UCL Division of Biosciences


Mark's bêtes noires

Now that I am an old man I going to start acting like one and be grumpy about the use of certain terms.

  • Ancestry Informative Marker (AIM): All alleles are 'ancestry informative'! In the population history inference literature an AIM is usually selected as an allele showing high allele fraction differences (high FST) between certain regions (usually between continents). Putting aside issues related to which regional population samples are selected to define these high FST AIMs, allele fraction differences is no indicator of the ancestry information content of an allele. Indeed, if you are interested in recent ancestry in closely-related populations, rare (and so low FST) alleles can be more informative.
  • Mutation (when referring to an allele): OK, the main culprits of this error are medics, but geneticists also make it. A mutation is the event that generates a new allele. When considering genetic variants in a population you are considering alleles. The only grey area is de novo alleles, where the mutation event generating the allele occurred in that individual the allele is observed in.
  • Incomplete lineage sorting (ILS): This term is usually applied when a gene tree does not conform to a population or species tree. Setting aside the fact that populations, and even species, only very rarely have a history that is truly tree-like, this is expected! The term ILS gives the impression that the drift process hasn't done a proper job of making sure those naughty, wayward lineages reflect the true and righteous population tree.
  • Genetic 'marker': This begs the question 'marker of what?' In population genetics the term 'marker' is usually used in such a way as to suggest a particular allele is a proxy for a particular population origin. Putting aside the problems of defining an ancestral source population, individual alleles are almost always very poor proxies for population origins.
  • Non-paternity / false paternity event (as applied to cases where the biological father is not the assumed father): OK, I have also used these terms, but they are silly. Clearly there was a paternity event so it can't be described as 'non-' or 'false'. 'Incorrectly assigned paternity event' would be a more accurate description.
  • High altitude population: People don't live at high altitude (except those on the international space station, and maybe Donald Trump). Some people do live at high elevation though.
  • Europe (as a continent): Its not a continent, it's a peninsula of the Eurasian continent. If Europe is a continent then the Indian 'sub-continent' should be promoted to the same status.
  • 'When humans left Africa': Should be 'when some humans left Africa'; I am quite sure most humans at the time had the good sense to stay in Africa.
  • "So we conclude that things are more complicated than previously thought": This begs the question "why the hell did you think things were simple in the first place"? I suspect this arises from people confusing models with reality; simple models are almost always justified and almost never correct.
  • Frequency (when meaning proportion): Sensu stricto frequency means  change with respect to time. If, for example, we are talking about how common a variant is in a population, we are really describing its proportion, or fraction, not its frequency.