Plant study hints evolution may be predictable

Evolution has long been viewed as a rather random process, with the traits of species shaped by chance mutations and environmental events -- and therefore largely unpredictable.

But an international team of scientists led by researchers from Yale University and Columbia University has found that a particular plant lineage independently evolved three similar leaf types over and over again in mountainous regions scattered throughout the neotropics.

The findings provided the first examples in plants of a phenomenon known as "replicated radiation," in which similar forms evolve repeatedly within different regions, suggesting that evolution is not always such a random process but can be predicted.

The study is published July 18 in the journal Nature Ecology & Evolution.

"The findings demonstrate how predictable evolution can actually be, with organismal development and natural selection combining to produce the same forms again and again under certain circumstances," said Yale's Michael Donoghue, Sterling Professor Emeritus of Ecology & Evolutionary Biology and co-corresponding author. "Maybe evolutionary biology can become much more of a predictive science than we ever imagined in the past."

For the study, the research team studied the genetics and morphology of the plant lineage Viburnum, a genus of flowering plants that began to spread south from Mexico into Central and South America some 10 million years ago. Donoghue studied this same plant group for his Ph.D. dissertation at Harvard 40 years ago. At the time, he argued in favor of an alternative theory in which large, hair-covered leaves and small smooth leaves evolved early in the evolution of the group and then both forms migrated separately, being dispersed by birds, through the various mountain ranges.

The new genetic analyses reported in the paper, however, show that the two different leaf types evolved independently, in parallel, in each of a number of mountain regions.

"I came to the wrong conclusion because I lacked the relevant genomic data back in the 1970s," Donoghue said.

The team found that a very similar set of leaf types evolved in nine of 11 regions studied. However, the full array of leaf types may have yet to evolve in places where Viburnum has only more recently migrated. For instance, the mountains of Bolivia lack the large hairy leaf types found in other wetter areas with little sunshine in the cloud forest in Mexico, Central America, and northern South America.

"These plants arrived in Bolivia less than a million years ago, so we predict that the large, hairy leaf form will eventually evolve in Bolivia as well," Donoghue said.

Several examples of replicated radiation have been found in animals, such as Anolis lizards in the Caribbean. In that case, the same set of body forms, or "ectomorphs," evolved independently on several different islands. With a plant example now in hand, evolutionary biologists will try to discover the general circumstances under which solid predictions can be made about evolutionary trajectories.

"This collaborative work, spanning decades, has revealed a wonderful new system to study evolutionary adaptation," said Ericka Edwards, professor of ecology and evolutionary biology at Yale and co-corresponding author of the paper. "Now that we have established the pattern, our next challenges are to better understand the functional significance of these leaf types and the underlying genetic architecture that enables their repeated emergence."

Read more at Science Daily

The importance of elders

According to long-standing canon in evolutionary biology, natural selection is cruelly selfish, favoring traits that help promote reproductive success. This usually means that the so-called "force" of selection is well equipped to remove harmful mutations that appear during early life and throughout the reproductive years. However, by the age fertility ceases, the story goes that selection becomes blind to what happens to our bodies. After the age of menopause, our cells are more vulnerable to harmful mutations. In the vast majority of animals, this usually means that death follows shortly after fertility ends.

Which puts humans (and some species of whale) in a unique club: animals that continue to live long after their reproductive lives end. How is it that we can live decades in selection's shadow?

"From the perspective of natural selection, long post-menopausal life is a puzzle," said UC Santa Barbara anthropology professor Michael Gurven. In most animals, including chimpanzees -- our closest primate brethren -- this link between fertility and longevity is very pronounced, where survival drops in sync with the ability to reproduce. Meanwhile in humans, women can live for decades after their ability to have children ends. "We don't just gain a few extra years -- we have a true post-reproductive life stage," Gurven said.

In a paper published in the Proceedings of the National Academy of Sciences, senior author Gurven, with former UCSB postdoctoral fellow and population ecologist Raziel Davison, challenge the longstanding view that the force of natural selection in humans must decline to zero once reproduction is complete.

