Systematics

Taste of quals: do phylogenetics and conservation biology walk side by side?

Photo by Letícia Soares.

Robbie Hart writes on the relationships between conservation biology and phylogenetic trees, systematics and species concepts. Photo by Letícia Soares.

Here I am again, with another example of a qualifying exam question, from the Ecology, Evolution and Systematics program of the University of Missouri-St Louis. This time, I’ll post a sample from the quals of Robbie Hart, a PhD candidate (very soon PhD to be) in our program. Robbie’s quals answers were pointed out by a former faculty faculty member as one of the best through out years of evaluating the quals from several student cohorts. When I told Robbie the great things I heard on the quality of his answers, I asked him if I could post a few of them in the blog, and that was his reaction:

Robbie Hart gives us a sample of his own qualifying exam. He is also a pro when it comes to crack nuts. Courtesy of Robbie Hart.

“Awwwww don’t make me blush! That’s certainly a nice complement, though it seems unlikely! Quals was upsetting and difficult for me as it is for everyone…and it involved an early version of dropbox eating one of my answers. […]. I found them [the answers], but can barely understand them now. I think I’ve spent too long in the field. I’ll share with you […] my excessively wordy evolution major and my superficial and incomplete conservation bio minor.”

So here it is, a conservation biology minor question, answered by Robbie Hart. If you want to catch up with this topic on how to prepare yourself for qualifying exams in ecology and evolution, check out our previous posts!

What information in classifications and phylogenies may help – or hinder – efforts in conservation?

To prioritize conservation actions, one must first ask the existential question of conservation biology: ‘what are we trying to conserve when we protect biodiversity?’. One answer to this question is based in utility to humans: the goal is ecosystem services (1), and in an uncertain world, continued diversity conserves ‘option value’ – net benefit of keeping various possibilities open (2). Another is based on evolutionary history – an organismal lineage is seen as taking a certain amount of time to evolve, and a loss of that lineage (extinction) is lost evolutionary time (3,4). Both of these may be seen as preserving distinctive features of organisms; most modern approaches to quantifying biodiversity take genetic diversity as a proxy for a multitude of unknown (and perhaps unknowable) ‘features’ (1,2). Phylogenies and classifications, therefore, are central to setting the units of conservation, as they are both maps of the diversity to be conserved.

Species are historically the units of conservation for the public, scientists and legislators. However, their very importance may make them especially unstable categories – driven by biological evidence, legislative criteria, or the adoption of different species concepts, species number may change drastically, often leading to confusion or changes in prioritization (“taxonomy as destiny”(5), also see (6, 7, 8)). Different species concepts may work better for the different taxonomic goals of listing and management (7), and even the quality of the species level as a uniquely real grouping has been called into question as another just another lump in the continuum (6,9). Infra-specific groupings have fared even less well; they are subject to differing taxonomic cultures across different taxa, and have little relation even to genetic subdivisions of species (10). Higher taxa are also commonly used, and to some advantage: they offer deeper insight into loss of evolutionary history, and they are potentially more stable than specific and infraspecific levels. It could be argued that evolutionary taxa sensu Simpson are to some extent based on features themselves. However, the arbitrary nature of the higher divisions make them less suitable for quantitative, comparative analysis (1,3).

In light of these troubles, other units have been proposed for conservation. Units may be ‘management’, consisting of any population groups differing in allele frequency (1); ‘designatable’, designed with pragmatic policy issues in mind (11); ‘evolutionarily significant’, defined either as historically isolated (12), reciprocally monophyletic (1), or more broadly defined (13); or any of a large set of distinct or partially overlapping terms. As classifications, these terms share an unfortunate dichotomy – a group is either a unit, or not (13).

Phylogenetic diversity methods move beyond this dichotomy and treat distinctness or originality as a continuum. Methods are similarly diverse here, but generally apportion to each organism the amount of tree for which they are responsible. This offers a detailed look at exactly how much phylogenetic history is lost with each species that goes extinct; and is a measure with significant stability to taxonomic revision. This method can be extended in various ways: to probabilistic measures that take into account each sister node’s threat levels (14); or combined with complementarity principles to quantify hotspots of phylogenetic endemism (15, 16).

In the past, taxonomies and classifications have posed hindrances to conservation efforts. Newer phylogenetic diversity methods show great promise in moving past dichotomous categories and quantifying the threat to the shared evolutionary history of organisms. The virtue and immediacy of these are highlighted by studies showing that nonrandom extinction can pose a particularly severe threat to evolutionary history (4, 17).

Works cited

1. Crozier RH (1997) Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annual Review of Ecology, Evolution, and Systematics 28:243-268.

2. Faith DP (1994) Phylogenetic pattern and the quantification of organismal biodiversity. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 345:45-58.

3. Avise JC, Johns GC (1999) Proposal for a standardized temporal scheme of biological classification for extant species. Proceedings of the National Academy of Sciences of the United States of America 96:7358-63.

4. Vamosi JC, Wilson JR (2008) Nonrandom extinction leads to elevated loss of angiosperm evolutionary history. Ecology Letters 11:1047-53.

5. May RM (1990) Taxonomy as destiny. Nature 347:129–130.

6. Isaac NJ, Mallet J, Mace GM (2004) Taxonomic inflation: its influence on macro ecology and conservation. Trends in Ecology and Evolution 19:464-9.

7. Mace GM (2004) The role of taxonomy in species conservation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 359:711-9.

8. Baker RJ, Bradley RD (2006) Speciation in Mammals and the Genetic Species Concept. Journal of mammalogy 87:643-662.

9. Mishler BD (2009) in Contemporary Debates in Philosophy of Biolgoy, Ayala FJ, Arp R (Wiley-Blackwell), pp. 110-122.

10. Zink RM (2004) The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 271:561-4.

11. Green DM (2005) Designatable Units for Status Assessment of Endangered Species. Conservation Biology 19:1813-1820.

12. Moritz C (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic biology 51:238-54.

13. Crandall KA, Bininda-Emonds OR, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15:290-295.

14. Faith DP (2008) Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conservation Biology 22:1461-70.

15. Rosauer D, Laffan SW, Crisp MD, Donnellan SC, Cook LG (2009) Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular ecology 18:4061-72.

16. Faith DP, Reid CA, Hunter J (2004) Intergrating Phylogenetic Diversity, Complementarity and Endemism for Conservation Assessment. Conservation Biology 18:255-261.

17. Purvis A (2000) Nonrandom Extinction and the Loss of Evolutionary History. Science 288:328-330.