Sunday, May 21, 2017

Reading up on biogeography part 3: Hopping between islands yes, hopping from continent to island no?

The third vicariance biogeography / panbiogeography paper in the special issue is

Grehan JR, 2017. Biogeographic relationships between Macaronesia and the Americas. Australian Systematic Botany 29: 447-472.

Despite being very long, its gist is easily summarised:

The mainstream explanation for the occurrence of plants and animals on the Macaronesian islands (Canary Islands, Madeira, etc.) is that they must have got there via long-distance dispersal, often from Africa but sometimes from the Americas, because the islands are of relatively young volcanic origin and distant from other land masses. However, the "model-based approaches" that this conclusion is based on cannot be accepted because they supposedly assume dispersal and ignore the possibility of vicariance.

This is followed by many pages of example cases of plants and animals illustrated with maps and phylogenies. It is not clear to me what that is supposed to show, because without a time axis it doesn't move the inference either way; at best it could show that some of the groups have a pattern that is consistent with vicariance, but if a lineage is too young then vicariance is still out, and the same if the lineage is much older than the island.

Finally, there is some speculation, again illustrated with maps, about whether there were always volcanic islands in the same area, all through from the time when the Atlantic started to open. They would have been transient on a geological scale, so the local lineages supposedly produced by vicariance when Africa and the Americas started moving apart would have had to island-hop as new volcanoes rose and older ones eroded away, over more than 100 million years.

In contrast to the previous two papers I did not really gain new insights into the methodologies favoured by vicariance biogeographers. In a sense the present paper is closer to an opinion piece or perhaps a review article than to a research study.

The supposed assumptions of "model-based approaches"

The paper claims
"Model-based approaches to Maccaronesian biogeography assume the that the [sic] sequence of phylogenetic relationships reflects a sequence of chance dispersal. Although often cited as Hennig's progression rule, it is not a rule but an assumption that does not address the equal applicability of sequential differentiation across a widespread ancestor."
And further on:
"Model-based methods use chance dispersal to explain divergence and allopatry, ..."
Unfortunately this claim at least is demonstrably false. There are various models available to do ancestral area inference (see this graphic as an example), and DIVA and very popular DEC, for example, include vicariance. That's what the V in the acronym DIVA means! If a model-based analysis with a model that allows vicariance infers no vicariance then we can assume it is not because the model does not allow vicariance, but because the data didn't support that conclusion.

I am also reasonably certain that Hennig's progression rule does not only apply to long distance ("chance") dispersal but would just as well apply to a series of range expansions followed by speciation events across a single land mass. It simply applies the principle of parsimony to historical biogeography, arguing that if several lineages along a grade occur in an area then that would probably, all else being equal, have been (at least part of) the ancestral range, because other explanations require more dispersal and/or extinction events.

It is interesting, by the way, how the word "model" seems to be used in this context, as if a mathematical description of a system is something bad.

What distribution patterns would we expect under vicariance and long-distance dispersal, respectively?

"The progression rule also assumes that a 'basal' grade is located in the source region or centre of origin, but some Macaronesian clades are basal to large continental clades, and there are also clades with 'reciprocal monophyly' in which a diverse Macaronesian clade is the sister group to a diverse continental clade. These phylogenetic and geographic incongruities do not arise in a vicariance interpretation of phylogeny, because a basal clade or grade marks only the location of the intial phylogenetic break or breaks within a widespread ancestral range."
I don't really understand the reasoning here. The idea seems to be that if an island clade is nested within a continental grade, then it may make sense to conclude dispersal, but if an island clade and a continental clade are sister to each other then it is somehow "incongruent" (with what?) and can only be explained by vicariance. Why?

I would look at the nearest outgroup to get more information, but even if that occurred in neither region then we would still have to ask if additional continental or island lineages may have simply gone extinct. The key questions are whether the lineage split is so recent that it happened considerably after continental break-up and whether an island lineage is older than the island(s). Really I don't see how we can conclude anything with confidence without a time axis.

Perhaps the idea is to equate "distribution of the species along a basal grade is evidence of a centre of origin" with "absence of such a basal grade is evidence of absence of a centre of origin"? If so, that would not be logical; absence of evidence for A is not evidence for not-A.

