Several geneticists have told me that I should never, ever, ever use the word “locus/loci” the way its is often used in the field of phylogenetic inference:
“A four-locus phylogeny of X…”
“…and all loci employed supported the monophyly of…”
“…no significant conflict among the loci was detected…”
etc.
"Locus", they argue, should be reserved for the strict definition: “the position of a gene (or other significant sequence) on a chromosome”.
So instead I've always used “genes” or “genetic markers” (or simply “markers”). The latter - “marker” - is useful when referring to, e.g., the ITS region, that does not fully qualify as a “gene”.
What’s your take on this?
I should have added: I'm asking because at least half of the papers I review consistently use "locus/loci".
"gene" is may be better. But the most precise is "marker", you can use single locus marker to set a single gene phylogeny or a multilocus marker approach to infer phylogeny of organisms.
Marker is the best choice of wording mainly because it has been used more often and also the fact that it has been used more cautiously which actually means it has yet its meaning boundary denoting to specific areas. Whereas Locus and Genes have been far more used in many diverse areas of molecular areas that alone in my opinion are not enough to refer to phylogenetic areas.
If I may, I'd like to suggest that all three names are appropriate, but are 'strictly' appropriate only for different 'types' of data. If you are constructing a tree based on phenetic information controlled by genes then either 'gene' or 'locus' could be used for each set of data. Similarly if you were using molecular approaches to analyse the SNPs or sequences responsible for those phenotypes I'd also use both interchangeably. If using several lengths of sanger sequence, without detailed functional information, I'd use locus for each since you probably have a chromosomal location, but not necessarily known function, and each could contain more than a single variant or 'marker' in different individual molecules. If using several directly detected SNPs and/or VNTR/SSR data then I'd use 'markers'. I wouldn't use 'gene' in these last cases, since there is no evidence that they are expressed or have any intrinsic relationship to any coding sequence or functional consequence for a protein. Of course, as the biology of genomics has become clearer over the last few decades, the connection between the theoretical terms 'gene' and 'loci', as they were originally coined, and their actually physical reality (and the data that we use in phylogenetics) has become more blurred rather than clearer. SO on one hand you could argue it doesn't matter which term you use, unless it creates an ambiguity within the reader's mind when reading your manuscript. And that has to be on a study by study or paper by paper basis. Marker is a universal term that covers all levels of genetic data and so is a good hedge if you don't want to be specific in any case.
Interesting topic.
These is complex concept and should understand in the context. Understanding differs among communities. Let's list the glossary part for these terms. I'm sure we can get some insights.
Evoluton. 2005. DJ Futuyma.
Gene: the functional unit of heredity.
Locus: A site on a chromosome occupied by a specific gene; more loosely, the gene itself, in all its allelic states.
Handbook of Statistical Genetics 3ed 2007. BJ Balding, M. Bishop & C. Cannings
Gene: a segment (not necessarily contiguous) of DNA that codes for a protein of function RNA.
Locus: the position of a gene on a chromosome.
just a primer from two books at hand. I remember these terms frequently appeared in Glossary Box in journal Trends in Ecology & Evolution.
Hope guys keep on listing.
Nice discussion. If I may add, my impression is that "marker" is a methodological term, that distinguishes between the qualitative properties of different kinds of genetic data. For instance, you may use "marker" to distinguish between SSR (microsatellites), RFLP, RAPD, VNTR, RAD, SNP, or Sanger sequencing markers. Now, "gene" may be used as a loose term for hereditary unit. However, these units express complete functions (a protein or ribosomal RNA), while most "genes" used in phylogenetics are partial entities of these "genes" (exons, introns, etc.). Nonetheless, It may be used to distinguish between units within the same "locus", for instance mitochondrial genes. Or to distinguish between ITS, 28S, 16S regions, which are essentially in the same "locus" or chromosomal region. The term "locus" or "loci" comes in handy when you want to distinguish explicitly between "genes" that are in different chromosomal locations. For instance, the ITS, tef1 and rpb2 are in theory distinct loci, but you couldn't say the same for ITS, 28S and 16S. And all of these, methodologically, are Sanger sequencing markers.
Cheers,
http://en.wikipedia.org/wiki/Genetic_marker
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