The circle of life—otherwise known as a tree
By Jeffrey Kluger
September 21, 2015

When it comes to identifying all of the species on the planet, there’s not much you can say with certainty. Unicorns don’t make the cut; bunnies do. Then there’s a lot of gray. Even estimating the total number of species, never mind naming them, has proven a monumental challenge—with the best guesses putting the count from a low of a few million to a high of 100 million.

Now, the job is getting easier—or at least more organized—thanks to a newly launched digital repository that researchers all over the planet can use to upload their findings, and allow curators to bring order out of the biological chaos. What Wikipedia did for everyday—and not-so-everyday—knowledge, the new site can do for the impossibly complicated business of figuring out every species of microbe, fungus, beast and tree that calls the planet home.

The Open Tree of Taxonomy (OTT), just announced in a paper in the Proceedings of the National Academy of Sciences, is the brainstorm of researchers from 11 institutions, led by evolutionary biologist Cody Hinchliff of the University of Michigan. There were a lot of reasons that trying to create a one-stop, go-to destination for all research on speciation was an audacious idea. For one thing, the studies are all over the map—literally. Biologists around the world have been finding and announcing new species in all manner of often-obscure journals for decades, if not centuries. Much of that work occurred before the age of digitizing and gene sequencing, which makes modern species research both more accessible and more reliable—and earlier findings less of both.

But genetic sequencing raises its own problems. The mere fact that a collection of genes appears to suggest a unique species of, say, fungus, does not mean it actually does—any more than a shadow on a star or a wobble in its position definitely means it is orbited by a planet. In both cases, more research is necessary. When it comes to organisms, these maybe-members of a particular taxon go by the unglamorous name operational taxonomic unit (OTU), a sort of place-holder classification pending more proof.

To assemble their Open Tree, the researchers both scoured the literature on their own and put out a call to biologists, inviting them to upload their work to a central site. Making their job a bit easier, Hinchliff and his colleagues weren’t hoping just to count heads—or whatever passes for a head—from every individual species out there. Rather, they were concentrating on studies of entire phylogenies, or whole groups of animals that trace their origins back to a single common ancestor. There’s no reason to go one-by-one through every paper that has ever identified a new kind of butterfly when a community of lepidopterists have already done the collating for you.

The initial response rate to the open call was less than the authors had hoped—just 16% so far. But that, plus the published papers they collected on their own, has produced a sample set of 6,810 taxonomic trees from 3,062 studies. That, in turn, produced an overall tree (which, in the new paper, looks more like a multicolored sun with inward pointing rays) with 2.3 million so-called tips—either named species or OTU’s.

None of those 2.3 million earned their spot on the tree easily. All of the uploaded studies went through a process of manual curation, with the methods being checked, the gene lines being traced, and multiple mentions of a single genetic sequence that might go by different names in different studies being compressed to just one. The result, the researchers hope, will mean all of the crowd-sourced upside of Wikipedia, with little of the downside risk of junk making it into the dataset.

The Open Tree team doesn’t pretend that the 2.3 million tips remotely amount to a complete species census. A well-conceived 2011 study by marine biologist Camilo Mora of the University of Hawaii used statistical sampling to come up with an estimate of 8.7 million currently extant species. And some people regard Mora’s findings as a lowball.

What’s more, across the more than 3.5 billion years life has existed on Earth, the exact population of the planet has always been a blink-and-you-miss-it kind of thing, with new species appearing and disappearing all the time. Human beings, alas, have accelerated those disappearances; Mora estimates a loss of 27,000 species per year due to habitat destruction alone. If the new tree helps us appreciate the planet’s biological riches before it’s too late, it will have accomplished more than the researchers themselves ever intended.


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