The plan is to get into a (fairly) regular habit of blogging about evolutionary genetics research (and perhaps a bit of running and biking stuff). Anyway, 1st post is about a meeting I recently attended in Trondheim.
The first Wild Animal Genomics meeting was run by Josephine Pemberton and I, using funds from our ERC grants. That took place in Scotland three years ago, and was aimed at bringing together researchers that were using, or planned to use, genomics tools to study quantitative genetics, selection and microevolution in wild populations. In June this year Henrik Jensen and Arild Husby put together a follow-up meeting, which was held just outside Trondheim. I really like these kinds of meetings – fairly small (~30-35 people) and everybody working on similar topics. The meetings are modelled on the WAMBAM meetings which have been running for around 10 years and have proven hugely successful in bringing together a community of researchers using ‘animal models’ to study quantitative genetics in pedigreed populations.
One of the most striking things at the Trondheim meeting was how quickly research in the field has moved on. Three years ago, we were only just starting GWAS analyses, virtually nobody had full genome assemblies, and a state-of-the-art SNP chip had 10,000 markers. There was a recognition that QTL mapping by linkage analysis was hugely under-powered, but a (in hindsight very naive) hope that association scans would get around this, and that many of the quantitative traits we were studying would harbour some loci of moderate-large effect that might explain measurable variation in fitness. At the recent meeting, there were examples where reseaerchers had sequenced whole genomes of >1000 individuals, and a number of presentations showing GWAS results with high density SNP chips or genotyping-by-sequencing methods. In general (and there were some exceptions) the attempts to find loci underpinning quantitative variation hadn’t found much. Lessons from studies of complex traits in humans suggest this isn’t suprising, although there are clearly some wild populations where patterns of high LD and recent admixture mean that some loci will be found.
So does this all mean that the genomic approach to understanding genetic variation in wild populations has failed? I don’t think so. If one regards ‘gene hunting’ as the main reason for doing this work, then sure, there will be some disappointed researchers. However, the most exciting thing about the recent advances in molecular quantitative genetics has been some of the cool research that has gone beyond a GWAS and given us genuine insight into the genetic architecture of quantitative traits. It isn’t necessary to find the loci that explain significant variation in order to perform analyses such as chromosome partitioning, genomic prediction, regional heritability mapping, and inbreeding coefficient estimation. Not only that, but these analyses do not require pedigrees and are robust to different kinds of genetic architecture. With that in mind, I still think these are exciting times for evolutionary genomics of wild populations. In the next few years we should expect to see research that describes the architecture of traits, identifies genetic changes in response to selection, gives us new insight into the mechanisms of inbreeding depression, helps us understand sexually dimorphic traits and no doubt addresses a whole load of other questions. Not only that, but we can start to do so in any population where phenotypes and DNA can be collected; the constraint of needing decades worth of pedigree data is no longer there, and so we should get broader taxonomic representation in this field. The biggest challenge will probably be in collecting good phenotypic data in large enough numbers to perform robust analyses. In other words, the most important researchers in the genomics era will still be the dedicated natural historians and ecologists that have underpinned so much of what we do today.