Genetic methods for counting new species may be a little too good at their jobs, a new study suggests.

Computer programs that rely on genetic data alone split populations of organisms into five to 13 times as many species as actually exist, researchers report online January 30 in Proceedings of the National Academy of Sciences. These overestimates may muddy researchers’ views of how species evolve and undermine conservation efforts by claiming protections for species that don’t really exist, say computational evolutionary biologist Jeet Sukumaran and evolutionary biologist L. Lacey Knowles.
The lesson, says Knowles, “is that we shouldn’t use genetic data alone” to draw lines between species.

Scientists have historically used data about organisms’ ecological distribution, appearance and behavior to classify species. But the number of experts in taxonomy is dwindling, and researchers have turned increasingly to genetics to help them draw distinctions. Large genetic datasets and powerful computer programs can quickly sort out groups that have become or are in the process of becoming different species. That’s especially important in analyzing organisms for which scientists don’t have much ecological data, such as insects in remote locations or recently extinct organisms.

Knowles and Sukumaran, both of the University of Michigan in Ann Arbor, examined a commonly used computer analysis method, called multispecies coalescent, which picks out genetic differences among individuals that have arisen recently in evolutionary time. Such differences could indicate that a population of organisms is becoming a separate species. The researchers used a set of known species and tested the program’s ability to correctly predict the right number of species given certain variables. The program is good — maybe too good — at detecting the differences, Knowles says. If scientists don’t take other factors, such as geographical separation, into account, they may call genetically different groups separate species when they are merely subgroups of the same species.

Then again, it depends on what you mean by a “species,” says Rampal Etienne, an evolutionary community ecologist at the University of Groningen in the Netherlands. He developed the method that Knowles and Sukumaran analyzed. By one definition, a species is a genetically distinct lineage. “If that’s your species concept then, no, it’s not true that there are more species discovered by this method than there actually are,” Etienne says.

Biologists have long defined species primarily based on mating behavior and physical traits, not genetic similarity. Species are said to be reproductively isolated when they don’t mate either because they can’t or because they don’t for some reason (such as female fish choosing to mate with only red or blue males). Reproductive isolation doesn’t exclude two species from mating once in a while, says evolutionary biologist Ole Seehausen of the University of Bern in Switzerland. What’s important is that species that breed in the same area remain distinct.
What’s more, “speciation is not a one-way road,” Seehausen says. When ecological conditions change, groups that had been going their separate ways may breed with each other again. For instance, female fish that choose mates based on color may breed with males of the non-preferred color when water becomes murky and obscures their vision. Computer programs can predict when speciation has started but can never forecast whether the groups will remain separate or will come back together, Seehausen says.

Using the biological criteria, the genetic method may seem to fall short, but genetic analyses simply aren’t designed to address such questions, Seehausen says. He agrees with Knowles and Sukumaran that genetic data should be used in combination with ecological and other studies to identify species.

Characterizing species based on their genes could still be a useful conservation tool, Etienne says, helping to preserve genetic diversity. A diverse set of genes can help a species adapt to changing environments, and a lack of diversity can doom it to extinction. Identifying diverse groups within a population could help researchers decide where to focus conservation efforts, Etienne says. “Whether they are two species or not is less important,” he says.

Estimates of global biodiversity are not affected by any shortcomings with the genetic analysis programs, Knowles says. Scientists use many types of data to determine the total number of species in a region or on Earth.

A cautionary tale in evolutionary theory is coming straight from the horse’s mouth. When ancient horses diversified into new species, those bursts of evolution weren’t accompanied by drastic changes to horse teeth, as scientists have long thought.

A new evolutionary tree of horses reveals three periods when several new species emerged, scientists report in the Feb. 10 Science. The researchers found that changes in teeth morphology and body size didn’t change very much during these periods of rapid speciation.
“This knocks traditional notions that rapid diversification of new species comes with morphological diversification as well,” says paleontologist Bruce MacFadden of the University of Florida in Gainesville. “This is a very sophisticated and important paper.”

The emergence of several new species in a relatively short time is often accompanied by the evolution of special new traits. Classic notions of evolution say that these traits — such as longer teeth with extensive enamel — are adaptive, enabling an animal to succeed in a particular environment. In horses, the evolution of such teeth might permit a shift from browsing on leafy, shrubby trees to grazing on grasses in open spaces with windblown dust and grit.

“You can’t live on a grassland as a grazer and have short teeth,” says MacFadden, an expert in horse evolution. “You’ll wear your teeth down and that’s not a recipe for success as a species.”

Similarly, a big change in body size can indicate a move to a new environment. Animals that live in forests tend to be smaller and more solitary than the larger herd animals that live in open grasslands.

Paleontologist Juan Cantalapiedra and colleagues compiled decades of previous work to create an evolutionary tree of 138 horse species (seven of which exist today), spanning roughly 18 million years. The tree reveals three major branchings of new species: a North American burst between 15 million and 18 million years ago, and two bursts coinciding with dispersals into Eurasia about 11 million and 4.5 million years ago.
The researchers expected to see evidence of an “adaptive radiation,” major changes in teeth and body size that allowed the new horse species to succeed. But rates of body size evolution didn’t differ much in sections of the family tree with low and high speciation rates. And rates of change in tooth characteristics were actually lower in sections of the tree with fast speciation rates, the team reports.

