June flashback: Massive Genetic Study Reveals 90 Percent Of Earth’s Animals Appeared At Same Time

Landmark new research that involves analyzing millions of DNA barcodes has debunked much about what we know today about the evolution of species.

In a massive genetic study, senior research associate at the Program for the Human Environment at Rockefeller University Mark Stoeckle and University of Basel geneticist David Thaler discovered that virtually 90 percent of all animals on Earth appeared at right around the same time.

More specifically, they found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.

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

What Is DNA Barcoding?

Over the last decade, hundreds of scientists collected around 5 million DNA barcodes from 100,000 animal species in different parts of the globe. Stoeckle and Thaler looked through these 5 million genetic imprints to find one of the most surprising discoveries about evolution to date.

There are two types of DNA. Most people know nuclear DNA. This is the DNA containing the genetic blueprint for each single individual. It is passed down from the parents to the offspring. The genome is made from kinds types of molecules arranged in pairs. There are 3 billion of these pairs, which are then used to form thousands of genes.

The other, less familiar type of DNA is one found in the mitochondria of cells. The mitochondria generate energy for the cell and contains 37 genes. One of these is the COI gene, which is used to create DNA barcodes. All species have a very similar mitochondrial DNA, but their DNA is also different enough so we can distinguish between species.

Paul Hebert, biologist and director of the Biodiversity Institute of Ontario, developed a new way to identify species by studying the COI gene.

Born Around The Same Time

In analyzing the COI of 100,000 species, Stoeckle and Thaler arrived at the conclusion that most animals appeared simultaneously. They found that the neutral mutation across species were not as varied as expected. Neutral mutation refers to the slight DNA changes that occur across generations. They can be compared to tree rings because they can tell how old a certain specie or individual is.

As to how that could have happened, it's unclear. A likely possibility is the occurrence of a sudden event that caused large-scale environmental trauma and wiped out majority of the Earth's species.

"Viruses, ice ages, successful new competitors, loss of prey — all these may cause periods when the population of an animal drops sharply," explains Jesse Ausubel, director of the Program for the Human Environment.

Such times give rise to sweeping genetic changes across the planet, causing new species to appear. However, the last time such an occurrence took place was 65 million years ago, when an asteroid hit the Earth and killed off the dinosaurs and half of all other species on the planet.

Did 90% of Animal Species Appear about the Same Time as Human Beings?

Many of you have seen headlines like this on social media recently. What is the origin of this flurry of excited claims? Do they have any merit?

The claims originate with a scientific paper titled, “Why should mitochondria define species?” published in May in a low-profile Italian journal, Human Evolution (not to be confused with the prestigious Journal of Human Evolution). Shortly after, the science media site Phys.org published a short summary. Authored by the Rockefeller Institute (the home institution of the lead author), this extended press release didn’t generate much reaction inside or outside of the scientific community. However, a follow-up article published on the same website oversimplified and misportrayed the conclusions of the paper: “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.” It was this mischaracterization of the original research that kicked off a firestorm of reactions, primarily amongst critics of evolution.

Are the results reported as surprising as the press release makes it sound? Did most animal species really come into being around the same time? To tackle these questions, we first must examine the original intent of the authors of this paper.

The lead author, Dr. Mark Stoeckle, is s a pioneer in the “DNA barcoding” initiative. The idea of DNA barcoding is that small pieces of DNA can be sequenced from many different species, and the genetic variation observed could be used as a rapid identification method for the millions of species on earth. Some advocates have gone as far as to suggest that DNA barcoding should be used as a method of defining species themselves, an idea captured in the title of the paper that we are discussing here. As a result, barcoding has been a contentious topic among biologists, not unlike the debates over the exact mechanisms behind evolution. These debates have provided fodder for critics of evolution, who often use disagreements among scientists to portray the whole field of evolutionary biology in crisis.

Mitochondrial DNA: A tiny genome we each inherited from our mother

Barcoding is one of several DNA “fingerprinting” techniques that take advantage of the unusual properties of a small genome that most of us never think about: our mitochondrial genome (mtDNA, for short). In most animals, this tiny genome—less than 20,000 nucleotides (compared to several billion in our full genome)—is passed down to offspring solely through the maternal line. Yes, your mtDNA genome is 100% your mother’s, and 0% your father’s. As it is copied and passed down from mother to child, mistakes may occur, creating new genetic variations. Hence, by examining the variation in living organisms, it is possible to trace distinct lineages in today’s world back to an ancient common ancestor.

