Did you read Matthew’s post on the okapi yesterday? I hope so, because I’m worried, in view of the paucity of comments on science posts, that people are skipping them. Perhaps that just reflects the dearth of things that non-scientist readers have to say. I hope that’s the answer, for it takes about four or five times more work to do a science post than, say, an anti-theist post.
So I’ll try once more today. This is a genetics paper that came out a few weeks ago, but I haven’t had time until now to read it and summarize it. It’s on the phenomenon of horizontal gene transfer (HGT), whereby genes move between the genomes of very distantly related species. Examples include the include the absorption of bacteria by other species (that’s how the mitochondria originated, a theory suggested by Lynn Margulis; and these mitochondria, once free-living bacteria, contribute their genes to the absorbing organism); the transfer of pigment genes from fungi to aphids, which give the aphids a red color that may help hide them; and the transfer of several enzymes from bacteria to insects, which help the insects use new plants as food.
The phenomenon of HGT has been called “non-Darwinian,” since it simply wasn’t envisioned by Darwin or, indeed, even in the early days (ca. 1930-1940) of the “modern synthetic theory” of evolution. But, contra some critics of evolution, HGT does not invalidate the modern theory of evolution. For the transfer of genes between distantly related species is simply a new source of genetic variation—like “normal” mutations—whose fate is still subject to whether the transferred genes are good or bad for the host. In the case of aphids, for instance, the acquired pigment genes rose in frequency in the pea aphid species by natural selection, but had they been deleterious they would have been eliminated.
This kind of gene transfer can occur in several ways: by eating of one organism by another, and then incorporation of that organism’s DNA into the genome; by infectious transfer of microorganisms followed by the same kind of incorporation; or simply by absorption of microorganisms into the body, as when rotifers rehydrate after they’ve become desiccated.
Infrequent HGT, then, doesn’t kill the theory of evolution, but expands it by showing that “mutations”—the raw material for evolution—can be acquired in a way we didn’t previously suspect.
Now if HGT was very, very common, then it would completely efface the evolutionary relatedness of organisms as seen from their DNA. If Drosophila species, for example, got genes repeatedly from microorganisms, and different fly species got different genes, then one might be completely thrown off by using DNA sequences to determine how related they are. You’d mess up your phylogeny by including horizontally acquired DNA from unrelated species in your tree-making algorithm. This was the basis of the infamous New Scientist cover that read “Where Darwin Went Wrong.” The “wrong” bit was supposedly that Darwin envisioned a branching bush of life, but HGT might mean that the branches were effaced by transfer of DNA from distantly related species, and we wouldn’t have easily defined bushes at all.
Fortunately for evolutionists, HGT isn’t that common—certainly not common enough to prevent us from reconstructing evolutionary relationships, as scientists recently did for families of birds (see here). Cries that “Darwin was wrong!” or “Evolutionary theory is disproven!” are simply wrong. The branching bush of life is still secure, though there are bits of bark that move between the branches.
A new paper in Genome Biology by Alastair Crisp et al. (reference and download below) is the first attempt to systematically find out how much HGT there is between three groups of metazoan organisms (nematodes, flies, and primates) and simpler ones (fungi, microbes, algae). What they did was perform genome scans of DNA sequences of species in all these groups, looking for those gene sequences in nematodes, flies, and humans that were far more similar to sequences in the other species than to more-closely related species of metazoans. For example, they could find a gene in one or several species of fruit flies that was far more similar in sequence to a gene in a bacterium than to any genes in other metazoans. That would imply that that gene had been transferred from bacteria to flies. (Another possibility is that the gene was not the result of HGT, but was present in the common ancestor of all of these species and was simply lost in all the non-fly metazoan species. But the authors used controls to rule out that possibility.)
The authors also divided up the genes that presumably moved by HGT into three classes, A, B, and C, differing in the assurance with which HGT occurred (i.e., the degree of difference in similarity of DNA between related and very unrelated species). “A” is the gold standard, with very high probability of HGT, while B and C have less assurance, but still probably still reflect HGT.
What Crisp et al. revealed was a moderate but not high frequency of HGT in two of the groups, and a low frequency in the other. The results suggest that there is indeed HGT, it’s not vanishingly rare, and that it can contribute to evolutionary change. But the level of HGT is not high enough to either efface phylogenetic trees or suggest that we revise evolutionary theory to say that genetic variation comes more often from HGT than from simple mutations in organisms.
The salient findings:
- First, a refresher: primates have roughly 20,000 genes, fruit flies about 15,000, and the nematode Caenorhabditis about 11,000. You can see that there’s not much difference in gene number between these species: a result that surprised evolutionists and developmental biologists when the data first came out. Perhaps solipsistically, we humans seem a lot more complicated than flies, but don’t have many more genes. The difference may reside in how those genes are used, that is, in the regulation of a fairly constant number of genes.
- How much HGT has occurred? In primates, the number of genes that have moved by HGT in classes A, B, and C are 32, 79, and 109, respectively. In Drosophila the numbers are 40, 25, and 4. In the nematodes it’s 68, 127, and 173, respectively. There’s much less HGT in flies than in the other groups, but still the extent of HGT is only moderate in worms and primates: about 0.2%- 1.5%, depending on which species you use and what class of genes you want to count as acquired by HGT. That’s not enough transfer to constitute serious problems for making phylogenetic trees.
- Most of the genes transferred to all three groups were those producing enzymes, which makes sense since they can confer immediate new functions on the recipient organism. Genes most often transferred affected the immune system, lipid metabolism, the modification of other large molecules, proteins produced when organisms are stressed, and antioxidant activities. This held across worms, flies, and primates.
- Curiously, one gene that may have been transferred horizontally is the Landsteiner blood group gene in primates: the gene producing different antigens on red blood cells that give us type A, B, AB or O blood.
- Finally, by placing the putatively transferred genes on the family tree of metazoans, they determined that gene transfer is both ancient and ongoing: HGT genes were acquired in both the ancient parts of a group’s phylogeny or in the more recent parts: say in the lineage of only one species of primate—which implies recent HGT since that one species diverged from other primates.
Where do the genes transferred into primates, worms, and flies come from? The authors provide this handy chart:
The recipients are in the column to the left, the donor groups along the bottom. As you see, most genes come from microbes: bacteria and protists. This isn’t surprising because those organisms can transfer genes by either ingestion or infection.
The upshot is that we have a nice new finding, with some surprises—the ABO blood group genes still amaze me, and I’d like more confirmation—but a finding that hardly endangers evolutionary theory. And though I find the extent of HGT low, especially in flies, the authors do try to make a case that it’s rather high. As they note in the paper’s conclusions:
Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages. Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans. The majority of these genes are concerned with metabolism, suggesting that HGT contributes to biochemical diversification during animal evolution.
Well, technically “173” is “hundreds,” but I think the actual numbers I gave above, and the percentages of genes in a genome acquired by HGT, show that its prevalence is less than the paragraph above would suggest.
Nevertheless, it’s clear that we have a new source of genetic variation, and one that can contribute to adaptive evolution. But remember as well that the frequency of HGT transfer must be low, since such events must be rare, so we’re not entitled to say either that the number or commonality of HGT events is substantially higher than the number of genetic novelties produced by the more conventional process of mutations occurring within a species’ genome. This is why the branching bush of life seems, for the time, secure.
Crisp, A., C. Boschetti, M. Perry, A. Tunnacliffe, and G. Micklem. 2015. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biology 16:50, doi 10.1186/s13059-015-0607-3.