“It’s very tempting to see some change in body size, for example, and say, ‘Oh, that’s adaptive radiation,’” says Cantalapiedra, of the Leibniz Institute for Evolution and Biodiversity Science at the Museum für Naturkunde in Berlin. “But that’s not what we see.”

Cantalapiedra and his collaborators speculate that during the periods of rapid speciation, the environment was so expansive and productive that there just wasn’t a lot of competition to drive the evolution of adaptive traits. Perhaps, for example, North American grasslands were so rich and dense that there was enough energy for various species to evolve without having to develop traits that gave them an edge.

That scenario might be special to horses, says MacFadden, but it might not. Similarly, classic adaptive radiation scenarios might be true in many cases, but as this work shows, not always.

Astronomers have caught a star exploding just hours after light from the eruption first reached Earth. Measurements of the blast’s light suggest that the star rapidly belched gas in the run-up to its demise. That would be surprising — most scientists think the first outward sign of a supernova is the explosion itself.

“Several years ago, to catch a supernova early would mean to detect it at several days, a week, or maybe more, after the explosion,” says astrophysicist Ofer Yaron of the Weizmann Institute of Science in Rehovot, Israel. Now, he says, “we talk about day one.” Although previous supernovas have been seen this early, the new observation is the earliest one with a spectrum — an accounting of the emitted light broken up by wavelength — taken six hours after the explosion, Yaron and colleagues report online February 13 in Nature Physics.
Astronomers observed the explosion — a type 2 supernova, triggered by the collapse of a dying star (SN: 2/18/17, p.24) — with the Intermediate Palomar Transient Factory, which surveys the sky on a regular basis using a telescope at the Palomar Observatory, near San Diego. The supernova appeared on October 6, 2013, in the galaxy NGC7610, 166 million light-years from Earth in the constellation Pegasus.

Spectra taken at several intervals after the explosion painted a picture of the aftermath. A shock wave from the supernova plowed through gas surrounding the star, stripping electrons from atoms, which later recombined, emitting certain wavelengths of light in the process. Those wavelengths showed up in the spectra, allowing scientists to deduce what had occurred. The gas had been emitted just before the explosion — within the previous year or so — they concluded.

“This is actually very exciting if you ask me,” says astrophysicist Matteo Cantiello of the Center for Computational Astrophysics in New York City, who was not involved with the research. For typical stars on the brink of collapse, he says, “this is the first clear evidence that … the last period of their lives is not quiet.” Instead, dying stars may become unstable, rapidly spurting out material.

“That’s very, very odd,” says astrophysicist Peter Garnavich of the University of Notre Dame in Indiana. Scientists typically assume that the outer layers of such stars are detached from the internal processes which trigger the collapse, Garnavich says. How an oncoming collapse could provoke eruptions preceding the explosion is unknown.

BOSTON — Rooted in place, plants can’t run away from arsenic-tainted soil — but they’re far from helpless. Scientists have identified enzymes that help rice plant roots tame arsenic, converting it into a form that can be pushed back into the soil. That leaves less of the toxic element to spread into the plants’ grains, where it can pose a health risk to humans, researchers reported February 17 at the annual meeting of the American Association for the Advancement of Science.

Once arsenic worms its way into rice plant roots and gets into the vascular system, “it’s transported into the leaves and the grain,” David Salt, a biologist at the University of Nottingham in England who conducted the recent research, said during a news conference. Inside the plant, arsenic “can accumulate to levels where it can potentially be toxic if it accumulates over long times.”
Since arsenic occurs naturally in soil, understanding the genetic basis for plants’ natural defense mechanisms might help researchers engineer plants that take in less arsenic, said Mary Lou Guerinot, a biologist at Dartmouth College.
Arsenic in the soil switches between two different forms — ions with different electric charges. That form depends on soil conditions, which in a rice field fluctuate between wetter and drier. Plants are more likely to pull in arsenite from the soggy soil of a flooded rice paddy, and arsenate when that soil dries out a bit. The plants use different chemical mechanisms to take in and process the different arsenic ions.

In arsenate-rich soil, the ion sneaks into the outer layer of root cells through specialized passageways, called transport channels, that normally carry phosphate ions through root cell membranes. Transforming arsenate into arsenite lets the roots push the element back into the soil through a process called efflux, but scientists weren’t sure how the plant changed arsenic’s form.
Salt’s team found that rice plants without working genes for enzymes called HAC1;1 and HAC1;2 couldn’t turn arsenate into arsenite. So more arsenate accumulated in the plants’ shoots. When the scientists made HAC1;1 and HAC1;2 genes in other rice plants produce more of the enzymes than usual, grains from those plants had lower concentrations of any form of arsenic.

It’s just one defense of many, Salt said, and it’s not bulletproof. Arsenate can still spread into plants’ vascular systems from the roots via phosphate channels.

When the soil is rich in arsenite, rice roots take arsenite up through the same channels that take in silicon. Although efflux is an efficient way for roots to get rid of arsenite, there’s a limit to how quickly the cells can push the ion out.

So to create rice plants that are better at dealing with arsenic, Salt and other scientists are looking not just at how roots push out arsenic once it gets in, but how they keep the toxin out to begin with. For example, engineering channels that are better at pulling in just phosphate or just silicon could lessen the amount of arsenic that co-opts those channels.

Since soil conditions in a rice field switch between dry and wet, plants need defense mechanisms for both forms of arsenic. “Once we know what forms the plant takes in and how it’s doing that, we’ll need a solution for arsenate and arsenite,” Guerinot says. “There’s no easy fix.”