They assert that a long post-reproductive lifespan is not just due to recent advancements in health and medicine. "The potential for long life is part of who we are as humans, an evolved feature of the life course," Gurven said.

The secret to our success? Our grandparents.

"Ideas about the potential value of older adults have been floating around for awhile," Gurven said. "Our paper formalizes those ideas, and asks what the force of selection might be once you take into account the contributions of older adults."

For example, one of the leading ideas for human longevity is called the Grandmother Hypothesis -- the idea that, through their efforts, maternal grandmothers can increase their fitness by helping improve the survival of their grandchildren, thereby enabling their daughters to have more children. Such fitness effects help ensure that the grandmother's DNA is passed down.

"And so that's not reproduction, but it's sort of an indirect reproduction. The ability to pool resources, and not just rely on your own efforts, is a game changer for highly social animals like humans," Davison said.

In their paper, the researchers take the kernel of that idea -- intergenerational transfers, or resource sharing between old and young -- and show that it, too, has played a fundamental role in the force of selection at different ages. Food sharing in non-industrial societies is perhaps the most obvious example.

"It takes up to two decades from birth before people produce more food than they're consuming," said Gurven, who has studied the economy and demography of the Tsimané and other indigenous groups of South America. A lot of food has to be procured and shared to get kids to the point where they can fend for themselves and be productive group members. Adults fill most of this need with their ability to obtain more food than they need for themselves, a provisioning strategy that has sustained pre-industrial societies for ages and also carries over into industrialized societies.

"In our model, the large surplus that adults produce helps improve the survival and fertility of close kin, and of other group members who reliably share their food, too," Davison said. "Viewed through the lens of food production and its effects, it turns out that the indirect fitness value of adults is also highest among reproductive-aged adults. But using demographic and economic data from multiple hunter-gatherers and horticulturalists, we find that the surplus provided by older adults also generates positive selection for their survival. We calculate all this extra fitness in late adulthood to be worth up to a few extra kids!"

"We show that elders are valuable, but only up to a point," contends Gurven. "Not all grandmothers are worth their weight. By about their mid-seventies, hunter-gatherers and farmers end up soaking up more resources than they provide. Plus, by their mid-seventies, most of their grandkids won't be dependents anymore, and so the circle of close kin who stand to benefit from their help is small."

But food isn't everything. Beyond getting fed, children are also taught and socialized, trained in relevant skills and worldviews. This is where older adults can make their biggest contributions: While they don't contribute as much to the food surplus, they have the accumulation of a lifetime of skills they can deploy to ease the burden of childcare on parents, as well as knowledge and training that they can pass on to their grandchildren.

"Once you take into account that elders are also actively involved in helping others forage, then it adds even more fitness value to their activity and to them being alive," Gurven said. "Not only do elders contribute to the group, but their usefulness helps ensure that they also receive from the surpluses, protections and care from their group. In other words, interdependence runs both ways, from old to young, and young to old."

"If you're part of my social world, there might be some kickback," Davison explained. "So to the extent that we're interdependent, I'm vested in your interest, beyond just simple kinship. I'm interested in getting you to be as skilled as possible because some of your productivity could help me down the road."

Gurven and Davison found that rather than our long lifespans opening up opportunities that led to a human-like foraging economy and social behavior, the reverse is more likely -- our skills-intensive strategies and long-term investments in the health of the group preceded and evolved with our shift to our particular human life history, with its extended childhood and unusually long post-reproductive stage.

In contrast, chimpanzees -- who represent our best guess as to what humans' last common ancestor may have been like -- are able to forage for themselves by age 5. However, their foraging activities require less skill, and they produce minimal surplus. Even so, the authors show that if a chimpanzee-like ancestor would share their food more widely, they could still generate enough indirect fitness contributions to increase the force of selection in later adulthood.

"What this suggests is that human longevity is really a story about cooperation," said Gurven. "Chimpanzee grandmothers are rarely observed doing anything for their grandkids."

Though the authors say their work is more about how the capacity for long life came to first exist in the Homo lineage, the implication that we owe it to elders everywhere is an important reminder looking forward.

