Review: Clarke, Warwick (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series, 216:265-278.

Feature Paper: DOWNLOAD * Clarke, Warwick (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series, 216:265-278.

Author Abstract: A further biodiversity index is proposed, based on taxonomic (or phylogenetic) relatedness of species, namely the ‘variation in taxonomic distinctness’ (VarTD, Λ+) between every pair of species recorded in a study. It complements the previously defined ‘average taxonomic distinctness’ (AvTD, Δ+), which is the mean path length through the taxonomic tree connecting every pair of species in the list. VarTD is simply the variance of these pairwise path lengths and reflects the unevenness of the taxonomic tree. For example, a species list in which there are several different orders represented only by a single species, but also some genera which are very species-rich, would give a high Λ+ by comparison with a list (of equivalent Δ+) in which all species tended to be from different families but the same order. VarTD is shown to have the same desirable sampling properties as AvTD, primarily a lack of dependence of its mean value on the sample size (except for unrealistically small samples). Such unbiasedness is of crucial importance in making valid biodiversity comparisons between studies at different locations or times, with differing or uncontrolled degrees of sampling effort. This feature is emphatically not shared by indices related to species richness and also not by properties of the phylogeny adapted from proposals in other, conservation contexts, such as ‘average phylogenetic diversity’ (AvPD, Φ+). As with AvTD, the VarTD statistic for any local study can be tested for ‘departure from expectation’, based on a master taxonomy for that region, by constructing a simulation distribution from random subsets of the master list. The idea can be extended to summarising the joint distribution of AvTD and VarTD, so that values from real data sets are compared with a fitted simulation ‘envelope’ in a 2 d (Δ+, Λ+) plot. The methodology is applied to 14 species lists of free-living marine nematodes, and related to a master list for UK waters. The combination of AvTD and VarTD picks out, in different ways, some degraded locations (low Δ+, low to normal Λ+) and the pristine island fauna of the Scillies (normal Δ+, high Λ+). The 2 indices are also demonstrated to be measuring effectively independent features of the taxonomic tree, at least for this faunal group (although it is shown theoretically that this will not always be the case). The combination of Δ+ and Λ+ is therefore seen to provide a statistically robust summary of taxonomic (or phylogenetic) relatedness patterns within an assemblage, which has the potential to be applied to a wide range of historical data in the form of simple species lists.

Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.

Review: Today is the first of three papers on how measurements of taxonomic similarity between populations are used to determine biogeographic affinities between locations. This paper is a bit complicated in that they introduce specific mathematical formulas for assessing taxonomic similarity. I won't go into the mathematics in my review because I aim to help both laypersons and new graduate students (or advanced undergraduates) understand the reviews. The basics of the mathematical principles are described in the author's abstract above in any event. I encourage those wishing to know more about the subject to follow the download link for a free copy of the complete article.

I also want to point out that prospective or current Master's of Science students should examine this article and others in the journal Marine Ecological Progress Series (MEPS) as one professor once told me that a Master's degree thesis is basically a MEPS-worthy paper. Use MEPS as yore guideline when trying to decide scope of a research project or when determining how much of an advisor's idea you can tackle in about one year of research and one year writing up the results for your thesis. Don't do more… trust me. Save that for your PhD and Postdoc.

Now, onto the review. As the first paragraph of the authors' article states: 

"Species richness measures have traditionally been the mainstay in assessing the effects of environmental degradation on the biodiversity of natural assemblages of organisms. However, the sampling problems associated with ascertaining true species richness and making comparable assessments with historical data are well-known, and it should be noted that richness is not the only measurable component of community level biodiversity, even when the data consist simply of lists of species presence/absences. The phylogenetic structure of the assemblage is also clearly important, and an assemblage comprising a group of closely related species must be regarded as less ‘biodiverse’ than an assemblage of the same number of more distantly related species, for example all belonging to different phyla. Measures of phylogenetic structure, based on analysis of cladograms of particular groups of organisms, have been proposed by conservation biologists as a means of assigning conservation priorities that preserve the greatest amount of phylogenetic diversity or ‘evolutionary history’ (May 1990, Vane-Wright et al. 1991, Williams et al. 1991, Faith 1992, 1994, Humphries et al. 1995, Nee & May 1997). Little attention, however, has been devoted to analysis of the ways in which environmental degradation affects phylogenetic structure on local or regional scales, and the extent to which properties of this structure can be used as measures of biodiversity for the purposes of biological effects monitoring."

I copied the entire paragraph because not only is it an excellent example of scientific writing, but it clearly states the problem the authors seek to address in their paper. To address the problem at hand (last sentence in the author introduction above), the authors use the concept of "taxonomic distinctness," which they define as "a measure of the average degree to which individuals in an assemblage are related to each other."

Oftentimes when researchers want to conduct global or large-scale analyses of target species, the highest resolution consistent data available are species presence-or-absence lists, also known as checklists. Usually, scientists use such lists to determine taxonomic diversity and total richness, but the authors propose determining "average taxonomic distinctness" of populations, for which they provide formulas (look to the original article).

But in essence, what the authors are trying to point out is that when confronted with only checklists, one needn't be restricted just to total species (or other taxonomic levels) richness. One can determine which locations are related to each other based on species compositions that are shared. Recall last Saturday's review (Week 5 Paper 2) where atolls have characteristic floras and faunas and how rainfall and island elevation can help structure and determine how related those floras and faunas are. 

The authors' taxonomic distinctness levels can be used to aid historical biogeography through determining sources of radiation or speciation events. The authors also use their metric to show how environmental degradation can skew species richness and thus can help determine which species are likely to "drop off" or go locally extinct. Thus, taxonomic distinctness can be used for management purposes, as well as for computer simulations to test various historical biogeography theories.

The authors also state that "Theories of island biogeography have largely been developed from data on species that are easily censused and for which complete inventories can be produced in relation to island size, such as birds, reptiles and certain groups of insects (MacArthur & Wilson 1967). For groups such as free-living nematodes, or other small cryptic taxa, a complete census is rarely possible, except for very small areas. [Taxonomic distinctness measures] therefore offer a useful alternative, and might also help to address longstanding questions concerning island biogeography that cannot be resolved by a count of the number of species alone: for example whether increasing numbers of species are a function of increasing island size per se, or are related to the larger number of habitats."

The authors then conclude with: "Because of the impracticality of routinely attempting comprehensive surveys, surrogacy methods will clearly become the norm in biodiversity estimation (Harper & Hawksworth 1994), and the search for appropriate indicators of marine and coastal biodiversity has become an important research goal (Feral 1999)."

In essence, this is what nearly all fieldwork is: gathering a sample subset of an entire population and hoping that you can sample enough to draw statistically powerful conclusions about the whole population. Furthermore, if certain "keystone" or important species are known to have a tight relationship with other organisms of interest, studying the one will often provide information about the state of the other. 

For example, butterflyfishes are mostly coralivorous, with many being obligate coralivores. This means that many butterflyfish species only eat living coral. Therefore, counting butterflyfishes on a reef and knowing a given reef area can help coral reef biologists determine approximate levels of coral cover needed to sustain such levels of butterflyfishes.

Next we'll look at how beta-diversity can be measured from another kind of taxonomic similarity index. Download links below as usual.