large proportion of PD. ” Red and black = high loss of deeper branches Huang et al (2011) Biol. Lett.

Key Biodiversity Areas (KBAs) • KBAs are sites of global significance for biodiversity conservation, “contributing significantly to the global persistence of biodiversity” (IUCN and partners) • KBAs typically are identified based on the presence of globally threatened (and/or geographically restricted) species. • A gap - KBAs at the genetic and phylogenetic levels. – Suggestions in Brooks et al (2015) – Expected PD calculations also might help fill this gap in providing information about both expected gains and expected losses.

• Brooks et al 2015 suggest: – (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; – (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and – (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the …phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism.

• Note Brooks et al (2015) “broaden the scope of the threatened species criterion to consider ‘threatened taxa’, as long as these are globally relevant. ” • for a phylogenetic key biodiversity area (or ‘PDKBA’), a direct analogue is any site that has one or more threatened branches (see Faith 2015) – (weighted) phylogenetic endemism (PE): • each branch length is inverse-weighted by the proportion of the total range extent of that branch that is represented in that area – define threatened PE (‘TPE’) as the PE score calculated only for designated threatened branches – area with high TPE arguably contributes significantly to the global persistence of PD.

• Note Brooks et al (2015) “broaden the scope of the threatened species criterion to consider ‘threatened taxa’, as long as these are globally relevant. ” • for a phylogenetic key biodiversity area (or ‘PDKBA’), a direct analogue is any site that has one or more threatened branches (see Faith 2015) – prioritise among these based on extent of the probable worst case losses, or the conservation gain in expected PD…… – extends Brooks et al, re consideration of occurrence of EDGE species (i. e. threatened phylogenetic diversity) in key biodiversity areas to prioritize conservation actions among sites

Two basic expected PD approaches – the gain in expected PD, if a given KBA area were protected (probabilities of extinction transformed to some small value). - Identifies places with a concentration of threatened PD. the loss in expected PD, if the area was lost (received no protection). - Identifies places with geographically restricted threatened PD. KBAs may naturally link to phylogenetic risk analysis – avoiding worst case losses

Laity et al (2015) document patterns of PD, PE for multiple taxonomic groups in Australia and suggest tracking PD plus PE or TPE for planetary boundaries acacias

Some changes are local, some are global • reduced PD within sites • changes in the phylogenetic diversity community composition • local/regional tipping points, worst case losses • changes in range, with new centres of range-restricted PD • possible global tipping points, worst case PD losses