"Despite elders being far more numerous today than ever before in the past, there's still much ageism and underappreciation of older adults," Gurven said. "When COVID seemed to be most deadly just for older adults, many shrugged their shoulders about the urgency of lockdown or other major precautions.

Read more at Science Daily

'Fuel of evolution' more abundant than previously thought in wild animals

The raw material for evolution is much more abundant in wild animals than we previously believed, according to new research from The Australian National University (ANU).

Darwinian evolution is the process by which natural selection results in genetic changes in traits that favour the survival and reproduction of individuals. The rate at which evolution occurs depends crucially on genetic differences between individuals.

Led by Dr Timothée Bonnet from ANU, an international research team wanted to know how much of this genetic difference, or "fuel of evolution," exists in wild animal populations. The answer: two to four times more than previously thought.

According to Dr Bonnet, the process of evolution that Darwin described was an incredibly slow one.

"However, since Darwin, researchers have identified many examples of Darwinian evolution occurring in just a few years," Dr Bonnet said.

"A common example of fast evolution is the peppered moth, which prior to the industrial revolution in the UK was predominantly white. With pollution leaving black soot on trees and buildings, black moths had a survival advantage because it was harder for birds to spot them.

"Because moth colour determined survival probability and was due to genetic differences, the populations in England quickly became dominated by black moths."

The study is the first time the speed of evolution has been systematically evaluated on a large scale, rather than on an ad hoc basis. The team of 40 researchers from 27 scientific institutions used studies of 19 populations of wild animals from around the world. These included superb fairy-wrens in Australia, spotted hyenas in Tanzania, song sparrows in Canada and red deer in Scotland.

"We needed to know when each individual was born, who they mated with, how many offspring they had, and when they died. Each of these studies ran for an average of 30 years, providing the team with an incredible 2.6 million hours of field data," Dr Bonnet said.

"We combined this with genetic information on each animal studied to estimate the extent of genetic differences in their ability to reproduce, in each population.

After three years of trawling through reams of data, Dr Bonnet and the team were able to quantify how much species change occurred due to genetic changes caused by natural selection.

"The method gives us a way to measure the potential speed of current evolution in response to natural selection across all traits in a population. This is something we have not been able to do with previous methods, so being able to see so much potential change came as a surprise to the team," Dr Bonnet said.

Professor Loeske Kruuk, also from ANU and now based at the University of Edinburgh in the United Kingdom, said: "This has been a remarkable team effort that was feasible because researchers from around the world were happy to share their data in a large collaboration.

"It also shows the value of long-term studies with detailed monitoring of animal life histories for helping us understand the process of evolution in the wild."

However, the researchers warn it's too early to tell whether the actual rate of evolution is getting quicker over time.

"Whether species are adapting faster than before, we don't know, because we don't have a baseline. We just know that the recent potential, the amount of 'fuel', has been higher than expected, but not necessarily higher than before," Dr Bonnet said.

According to the researchers, their findings also have implications for predictions of species' adaptability to environmental change.

"This research has shown us that evolution cannot be discounted as a process which allows species to persist in response to environmental change," Dr Bonnet said.

Dr Bonnet said that with climate change predicted to increase at an increasing rate, there is no guarantee that these populations will be able to keep up.

Read more at Science Daily

Sudden evolutionary change in flowers

When Charles Darwin first codified the theory of evolution by means of natural selection, he thought of it as a gradual process. "We see nothing of these slow changes in progress, until the hand of time has marked the long lapse of ages," he wrote in his seminal work, "On the Origin of Species."

But Darwin didn't have the full picture. "Evolution doesn't necessarily take all these small changes like Darwin proposed," said Scott Hodges, a professor in UC Santa Barbara's Department of Ecology, Evolution, and Marine Biology.

Hodges, doctoral student Zachary Cabin and their colleagues just have identified a case of a sudden evolutionary change. In the journal Current Biology, the scientists describe a population of columbines that have lost their petals, including the characteristic nectar spurs. A drastic change caused by a mutation in a single gene. The finding adds weight to the idea that adaptation can occur in large jumps, rather than merely plodding along over extended timespans.

