Understanding Phylogenies: Use in Conservation Planning

Deciding which species to invest time, money, and political capital in is a primary challenge of biodiversity conservation. (There is a subsequent challenge of deciding which conservation actions to pursue after determining which species to target; however, today I focus on species selection.) Phylogenies can inform conservation planning. Using the candy bar phylogeny I’ll discuss the roles of incomplete sampling and phylogenetic distinctiveness in conservation decision making.

Figure 2- Fully bifurcating candy bar phylogeny with traits mapped onto tree topology.  Red slash over a trait means "loss of" that trait on the tree.
Figure 2- Fully bifurcating candy bar phylogeny with traits mapped onto tree topology. Red slash over a trait means “loss of” that trait on the tree.

Incomplete Sampling
A number of commenters on Twitter and the original Candy Bar Phylogeny post noted that their favorite candy bar was missing. But that’s research, right? We’re constantly making decisions about depth and breadth of sampling in the face of constraints such as time, access to sampling locations, and research budget. Further, sampling often depends on the research question. For the candy bar phylogeny, my goal was to describe overall diversity in American candy bar flavors and how flavors were repeated across the tree. However, if my question had been to describe variation in solid chocolate bars, I would have needed a vastly different sampling scheme.

How does my not sampling Baby Ruth or Mr Goodbar relate to conservation? Well, I don’t even remember seeing a full size Mr Goodbar in any of the three stores (aka- sampling locations) I went to! Researchers cannot sample taxa that they do not encounter; for the Mr Goodbar example, this would be an absence, the taxon was known but not present (or missed, called a pseudoabsence) during sampling. In contrast but more importantly, researchers cannot sample taxa that they do not know about. As an example, in 2013 the olinguito (Bassaricyon neblina) was discovered. We can neither place this species in the mammalian phylogeny nor develop conservation measures for undescribed species. However, now that the olinguito, a member of the raccoon family (Procyonidae), has been described, researchers can use morphological and genetic data to place the species within the family. Researchers may find through further study of the ecology and distribution that the olinguito should receive conservation actions. While this example is rare for mammals, there are many species of invertebrates and plants yet to be found, described, and classified. With additional sampling from multiple research groups, we can update phylogenies and hopefully use this information to inform conservation prioritization.

Phylogenetic Distinctiveness
One distinct result of the candy bar phylogeny was that clade size was uneven. In particular, the caramel clade had the most taxa (n=10 although two taxa lost caramel) while the cherry clade only had one taxon. When thinking about conservation planning, phylogenetic distinctness may be a consideration. In this scenario of allocating conservation resources between the clade with the most taxa (caramel) and the least (cherry) while only considering phylogenetic distinctness, resources would be allocated to the Cherry Mash to help conserve that candy for the future.

That said, conservation planners take multiple lines of evidence into planning, not just phylogenetic distinctness. Rarity and endemism may also be considered when allocating resources. The mint clade had the same number of taxa as the cherry clade, one taxon each. However, York Peppermint Patties and Cherry Mash have different levels of rarity and endemism. If you’ve never heard of a Cherry Mash, that may be because it’s a regional Missouri candy (aka- it’s endemic to a few counties in the Midwest USA). Not only is it a regional candy bar, but it is also rare in stores (aka- sampling locations) where regional grocery stores carry it but national chains do not. In contrast, York Peppermint Patties are found across the US and in most stores. If a conservation planner wanted to conserve endemic and/or rare taxa, in this example the Cherry Mash would be prioritized over the Peppermint Patty despite equal phylogenetic distinctness within the phylogeny.

A real world example of conservation prioritization based on phylogenetic distinctness is that of the tuatara (Sphenodon punctatus). The tuatara’s got it all, it’s the last reptile of the Rhynchocephalia lineage, it’s endemic to New Zealand, and it’s adorable. Investing in tuatara conservation helps protect the last species of this evolutionary lineage. However, this is controversial as some conservationists would prioritize clades with high evolutionary potential (ascertained as species rich clades) over clades with a single species, also termed “living fossils.” The idea is that species rich clades have greater potential for adaptation and/or speciation in an ever changing environment, and that evolutionary potential is what we should preserve over distinctness or rarity. These are just a few of the competing considerations in conservation prioritization.

To learn more about the interplay between phylogenies and conservation see the book Phylogeny and Conservation edited by Purvis, Gittleman, and Brooks.

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