This simple inheritance pattern (in contrast to the tangled web of interactions which characterize the nuclear genome) makes it relatively easy to trace lineages. However, there are limits to the inferences we can draw solely from mtDNA, and those limits are the source of some of the confusion observed on social media reactions to this paper.

What did the paper actually demonstrate, and why is it important?

First, Stoeckle and Thaler examined the variation in a 600-nucleotide region of one gene in the genome of the mitochondria for five million individual animals representing 100,000 animal species. They concluded that the genetic diversity of mtDNA is relatively low (about 0.2% differences in the gene they examined, or about a 1 nucleotide difference) within most species. This is true whether that species had a restricted geographical range and/or population size (e.g. African elephants) or if the species had a large population and geographic range (e.g. humans). As we will see, it is this result that has led to the incorrect claim that most species originated about the same time.

The overriding interest in barcoding life is a desire to find a practical method for identifying a species—which is the basic unit of taxonomy. Stoeckle and Thaler propose in their paper that mitochondrial DNA can provide a reliable tool for identifying distinct lineages or organisms. They equate those distinct lineages of mtDNA with what we commonly identify as species. Their analysis suggests that, for many animals, using this small portion of the mtDNA inherited from the mothers is a good practical marker for species.

Stoeckel and Thaler have relied on analyses of a single gene to come to these conclusions. Will the general patterns they have observed hold true with additional data collection and analysis? Only time will tell.

Did Stoeckel and Thaler conclude that “90% of animal species appeared at same time as humans”?

The answer is No. Here is the relevant quote from the published paper:

the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.

In other words, the genetic diversity observed in mitochondrial genomes of most species alive today can be attributed to the accumulation of mutations from an ancestral genome within the past 200,000 years.

Their conclusions are interesting (and to some extent unexpected) but they are not shocking, nor do they defy evolutionary theory. To see why, let’s unpack what the authors have claimed. First, it is important to note that the authors never claim that most “species” came into existence within the past 200,000 years. Rather, what has come into existence within that time frame is the genetic variation observed in one gene in the mitochondrial genome. By tracing the mutations in that one gene, we can trace the origin of the gene back to the last common female ancestor of all living members of a certain species (the so-called “mitochondrial Eve”). But this discovery, at best, tells us the minimum age of the species. It tells us little to nothing about the maximum age of a species.

To understand the difference between “minimum” and “maximum” age for a species, consider the cheetah (Acinonyx jubatu). The cheetah has remarkably little genetic variation in both its nuclear and mitochondrial genome. Using the same methods employed by Stoeckle and Thaler, this species appears to be no more than 12,000 years old (unlike 90% of other mammal species, which are hundreds of thousands of years old). However, the fossil record of the cheetah species extends back several hundred thousand years. These two observations are not contradictory. The species is very old, but its mitochondrial DNA appears quite young. 12,000 years ago, at the end of the last Ice Age, cheetahs were migrating—presumably as a result of large climatic changes—from their native Asian point of origin to their present home in Africa. It appears this move resulted in a significant population bottleneck, wherein only a small number of cheetahs made it to Africa; the ancestors of the present population. All other cheetahs in Asia—along with their genetic diversity—went extinct. The mitochondrial genetic “clock” was reset by the genetic bottleneck. Examining mitochondrial DNA variation alone, we can only predict when the most recent bottleneck occurred for the mtDNA lineages found in cheetahs. We cannot predict the age of the cheetahs as a species.

The scenario above can be played out for most species. An examination of the mitochondrial genome of any species will only tell us when the common ancestor of all modern members of this species existed, which will almost invariably occur after the evolutionary origin of the species. What Stoeckle and Thaler have potentially discovered, by examining the variation of a single gene in the mtDNA, is that most species experienced a mitochondrial genetic “bottleneck” between 100 and 200 thousand years ago.

How might this bottleneck have occured? Stoeckle and others have provided several hypotheses. One scenario invokes the effects of significant ice ages during this time period. Such dramatic climate change has the effect of causing mass migrations, leading to rapid contractions and expansions of populations. In such times, variation in mitochondrial lineages is squeezed out of many species, even as they may retain a considerable amount of variation in their main (nuclear) genomes. In this respect, the results reported in this paper are not particularly surprising, because they fit well with what we already know about this phase of natural history.

In summary: Do Stoeckle and Thaler’s findings undermine evolutionary theory and prove that most animals were created recently? Definitely not.

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