Genetics vs Genomics in a Conservation Context

I’ve been asked a few times the difference between genetics and genomics, so I thought I’d take the time to explain how I see each differently, specifically in a conservation context. Genetics, in a classic sense, deals with genes. Genetics may tackle topics such as what gene underlies a trait of interest; how does overexpression, underexpression, or knocking-out a gene effect growth and development; where does a gene fit into a regulatory or metabolic pathway; or what are the functional differences between alleles? Genetics also deals with inheritance, including understanding that alleles can be dominant or recessive; the frequency of lethal alleles of a genetic disease in a population; X-inactivation in cells for dosage compensation; or fitness coefficients for phenotypic traits.

Genomics differs in that it considers the whole genome, so genes + non-coding sequence + tagging of genes (via phosphorylation or methylation) for expression + local inversions or rearrangements of chromosomes. Genomes interact with the environment where a stress on the organism may turn on or off (or change the level of expression of) different gene products; thereby producing variation in response to the environment. While we continue to learn more about inheritance at the genomic level (eg- inheritance of the epigenome), a lot of research, especially in humans, focuses on how traits are associated with these genome-by-environment interactions.

I think part of the lack of understanding between genetics and genomics in a conservation context is that conservation genetics uses a multi locus approach. When genetics is defined in a single locus = single gene context, it can be easy to think of the 10-20 microsatellites or hundreds of amplified fragment length polymorphisms (AFLPs) as being genome studies. Sure, multiple evenly spaced markers will give more information about parameters of interest to conservation genetics (including population genetic diversity, inbreeding level, individual heterozygosity, and/or gene flow), but it’s not genetics in the classic sense as the markers are at neutral loci not genes. But that’s okay because conservation geneticists know they are doing population genetics not classical genetics. That said, when the conversation turns to conservation genomics, it seems like an issue of increasing the number of loci and estimating those same parameters with more markers representative of a larger proportion of the genome. But it’s not, because genomics does not just offer a finer scale of measurement but different measurements. If studies are only using genomics to refine traditional population genetic parameters, we should question whether the study is truly conservation genomics or simply conservation genetics with a lot of markers (and potentially higher power).

This always leads me to think (and feel free to disagree) that conservation genomics is not a real sub-discipline. I have yet to see a study that took a genomics approach to answer a conservation question. I think genomics provides the tools for detailed evolutionary studies which some researchers frame as conservation studies. No doubt the development of next-generation sequencing and non-reference genome based analyses has allowed for expanded evolutionary studies of species of conservation concern; but evolutionary genomics of species of conservation concern does not equal conservation genomics. Moving forward, is conservation genomics simply a buzz phrase or will it develop into a meaningful sub-discipline for the conservation of biodiversity?

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One Comment Add yours

  1. Hi guys, I think this post deals with an important topic: the danger of using the latest catch phrases to dress up evolutionary focused studies to look like conservation. It is important that all conservation geneticists are careful not to do this. However, I have a bit of a different take on one of the points you made: I think that a study that uses a genomics approach can be highly relevant for conservation, even if it is not ‘front line’ conservation itself, and therefore I would argue that it is still ‘conservation genomics’. I can give an example from my own field: Kevin Glover, from the Institute of Marine Research in Norway has been conducting what I would call ‘conservation genomics’ research to discover genetic markers (SNPs) that can be used to distinguish wild vs aquaculture raised Atlantic salmon using a 7K SNP chip ( e.g. http://www.ncbi.nlm.nih.gov/pubmed/21429178). Under your definition, this does not classify as ‘conservation genomics’ as it does not answer a specific conservation question. Essentially it is just developing tools for conservation. In a later study however (http://www.biomedcentral.com/1471-2156/14/74 ), they use this information to genotype 99 of the most diagnostic SNPs (much more economical than genotyping 7,000 SNPs) in a large number of populations in order to assess levels of aquaculture escapee introgression in wild populations. So, a clear conservation study, but ‘only’ conservation genetics, not conservation genomics, by your definition (unless the line for a ‘genomics’ definition is below 99 markers!).

    So personally, I think that studies using genomics approaches can be highly relevant for conservation, even if they do not directly answer a conservation question. But at the end of the day, maybe it is not that important whether something is ‘conservation genetics’ or ‘conservation genomics’ (same as e.g. ‘molecular ecology’ vs ‘ecological genomics’), but if we, as researchers, truly believe that our work can be of benefit in a conservation context, then why not use the catch phrases that might help get the funding or get more publicity for a study? Further, (this doesn’t relate directly to your post, but anyway) I don’t think we should feel guilty about also squeezing non-conservation related studies out of the same data. That’s just being efficient.

    But we, as conservation genetics researchers have to be responsible and make sure the limited research dollars are well spent.

    Keep up the good work guys!

    Craig

    PS- I’ll be talking at a workshop in Sweden in March that deals specifically with these issues: http://www.ebc.uu.se/Research/IEG/evbiol/congenomics/

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