The paper also discusses other patterns, in this case non-overlapping ranges of related species (allopatry):
"Model-based methods use chance dispersal to explain divergence and allopatry, and yet allopatric divergence requires isolation, which cannot exist if there is effective dispersal."
The point of the second half of this sentence is a false dichotomy set up between dispersal that is so frequent that it makes speciation impossible and no dispersal at all. It seems obvious to me that the excluded middle is dispersal that happens but is too rare to make speciation impossible.
"In the same way that allopatric lineages within Tarentola are incongruent with the expectations of chance dispersal, so too is the allopatry of Tarentola and its New World sister group."
Again this makes no sense to me whatsoever, and again there seems to be some very black-and-white reasoning behind it: if species can disperse to distant islands everything should occur everywhere; but we observe that all species do not occur everywhere, so we have to conclude that dispersal is completely impossible. But this is one-to-one equivalent to the argument that you cannot produce random numbers with a die because when you cast it the second time it came up with a different number than the first time. Really, that seems to be the logic here.

One might also add that there is another fairly obvious reason why one would find patterns of allopatry even if the same region was reached two or three times by the same lineage: competitive exclusion. It is a well established, empirically tested insight of biogeography that islands (and by extension restricted areas in general) have a carrying capacity, both in overall diversity and in the number of species trying to occupy about the same ecological space. In the case of islands in particular, their species diversity is a function of size (the more land, the more species, mostly because lower area increases extinction rate) and distance from the nearest larger land mass (the closer, the more species, mostly because of higher immigration / dispersal rates filling up the species pool).

This makes a lot of intuitive sense. Assume you have a seed of a continental shrub species blown onto an island that so far has only been colonised by mosses, lichen, one species of grass, and a bunch of insects eating the former. Your shrub niche is still free, and there is nothing on the island that is adapted to eating you, so even if at first you are in a bit of trouble genetically (inbreeding) and ecologically (not used to this soil and climate) you have a reasonable chance of establishing. Now fast forward 500,000 years, and the single seed of that shrub has diversified into six species occupying every niche on the island that they could adapt to in that time, forming thick scrubland from coastal dunes to the highest peak. A new seed of a related continental shrub species ends up on the island - but now everything is occupied by relatives that have become well-adapted to this new environment. Are we really surprised that the second comer will have a harder time establishing?

Time-calibration of phylogenies, again

We had that one already in the Ung et al paper, but once more:
"Model-based methods, with rare exceptions, present molecular divergence ages as falsifications of early origins, at or before continental breakup, even though they are calibrated by fossils that can generate only minimal divergence dates. Although it is widely claimed that molecular-clock analyses are generate [sic] evidence of dispersal (Sanmartin et al., 2008), molecular divergence estimates artifically constrain the maximum age of taxa that may be much older than their oldest fossil or the age of the current island they occupy (Heads 2009a, 2012, 2014a, 2014b, 2016)."
I like the little caveat "with rare exceptions", although it is unclear what it refers to. But it is not a method, but the researcher using a method, who would draw the conclusion that a lineage diverging 12 Mya would not have diverged because of a tectonic event that happened 120 Mya. And yes, that conclusion makes a lot of sense to me, and no, "model-based" methods do not magically transform minimum ages into maximum ages. This has been discussed repeatedly in rebuttals to Heads' papers. What is more, people have run analyses using the alternative approach suggested by Heads and in the present paper and found that the results are generally absurd, such as pushing the age of the daisy family back before the origin of multi-cellular life.
"The timing of ancestral differentiation may be assessed either by fossils (including molecular extrapolations) or tectonic-biogeographic correlation."
First, fossil calibration or using estimated substitution rates are really two completely different data sources, so the former does not really "include" the latter. Second, using continental breakup to calibrate splits in the phylogeny would, as mentioned before, be circular reasoning. It would build the assumption of vicariance into the analysis to subsequently conclude vicariance as a result. I think that's not how science is supposed to work.
"Fossil data provide only the minimum known-age of taxa and [sic] fossils are often lacking for clades of interest to Macaronesia. In tectonic correlation, the estimate of clade age is more precise, because it refers to a particular, dated event, rather than a minimal (fossil-calibrated) age."
Yes, a fossil provides a minimum age. But unless I severely misunderstand something, a continental break-up could, at best, provide only a maximum age, if we assume that divergence would not have been possible before break-up. (And even that seems fishy to me, given that there are plenty of speciation events on the same landmass.) If it were to be taken as "precise" that would, once more, automatically exclude the possibility that the divergence happened later, after dispersal from one continent to the other, and that would be circular reasoning.

Even the vicariance approach would need long distance dispersal to work

Finally, I am puzzled by the idea of how the lineages would have stayed in place after the supposed vicariance event that would have happened long before the present islands came into existence:
"Island biota survives erosion and subsidence of island habitats by local dispersal onto newer volcanoes"
What I don't get is this: if a vicariance biogeographer can accept that a species hops across the ocean from one volcanic island to another, why can they not accept that it hops across the ocean from Africa onto one of the volcanic islands? What's the difference? Why is this discussion taking place again? I must be missing something very subtle here.

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