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Number of species depends how you count them

Using genetic analysis alone can overestimate count

3:00pm, February 8, 2017
Hercules beetles

DRAWING LINES  Scientists sometimes have difficulty determining whether organisms, such as these Hercules beetles, are members of different species. Genetic analysis alone may divide populations into species that don’t exist by other biological criteria.

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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.


J. Sukumaran and L.L. Knowles. Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences. Published online January 30, 2017. doi: 10.1073/pnas.1607921114. 

Further Reading

T.H. Saey. Killer whales are (at least) two species. Science News Online, July 11, 2013.

S. Milius. DNA suggests North American mammoth species interbred. Science News. Vol. 180, December 3, 2011, p.13.

T.H. Saey. Genes separate Africa’s elephant herds. Science News. Vol. 179. January 15, 2011, p. 16.

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