Thursday, May 11, 2017

Panbiogeography and area cladistics galore

Today the newest issue of Australian Systematic Botany came out, and oh boy is the content interesting. It is the first in a series of special issues on biogeography - but that is not the main point, to which I will come later.

I have tried before to systematise for myself what biogeography is actually about. What is its research program? Trying again, and perhaps in a way that reflects my current thinking:

1a. Inferring ancestral ranges, and closely related to that...
1b. Inferring biogeographic events and their timing.

This kind of research is focused on a given clade and tries to understand how its species came to occupy the ranges they do today. It uses a number of approaches and software tools that attempt to infer ancestral ranges given a generally time-calibrated phylogenetic tree of the study group, contemporary distributions at the tips of the tree, and a model specifying what biogeographic processes are 'allowed' to happen. Examples include originally parsimony-based Dispersal And Vicariance Analysis (DIVA), the Dispersal, Extinction and Cladogenesis model (DEC), and others.

A typical result would be on the lines of, "the ancestral range of this genus was in the south-east of the continent, and we estimate ca. three sympatric speciation events and ca. two vicariance events in its history", often illustrated with a phylogeny whose branches are labelled with the relevant ancestral ranges and biogeographic events.

2. Species distribution modelling

Research in this field tries to estimate where a species can occur, usually given presence data for the species and climatic, soil and other data for those known locations. This can be used, for example, to predict to where approximately in Australia an invasive species could spread out if it were introduced from its native range in, say, South America. Computationally intensive, species distribution modelling is a relatively recent development. That being said, it was the big hot new thing when I did my first postdoc, so recent is to be taken relative.

Obviously, a typical result would be a map with different colours indicating different probabilities of the species being able to exist in those locations.

3. Spatial studies

This field divides a study region into cells, often equal area grid cells, and attempts to quantify diversity metrices such as species richness, endemism, and phylogenetic diversity. Hotspots of diversity can then be targeted for conservation, or they simply provide information on the evolution of present diversity, especially if they are hotspots of palaeo- or neoendemism. This work has only really become possible with the availability of large biodiversity databases of geo-coded specimens.

A typical results would be on the lines of, "the study group shows the highest endemism scores in the south-west and the tropics".

4. Bioregionalisation

The idea here is to distinguish bioregions across the landscape that are significantly different from each other in their species or lineage content, and to figure out where their approximate borders are. Traditionally this was done very intuitively and based mostly on the presence or absence of key taxa. Today researchers often use computers and grid cell-based approaches similar to those in spatial studies, only that they compute pairwise dissimilarity scores between grid cells. Cells are then clustered into bioregions or, in the most novel approaches, submitted to network analysis.

A result might read: "Our analysis shows four major bioregions, the monsoonal tropics, the Eremaean, the south-west, and the temperate south-east. The border between the monsoonal tropic cluster and the Eremaean cluster is, however, considerably further south than estimated by a previous study..."

5. Area cladograms

And this is where I am leaving my comfort zone, because while I have used #1 and #3 and at least dabbled in #2 and #4, this one is weird to me and will probably remain so.

The idea in this case is to use areas or bioregions as the units of an analysis that is supposed to show how the areas are related. In other words, something like a phylogenetic analysis of areas, using their species content as data, and with a result on the lines of "the Australian temperate rainforests are sister to the New Zealand temperate rainforests, and together they are sister to the Patagonian ones" (not necessarily a true result, just to get the concept across). There are a few methods available for this, and they are generally parsimony based and by now quite dated.

The obvious problem here is that this whole procedure is based on a number of assumptions that I can only consider dubious. Just like phylogenetic reconstruction of the tree of life must assume, in that case rather sensibly I believe, that there is no significant gene flow between, say, cattle and primroses, building a tree of bioregions must assume that there is no significant dispersal or species exchange between the various area it uses as units of analysis. And that is where it all falls down for me, because of course species disperse happily from area to area. There are no barriers that are remotely as strong as as the barriers to gene flow between different species.

The present issue of Australian Systematic Botany

So we arrive at the present issue of Australian Systematic Botany, which is, as mentioned, the first in a planned series on biogeography. My personal perception is that of the above fields of research, the cutting edge is today in ancestral range inference and spatial studies. Species distribution modelling is often more seen as part of ecology rather than systematics; the scope for large numbers of bioregionalisation studies is obviously somewhat limited, given that there are considerably fewer bioregions than species; and I thought that area cladograms were more a thing of the 1980s or so.

But the papers in the present issue show that they are still being done - and so is panbiogeographic track analysis!

This is going to be very interesting, because when I read either of these approaches I have the same feeling as when examining some of the pro-paraphyly literature: intellectual challenge in the sense of having to understand a mode of thinking that is very, very alien to me. But that just makes it more important to try and follow the reasoning, even should it ultimately not be found convincing.

In particular I am looking forward to seeing a track analysis in action when I come to those papers, because so far it really has not clicked for me what they are supposed to show and how their conclusions can possibly be justified.

To summarise, the articles in the issue are:

1.&2. Two very short introductions.

3. Alan de Queiroz rebutting an earlier article by panbiogeographer Michael Heads. This one is open access, and otherwise stands out in that it seems to be the only article by a mainstream biogeographer. As I pretty much agree with everything it says I will not have any comments on it.

4. Ung et al. constructing an area cladogram for "southwest Pacific biotas", with the abstract indeed containing phrases such as "the islands of the Southwest Pacific are more closely related to each other than they are to Australia". Interestingly, they call their results a "model".

5. Romano et al's panbiogeographic track analysis of agaricoid fungi of the Patagonian forests.

6. An extremely long article by panbiogeographer John Grehan on relationships between America and Maccaronesia.

7. Martinez et al. conducting a panbiogeographic track analysis on plants and animals of the Argentinean pampas.

8. And with Corral-Rosas & Morrone another area-cladistic analysis, this time with Mexico as the study area.

Ancestral range reconstruction for individual clades or spatial analyses, on the other hand, are clearly MIA. So at a minimum one would have to say that this is, at the moment, still a rather narrow representation of the field of biogeography.

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