Found this on Phys.org: Sweeping gene survey reveals new facets of evolution

"Who would have suspected that a handheld genetic test used to unmask sushi bars pawning off tilapia for tuna could deliver deep insights into evolution, including how new species emerge?

And who would have thought to trawl through five million of these gene snapshots—called "DNA barcodes"—collected from 100,000 animal species by hundreds of researchers around the world and deposited in the US government-run GenBank database?

That would be Mark Stoeckle from The Rockefeller University in New York and David Thaler at the University of Basel in Switzerland, who together published findings last week sure to jostle, if not overturn, more than one settled idea about how evolution unfolds.

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.

But is that true?

"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.

The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

That reaction is understandable: How does one explain the fact that 90 percent of animal life, genetically speaking, is roughly the same age?

Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean?

[...]

On the one hand, the COI gene sequence is similar across all animals, making it easy to pick out and compare.

On the other hand, these mitochondrial snippets are different enough to be able to distinguish between each species.

"It coincides almost perfectly with species designations made by specialist experts in each animal domain," Thaler said.

In analysing the barcodes across 100,000 species, the researchers found a telltale sign showing that almost all the animals emerged about the same time as humans.


What they saw was a lack of variation in so-called "neutral" mutations, which are the slight changes in DNA across generations that neither help nor hurt an individual's chances of survival.

In other words, they were irrelevant in terms of the natural and sexual drivers of evolution.

Environmental trauma is one possibility, explained Jesse Ausubel, director of the Program for the Human Environment at The Rockefeller University.

"Viruses, ice ages, successful new competitors, loss of prey—all these may cause periods when the population of an animal drops sharply," he told AFP, commenting on the study.

"In these periods, it is easier for a genetic innovation to sweep the population and contribute to the emergence of a new species."

But the last true mass extinction event was 65.5 million years ago when a likely asteroid strike wiped out land-bound dinosaurs and half of all species on Earth. This means a population "bottleneck" is only a partial explanation at best.

"The simplest interpretation is that life is always evolving," said Stoeckle.

"It is more likely that—at all times in evolution—the animals alive at that point arose relatively recently."

In this view, a species only lasts a certain amount of time before it either evolves into something new or goes extinct.

And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there's nothing much in between.

"If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space."

The absence of "in-between" species is something that also perplexed Darwin, he said.

"


The study in question is the Why Should Mitochondria Define Species? by Mark Y. Stoeckle and David S. Thaler (officially published in Human Evolution here). Here is the abstract:

"More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years."


The most interesting finding is that species quickly evolve into new species then seem to stabilise for a long period of time before the next evolutionary spurt. What is fascinating is that this process seems to have occurred roughly around the same time, 100,000 to 200,000 years ago, for 90% of species on Earth, and that mtDNA mutations alone are enough to identify and define those species.

They argue that the mitochondrial mutations defining species are neutral. But I am not so sure about it. They should read my article Mutations in Coenzyme Q gene define most major mtDNA haplogroups, where I demonstrate that positive selection for beneficial polymorphisms in the MT-CYB gene appear to have played a major role in mitochondrial evolution in human populations, and that major mtDNA haplogroups are actually defined by such mutations.

The last glacial period started 110,000 years ago and ended 11,700 years ago. It would appear that most modern species took form just before that. It could be that the absence of "in-between" species could have been caused by population bottlenecks during the Last Ice Age itself, what has been called the quaternary extinction event and which led to mass extinctions in Afro-Eurasia and the Americas during the transition from the Pleistocene to the Holocene. This period also corresponds to the expansion of Homo sapiens from Africa to all other continents, an event that surely had an impact on the local ecosystems, disrupting the whole balance of the food chain, at least for large terrestrial animals.