Wednesday, May 21, 2008

Shaffer & Thomson 2007

Shaffer, H.B. and R.C. Thomson. 2007. Delimiting Species in Recent Radiations. Syst. Biol. 56(6): 896-906.

This paper is yet another example of how species delimitation is becoming heavily reliant upon population processes. To analyze population processes using molecular data, you really have to have quite a large sample size (at least 20 individuals per population so I've been told from the experts). Alas, I unfortunately do not have that many samples for my PhD work. Maybe in the future...

In this work, Shaffer and Thomson make use of SNP's (Single nucleotide polymorphisms) to delimit turtle species and find that they are useful. However, because the turtle case study was an example of very distantly related taxa and they only discuss how SNP's can be good for recent radiations, I think their title may be a bit misleading.

Also, I'm not too sure on what exactly a single nucleotide polymorphism is. It must be some sort of stretch of DNA because they talk about designing primers for it. They compare SNPs to microsatellite loci but say SNPs are generally biallelic and contain less info than microsats. They also compare SNPs to AFLPs and RAPDs. However, I thought I was told that AFLPs and RAPDs don't actually use evolutionary derived traits and so they should not be used in phylogenetic analyses. Well I guess this isn't a phylogenetic analysis, it is a population analysis so that could be different, and anyway, SNPs are probably completely different from the other two.

Interesting notes/quotes from the paper:

"In practice, older species have often had time to accumulate a range of features: reproductive isolation, fixed apomorphies, and gene-tree monophyly, whereas young taxa often lack these features".

"Tree-based methods [of species delimitation] tend to require demonstrable monophyly, whereas non-tree-based methods more often focus on the discovery of differentiation associated with the earliest stages of lineage diversification". Such as??? I guess I will have to see Sites and Marshall (2003, 2004) for specifics. But I'm assuming non-tree methods are derived from population genetics like the ones used in this paper.

-the authors hope that both tree-based and non-tree based methods will be used together to delimit species

-the authors give four examples of famous species radiations that lack clear evidence on actual species boundaries: 1) Darwin's finches, 2) cichlid fishes, 3) Galapagos Tortoises, and 4) Tiger salamanders.

"Under the neutral coalescent the expected time to monophyly for even a single nuclear gene is often long (Hudson and Coyne 2002) suggesting that many real species exist that have not yet achieved monophyly for even a few genes".

"This reliance on multiple markers [many genes to delimit a species] implies that species in their very earliest stages will probably not be recognized, but it is the price one pays for the taxonomic stability that follows from only recognizing comparatively well-differentiated species". Interesting quote. It makes me think about the future of taxonomy, and whether one wants to focus on the process or the pattern. If you want to focus on the pattern, you will want to work on delimiting well-differentiated species. If you want to focus on the process, you might want to research species in their early stages. Or is it better to be experienced in both? Probably.

-the authors find parametric approaches that simultaneously estimate ancestral population size, migration rate and divergence times appealing for testing species taxa

-"melding of population genetics and speciation biology" -I'm seeing this phrase everywhere!