How ancestors’ genes change to produce different descendants is largely unknown. This is to say, 153 years after the Origin of Species, and nearly 60 years after the DNA helix discovery, that we are largely ignorant of how DNA alterations produce new species. Whole genome analysis, it might seem, could dispel the ignorance easily, as it spells genomes out, gene by gene. Doesn’t this make species’ differences obvious? No, it turns out. Differences are so numerous – in the millions – that even the question “what is a distinct species?” – is hard to answer. 

The stickleback was a saltwater fish thousands of years ago, and still is. At the end of the Ice Age, 10,000 years ago, freshwater streams and lakes opened up as glaciers retreated. Sticklebacks began invading the new niches. Today, descendants of saltwater ancestors inhabit freshwater habitats in Japan, North America, Iceland and Europe. These species differ from the ancestors, and from each other. Salt water types have bony armor and spines, for instance, presumably to fend off marine predators. Freshwater species have less armor, or none. Body shape, size and color differ too between marine and freshwater, and between species in streams and in lakes. Invisible differences abound too, beyond the obvious metabolic adaptation to freshwater.

Two adult males

To learn the genetic changes that created the new species, researchers analyzed genomes of 21 sticklebacks: one from Alaska, and 10 pairs – one marine, one freshwater — from Japan, North America and Europe. A fish from a Scotland river, for instance, paired with one from Scotland’s North Sea coast. “Whole genome” means gene by gene spelling of genomes for 21 animals. 

One finding seemed logical, namely, that a certain set of genes seemed to handle freshwater adaptation everywhere in the world. A marine fish’s problem of adapting to rivers seems identical from all oceans. One might expect fish to solve it the same way.

And, partly, it seemed that they did. Every freshwater species – from Japan,Alaska, and   Canada, and Europe– had 147 genome “regions” in common, and saltwater species lacked them. (Multiple genes may lie in a “region”.) So perhaps the regions contain the universal toolbox, “invented” at the end of the Ice Age to invade freshwater niches.

But sticklebacks didn’t stop varying with that toolbox. Far from it. Over 5.8 million “letters” in DNA were different among freshwater species, and less than ½% of them were in the toolbox regions.  In other words, over 99% of the rest of these freshwater genomes were sprinkled with millions of differences.

What does this show about how evolution originates species? “Messily,” is one answer. “Sticklebacks” is a noun for evolution’s freshwater species, just as “Americans” names the citizens of our country. Neither noun tries to define similarities or differences. But while we don’t expect genetics to define “an American,” we do expect solid answers to the question: “what defines a stickleback?” Genetics, today, should be the way a “species” is defined.

But today, the answer is ambiguous. It is not yet possible to know which of the millions of genetic differences were essential – that is, truly propelled evolution of the freshwater fish.

Worse, the difficulty was aggravated by another finding, concerning the different types of mutations at work. The most prevalent type is the hardest to detect.

The first sort of genetic difference is what evolution expects, namely that mutations alter ancestors’ protein coding genes, and the novel proteins make different descendants. Armor in marine species, for instance.  Certain genes make proteins that become armor. Mutation might cripple one of these genes, leaving a descendant armor-free. But with marine predators absent, the leaner fish might thrive in freshwater. The mutant gene could become prevalent in the new species’ genome.

But this wasn’t evolution’s common tool with sticklebacks.  Only 17% of genome differences were in protein coding regions. 

Evolution’s second tool leaves ancestors’ protein-coding genes unchanged, but uses them differently. What mutates are DNA regions whose products regulate protein protein production. They control how much protein a gene fabricates, for instance, or for how long. Bony armor might be abolished by tamping down – but not altering — genes that make it.

And this is where 83% of the differences were. (I pass over some cautious qualifications of the researchers.) It was differences of degree that most genomic changes caused (“How long is that protein gene ‘on’?”) not differences of kind (“Are mutated proteins in that descendant or not?”). Differences of degree are more difficult to detect, for they operate in the tumult of living cells’ metabolism. The fact that stickleback evolution seemed to have worked mostly by regulating ancestor protein genes, not altering them, makes it much harder to read from genomes exactly how different species originated.

What phenomenon in nature?

Species arise by descendants gradually differing from ancestors.

What did this discovery show?

It correlated genome differences with differences in bodies between ancestors and descendants. Some commonalities were revealed, along with a welter of differences.

What was known before? 

A very few correlations of genome changes with species differences. (See another one, in “Evolution caught in the act,” on this website.)

What remains unknown?

Why such copious variations among species? What, really, makes a stickleback a stickleback, since millions of differences infest DNA of different species? And how come some species haven’t differentiated entirely out of the “stickleback” category since the Ice Age?

F. Jones, et al., The genomic basis of adaptive evolution in threespine sticklebacks, 484 Nature 55-61, 5 April 2012.

 H. Hoekstra, Stickleback is the catch of the day, 484 Nature 46-47, 5 April 2012.