RESEARCH ON COMPETITION TO SURVIVE

FROM:  NATIONAL SCIENCE FOUNDATION 

Study suggests survival isn't always about competition

New research findings contradict one of Darwin's hypotheses, which encourages prioritizing species for conservation based on evolutionary or genetic uniqueness
May 1, 2014

One of Charles Darwin's hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists have long accepted this to be true.

Thus, three researchers were more than a little shaken to find that their experiments on fresh-water green algae failed to support Darwin's hypothesis.

"It was completely unexpected," says Bradley Cardinale, an associate professor in the University of Michigan's school of natural resources and environment. "We sat there banging our heads against the wall. Darwin's hypothesis has been with us for so long, how can it not be right?"

The researchers--who also included Charles Delwiche, a professor of cell biology and molecular genetics at the University of Maryland, and Todd Oakley, a professor in the department of ecology, evolution and marine biology at the University of California, Santa Barbara--were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.

"The hypothesis is so intuitive that it was hard for us to give it up. But we are becoming more and more convinced that he wasn't right about the organisms we've been studying," Cardinale says. "It doesn't mean the hypothesis won't hold for other organisms, but it's enough that we want to get biologists to rethink the generality of Darwin's hypothesis."

Preserving species

The assumptions underlying Darwin's hypothesis are important for conservation policy, since they essentially encourage decision-makers to prioritize species preservation based on how evolutionarily or genetically unique they are. "We don't have enough time, people or resources to save everything," Cardinale says. "A large number of species will go extinct and we have to prioritize which ones we will save.

"Many biologists have argued that we should prioritize for conservation those species that are genetically unique, and focus less on those species that are genetically more similar," he adds. "The thinking is that you might be able to tolerate the loss of species that are redundant. In other words, if you lost a redundant species, you might not see a change."

But if scientists ultimately prove Darwin wrong on a larger scale, "then we need to stop using his hypothesis as a basis for conservation decisions," Cardinale says. "We risk conserving things that are the least important, and losing things that are the most important. This does bring up the question: How do we prioritize?"

The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh-water green algae so they could provide conservationists with useful data for decision-making. "We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists," Cardinale says. "When we started coming up with numbers that showed he wasn't right, we were completely baffled."

The National Science Foundation is supporting the work with $2 million over five years, awarded in 2010.

Experiments with green algae

The researchers sequenced 60 species of algae most common in North America and can describe with a high certainty their evolutionary relationships. "We know which ones are ancient and have become genetically unique, and which are new and recently diverged," he says.

Their experiments involved taking closely related species and putting them into competition, and taking evolutionarily ancient distantly related species and similarly pitting them against each other.

They also sent graduate students into natural lakes to gather samples, including one lake with "the most spectacular group of green algae," as well as something else, prompting the nickname "Leech Lake."

When the students stood in the water to collect their samples, "the entire bottom of the lake would start moving toward them," Cardinale says. "They would congregate on their boots, and start crawling up their legs. The challenge was to get the samples before the leeches got into their waders."

Samples obtained, they put species that have different evolutionary histories into bottles and measured how strongly they competed for essential resources such as nitrogen, phosphorus and light.

"If Darwin had been right, the older, more genetically unique species should have unique niches, and should compete less strongly, while the ones closely related should be ecologically similar and compete much more strongly – but that's not what happened," Cardinale says. "We didn't see any evidence of that at all.” They found this to be so in field experiments, lab experiments and surveys in 1,200 lakes in North America.

"If Darwin was right, we should've seen species that are genetically different and ecologically unique, doing unique things and not competing with other species," he adds. "But we didn't."

Traits and the quality of competition

Certain traits determine whether a species is a successful competitor or a poor competitor, he says. "Evolution does not appear to predict which species have good traits and bad traits," he says. "We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can't be predicted from the Tree of Life."

The scientists have a few ideas of what may be going on, and why Darwin's hypothesis is incorrect, at least for this group of organisms.

"Organisms like algae can be plastic. Maybe they all have the same genes that do the same things and can turn them off and on at different times," he says. "Maybe they sometimes can flip a switch for nitrogen on or off, or all at the same time. If we are correct, and they are not diverging in the genes that control competition, maybe they are diverging in other genes."

Darwin "was obsessed with competition," Cardinale says. "He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don't grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected.

"Maybe species are co-evolving," he adds. "Maybe they are evolving together so they are more productive as a team than they are individually. We found that more than one-third of the time, that they like to be together. Maybe Darwin's presumption that the world may be dominated by competition is wrong."

Cardinale's broad research goal is to gain a better understanding of how human alteration of the environment affects the biotic diversity of communities and, in turn, the impact of this loss on fluxes of energy and matter required to sustain life. "I focus on this because I believe that global loss of biodiversity ranks among the most important and dramatic environmental problems in modern history," he says.

Editor's Note: This Behind the Scenes article was first provided to LiveScience in partnership with the National Science Foundation.

-- Marlene Cimons, National Science Foundation
Investigators
Todd Oakley
Xiaoxia Lin
Phillip Savage
Bradley Cardinale
Related Institutions/Organizations
University of Michigan Ann Arbor

THE MUTANT PIGEON GENE

Victoria Crown Pigeon.  Credit:  Wikimedia Commons.

FROM: NATIONAL SCIENCE FOUNDATION
Mutant Gene Responsible for Pigeons' Head Crests
Decoded genome reveals secrets of pigeon traits and origins
January 31, 2013

Scientists have decoded the genetic blueprint of the rock pigeon, unlocking secrets about pigeons' Middle East origins, feral pigeons' kinship with escaped racing birds and how mutations give pigeons traits like feather head crests.

