Species and systematics
evolvingthoughts | June 19, 2006
When we attempt to apply to organisms that are not obligately sexual (that is, which don't have to have sex to reproduce) concepts that were specified to use with those that are, we have problems. The Recombination Model is one such attempt. Sure, some microbial species exchange genes. Others do it more frequently and more completely. There appears to be a continuum of gene exchange all the way from almost never to almost every time. So why should we expect that gene transfer will provide us with the sort of homogeneity of lineages and quasispecies that it does in obligate sexuals?
In part…
evolvingthoughts | June 18, 2006
The second main approach to a natural conception of microbial species (by which I mean, as opposed to operational, practical or conventional ones, collectively called "artificial" conceptions) is what I will call the Quasispecies Model. According to the concept developed by Manfred Eigen for viral species, a quasispecies ("as-if-species") is a cluster of genomes in a genome space of the dimensionality the number of loci. A quasipecies is in effect a cloud of genomes, clustering around a "wild-type" coordinate (that is, genome) that may or may not actually have an extant or extinct instance…
evolvingthoughts | June 17, 2006
The cluster of genomes of asexual organisms forms what is called a "phylotype" (Denniston 1974, a term coined by C. W. Cotterman in unpublished notes dated 1960; I like to track these things down). Phylotype is a taxon-neutral term, though, that is determined entirely by the arbitrary level of genetic identity chosen. For example, "species" in asexuals might be specified as being 98%+ similarity of genome, or it might be 99.9%+ (I have seen both in the literature). A phylotype of, say 67% or 80% might be used for other purposes (such as identifying a disease-causing group of microbes).
The…
evolvingthoughts | June 16, 2006
Reposted from the old blog.
OK, this is one of a series of posts in which I will play with ideas that might will become a paper.
The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).
But many microbial species either do not share genes to reproduce, or they can but do not need to. So, the question is sometimes raised whether microbes (of this kind) form species at all…
evolvingthoughts | June 15, 2006A recent paper in Nature, Speciation by hybridization in Heliconius butterflies is getting a fair bit of comment on the internet. This is a case where the researchers, wondering if an Andean butterfly species was a hybrid of two others, decided to test the hypothesis by re-evolving it deliberately.
The process is called "homoploid" because there was no change in chromosome number. Previous studies in various organisms, particularly in plants, but not restricted to them, had shown cases of speciation by hybridisation where disparate numbers of chromosomes in the hybrid were equalised by a…
evolvingthoughts | June 13, 2006[This is another repost from my old blog. I am sitting at home suffering with a hole in my jaw where a tooth, or its remnants was extracted with extreme prejudice, so I don't feel much like blogging.]
The evil that men do lives after them;
The good is oft interred with their bones;
So let it be with Caesar.
After a decent period to mourn the death of one of the greatest biologists of the century on any measure, perhaps it is time now to reassess how Mayr's legacy is to be presented. I have no competence to debate his scientific ideas - if speciation is mostly allopatric, or if it is…
evolvingthoughts | June 12, 2006An archival post from a year and a half ago.
I recently attended my last Systematics Forum at the Melbourne Museum. This lovely little series covers issues at a technical and theoretical level to do with classification in biology, which is my obsession du jour.
The forum was a special one, a talk by Michael S. Y. Lee (aka Mike) of the South Australia Museum, and the University of Adelaide, entitled Whale teeth, bird hands and snake legs: why palaeontologists need to talk to molecular biologists (and vice versa).
Mike is one of those way too handsome and way too young types who seems to have…