In the first paper being discussed in the tutorial (~journal club) of Genomics-Ecology-Evolution etc., the authors (Bernatchez et al.) had a pleasant task of reviewing their own long-term study on white fish species-pair (Coregonus clupeaformis and C.lavaretus). The paper gives a well-structured example how, and also why, a non-model organism can be used to study ecological genomics. One thing is for sure based on this paper; it requires a lot of time and work. The authors have come a long way to actually make their study organism an excellent target for the study of ecological genomics with a large dataset of both ecological and genetic studies.
Since the participants of this tutorial have quite different backgrounds, first the discussion was focused on the definitions of the main terms use here, such as “species” and “sympatric”. Can we talk about two sympatric species that are able to hybridize and live in the different water layers? Authors also don’t seem to be quite sure if species is the right term here and sometimes they use terms “species pair” and sometimes “two forms”. I suppose one could discuss the definitions forever but the main point here, however, is that the divergence of these two forms is quite recent (<15000yr), and after geographical (genetic) isolation during the Pleistocene, they have evolved different phenotypes (“dwarf” vs. “normal”) in sympatry. Therefore, this system is very ideal for detecting genes behind adaptive phenotypic traits because probably only the genes with strongest adaptive importance show some differences between the forms. The longer the genetic isolation lasts the more also non-adaptive, or weakly adaptive, genes differentiate making it more difficult to detect the genes and traits that play the major role in the beginning of speciation.
As my research topics are not related to ecological genomics (although it could be easily included), I have difficulties to evaluate the methods used in different parts of the paper. And because it’s a review, the methods are also not explained very detailed here. However, some critics, or at least questions, concerning the methods were raised during the discussion. For the microarray analysis the Atlantic salmon microarray was used (because there is none available for whitefish). There were some doubts that this non-specificity could affect the results. This is of course one general weakness of using non-model organisms and difficult to control. Basically one can just hope that the microarray works for the study species. With the Fst outlier analysis, it is often problematic to decide which one are really outliers. One should control for the amount of markers used, but this is often ignored. Meaning, then many false “candidate genes” are detected. On the other hand, maybe it’s better to select too many than too few candidates for the further studies, if there are enough resources for analyzing more.
The authors have so far come to the stage where they have some candidate genes for adaptive divergence and reproductive isolation and their next step is to confirm the specific role and importance of them. So basically their future plan is to make similar studies but with next-generation sequencing. They have a nice study system and hopefully they get some more detailed results. I think the main merit of this review is to give a main protocol for studying ecological genomics of non-model species because they might give a better idea about speciation in nature than using model organisms that haven’t really been under natural conditions for several generations. Therefore, besides developing the methods for certain steps on this protocol it’s also important to improve the protocol itself and thus making it easier to include more non-model organism into the studies of ecological genomics.
Bernatchez, L., Renaut, S., Whiteley, A., Derome, N., Jeukens, J., Landry, L., Lu, G., Nolte, A., Ostbye, K., Rogers, S., & St-Cyr, J. (2010). On the origin of species: insights from the ecological genomics of lake whitefish Philosophical Transactions of the Royal Society B: Biological Sciences, 365 (1547), 1783-1800 DOI: 10.1098/rstb.2009.0274
Originally posted by Mikko. Reposted by MRR to allow collection by research blogging.