On the origin of species insights from the ecological genomics of lake whitefish: Louis Bernatchez1 et al; Phil. Trans. R. Soc. B (2010)


Evolution, as explained by Darwin’s theory of origin, is a process of population divergence and speciation by natural selection and adaptation driven by ecological heterogeneity and competitive interactions. Several studies conducted in light of this theory as well as large amount of ecological information, provides a support for the role of divergent natural selection as main cause of evolution. But having a thorough understanding of the genomics underlying these evolutionary process will provide further strong grounds for this theory of evolution.
The review “On the origin of species: insight from the ecological genomics of lake whitefish” provides the genetic basis of evolutionary change and diversification driven by natural selection by reviewing the main findings of the long term research program conducting the ecological genomics of sympatric population of whitefish (Coregonus sp) engaged in the process of speciation. The review provides an example as how by applying a combination of multiple research approaches under the conceptual idea of adaptive radiation provides an insight into the evolutionary processes in a non-model species.
Adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Starting with a recent single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits with which they can exploit a range of divergent environments.
The genus Coregonus used in this review is the most speciose genus within family Salmonidae. Since the Pleistocene, the members of this species have evolved both allopatrically and sympatrically. The review involves study of dwarf and normal whitefish, which have developed reproductive isolation because of accumulation of genetic differences during allopatric geographical isolation and subsequent ecological divergence in sympatry.
Allopatric speciation occurs when population of same species are isolated due to geographical changes. Sympatric speciation is evolution of new species from a single ancestral species while inhabiting the same geographical region. It could occur due to genetic polymorphism.
The basic strategy for the study of ecological genomics used in the review, consists of four steps:
1. Identifying the phenotypic traits most likely to be adaptive. This involves Fst/Qst analysis and gene expression, microarray studies to get insight from transcriptome. Parallel pattern of gene expression, as well as inter-individual variance in expression were also observed through these experiments. Thus, this provides strong evidence for the role of natural selection in the evolution of differential regulation of genes involving a vast array of physiological processes.
2. Elucidating the genetic bases of these phenotypes. This involves mapping genetic regions underlying the expression of phenotypes for documenting the number, location and effect of genomic locations contributing to differentiation within and among the populations or species. It includes eQTL and pQTL and identifying the co-localization between eQTL and pQTL. This helped in determination of the extent to which genes controlling transcriptional variation may underlie adaptive divergence in dwarf and normal whitefish.
3. Finding the evidence for natural selection at the genome level in the wild. This involves genotyping of large number of loci to accurately estimate the expected level of genetic differentiation under neutrality, and the proportion of loci linked to genes implicated in adaptation and reproductive isolation. Genome scans also reveal the parallel trends of divergence through the analysis of multiple populations, consequently offering stronger support for the role of natural selection in adaptive trait evolution
4. Identifying mechanisms of reproductive isolation and elucidating their molecular basis. This involves investigating intrinsic and extrinsic factors influencing reproductive isolation. This is done by combining experimental studies and pQTL, eQTL mapping with a comparative analysis of genome-wide transcription patterns.

Thus, by integrating various methodologies like gene mapping, population genomics and transcriptomics, the authors tried to identify genes representing a large number of physiological functions that could be the probable candidates for the adaptive divergence and reproductive isolation of dwarf and normal whitefish. For future works they intend to focus their research on finding the exact role of these genes.
Being from proteomics background, as much I understood this paper I think it’s a good attempt by the authors to integrate genomics, evolution and ecology. But as discussed in the group discussion, it is more like a paper-by-paper compilation of the results of the experiments conducted by the group. Thus, it’s not like a global review involving different works on the ecological genomics but more as a compilation of their own data and results. They performed quite a number of experiments and integrated the results of those different varied experiments to provide an insight on the genetic basis of adaptive evolution. Thus, they cover lot of methods involved in such analysis. However, the review as such is not so clear and easy to understand as it involves lots of experiments whose methods and motives are not explained in the review. From the discussions, it was concluded that results of some of the experiments are not really exclusive, like the result of microarray studies showing upregulated genes in dwarf and normal whitefish represented by the heat map is not very exclusive as it states an obvious result of the phenotypic traits (fig.2). Thus, some of such results are technologically biased. Similarly, the result shown in fig.5 explaining the comparison of simulated and observed distribution of Fst for dwarf and normal fish from three different lakes is also not so clear as they are not correlated. Since, they conducted lot of experiments and did a detailed study so they have lot of data but the results presented in the review are not very correlated.
Thus, overall, the review is a good example to explain the combination of different research approaches targeting various functional and biological levels. It explains a good strategy for deciphering the genetic basis of evolutionary changes and diversification driven by natural selection and is also a good example to explain the integration of genomics, ecology and evolution.

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 nicee.srivastava. Reposted by MRR to allow collection by research blogging.