"Birds are a huge part of life on Earth, but we know surprisingly little about their genetics," says Michael Shapiro, one of the study's two principal authors and a biologist at the University of Utah.

In the new study, "we've shown a way forward to find the genetic basis of traits--the molecular mechanisms controlling animal diversity in pigeons," he says. "Using this approach, we expect to be able to do this for other traits in pigeons, and it can be applied to other birds and many other animals as well."

The findings appear in a paper published this week in the online journal Science Express.

Shapiro conducted the research with Jun Wang of China's BGI-Shenzhen (formerly Beijing Genomics Institute) and other scientists from BGI, the University of Utah, Denmark's University of Copenhagen and the University of Texas M.D. Anderson Cancer Center in Houston.

"The research identified the genes contributing to variation in the avian head crest, using the domesticated pigeons that so fascinated and inspired Charles Darwin in developing his theory of natural selection," says George Gilchrist, program director in the National Science Foundation's (NSF) Division of Environmental Biology, which funded the research. "This finding illustrates the power of comparative genomics."

Pigeons were domesticated some 5,000 years ago in the Mediterranean region. Key results of this study include sequencing of the genome of the rock pigeon Columba livia, which is among the most common bird species.

There are some 350 breeds of rock pigeons--all with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and head--including head crests in shapes known as hoods, manes, shells and peaks.

The pigeon's genetic blueprint is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and a common parakeet known as a budgerigar or budgie. "This will give us new insights into bird evolution," Shapiro says.

Using software developed by paper co-author Mark Yandell, a geneticist at the University of Utah, the scientists revealed that a single mutation in a gene named EphB2 causes head and neck feathers to grow upward instead of downward, creating head crests.

"This same gene in humans has been implicated as a contributor to Alzheimer's disease, as well as prostate cancer and possibly other cancers," Shapiro says, noting that more than 80 of the 350 pigeon breeds have head crests, which play a role in attracting mates in many bird species.

The researchers compared the pigeon genome to those of chickens, turkeys and zebra finches. "Despite 100 million years of evolution since these bird species diverged, their genomes are very similar," Shapiro says.

A genome for the birds, a gene for head crests

The biologists assembled 1.1 billion base pairs of DNA in the rock pigeon genome; the researchers believe there are about 1.3 billion total, compared with 3 billion base pairs in the human genome. The rock pigeon's 17,300 genes compare in number with the approximately 21,000 genes in humans.

The researchers first constructed a "reference genome"--a full genetic blueprint--from a male of the pigeon breed named the Danish tumbler.

Shapiro says the study is the first to pinpoint a gene mutation responsible for a pigeon trait, in this case, head crests.

"A head crest is a series of feathers on the back of the head and neck," Shapiro says. "Some are small and pointed. Others look like a shell behind the head; some people think they look like mullets. They can be as extreme as an Elizabethan collar."

The researchers found strong evidence that the EphB2 (Ephrin receptor B2) gene acts as an on-off switch to create a head crest when mutant, and no head crest when normal.

They also showed that the mutation and related changes in nearby DNA are shared by all crested pigeons, so the trait evolved just once and was spread to numerous pigeon breeds by breeders.

Full or partial genetic sequences were analyzed for 69 crested birds from 22 breeds, and 95 uncrested birds from 57 breeds. The biologists found a perfect association between the mutant gene and the presence of head crests.

They also showed that while the head crest trait becomes apparent in juvenile pigeons, the mutant gene affects pigeon embryos by reversing the direction of feather buds--from which feathers later grow--at a molecular level.

Other genetic factors determine what kind of head crest each pigeon develops: shell, peak, mane or hood.

Tracking the origins of pigeons

A 2012 study by Shapiro provided limited evidence of pigeons' origins in the Middle East and some breeds' origins in India and indicated kinship between common feral or free-living, city pigeons and escaped racing pigeons.

In the new study, "we included some different breeds that we didn't include in the last analysis," Shapiro says. "Some of those breeds only left the Middle East in the last few decades. They've probably been there for hundreds if not thousands of years. If we find that other breeds are closely related to them, then we can infer those other breeds probably also came from the Middle East."

The scientists found that the owl breeds--pigeon breeds with very short beaks that are popular with breeders--likely came from the Middle East. They're closely related to breeds from Syria, Lebanon and Egypt.

The research also uncovered a shared genetic heritage between breeds from Iran and breeds likely from India, consistent with historical records of trade routes between those regions. People were not only sharing goods along those routes, but probably also interbreeding their pigeons.

As for the idea that free-living pigeons descended from escaped racing pigeons, Shapiro says his 2012 study was based on "relatively few genetic markers scattered throughout the genome. We now have stronger evidence based on 1.5 million markers, confirming the previous result with much better data."

The scientists analyzed partial genomes of two feral pigeons: one from a U.S. Interstate-15 overpass in Utah's Salt Lake Valley, the other from Lake Anna in Virginia.

"Despite being separated by 1,000 miles, they are genetically very similar to each other and to the racing homer breed," Shapiro says.

"Darwin used this striking example to communicate how natural selection works," he says. "Now we can get to the DNA-level changes that are responsible for some of the diversity that intrigued Darwin 150 years ago."

The study's co-authors from the University of Utah include Yandell, Eric Domyan, Zev Kronenberg, Michael Campbell, Anna Vickery and Sydney Stringham; Chad Huff is a co-author from the University of Texas.

The study was also funded by the Burroughs Wellcome Fund, the University of Utah Research Foundation, the National Institutes of Health and the Danish National Research Foundation.

-NSF-