Ever since the theory of evolution was put forward, biologists have debated whether it always occurs in small, gradual steps over long timespans or sometimes as an equilibrium punctuated by abrupt changes. Often, large morphological changes appear within short geologic timescales where intermediate forms may not have fossilized. The question then remains whether many small changes occurred in a short period of time, or perhaps whether single large-scale mutation might be responsible. So, researchers really have to catch the development in action if they hope to build a case that sudden changes can drive evolution.

Enter the Colorado blue columbine. In one population, a mutation has caused many of the plants to lose their petals with the iconic nectar spurs. While not an uncommon occurrence in columbines, spurlessness seems to have stuck around in this area: About a quarter of the plants lack the distinctive feature.

A single gene

The team plumbed the plant's genome to find the source of the unusual morphology. They considered a gene, APETALA3-3, known to affect spur development. They found that this single gene controlled the entire development of the flower's spurs and nectaries.

"The gene is either on or off, so it's about as simple of a change you can get," said lead author Zachary Cabin. "But that simple difference causes a radical change in morphology."

A single broken gene causes mutant plants to develop flowers with no petals or nectar spurs.

If these flowers were preserved in the fossil record, scientist could well sort them into two wholly different genera. And there would also be a puzzling gap: no intermediate form documenting a transition from one morphology to the other.

"This finding shows that evolution can occur in a big jump if the right kind of gene is involved," Hodges said. APETALA3-3 tells the developing organ to become a petal. "When it's broken, those instructions aren't there anymore, and that causes it to develop into a completely different organ, a sepal," he explained.

APETALA3-3 is a type of homeotic gene, one that specifies the development of an entire organ. A mutation in one of these genes can have a drastic effect on an organism's morphology. For instance, one homeotic mutation causes a fly to develop legs where it should have antennae. "Most of the mutations of this nature are going to be like that, just awful," Hodges continued. "The animal won't have any chance of surviving. Biologist Richard Goldschmidt called them 'hopeless monsters.'"

But once in a very long while, one of these radical changes might provide a beneficial trait in a particular environment, creating a "hopeful monster." And a hopeful monster would show that evolution can proceed in single, large jumps, supporting the punctuated equilibrium hypothesis.

"We did not have a good example of a hopeful monster due to a single genetic change," said Hodges, "until now." Researchers have to catch these abrupt changes as they're happening, otherwise they disappear into an organism's genome. For example, other relatives of columbines have lost their petals and nectaries in the past, but it's now impossible to tell if these events occurred in one fell swoop. The fact that it is actively happening in the Colorado blue columbine enabled the team to confirm their status as a hopeful monster.

"There's definitely some luck involved with us being around at the right time to capture this," Cabin said.

Surprising selection

Catching the change in action offers another benefit as well: the opportunity to study the genetics and selective pressures at work.

The team discovered five versions, or alleles, of APETALA3-3, only one of which codes for a petal with a functional nectar spur. The other four were broken, as Hodges put it. They also determined that spurlessness is a recessive trait. The flower will develop normally as long as the plant has one copy of the functional allele. But any two of the mutant alleles together will prevent this. "You can mix and match them," Cabin explained.

About a quarter of Colorado blue columbines in this area display the recessive trait of spurlesness, more than can be attributed to mere chance.

Across all species of columbines it's possible to find rare individuals that develop flowers without nectar spurs. But with a quarter of the Colorado population missing the feature, Cabin and Hodges knew this was more than a chance occurrence. "To get that many of this mutant type really suggests that there's selection favoring it somehow," Hodges said, which he finds odd, since the spur produces nectar that attracts the plant's pollinators.

Hodges is deeply familiar with columbines, and all of his previous research suggests that nectar spurs are important to the group. Even slight changes to the structure have driven speciation and diversification in the genus. "So, how the heck can you lose your spurs and still be favored?" he asked.

Attracting pollinators is only one factor contributing to reproductive success. It turned out the mutant plants actually produced more seeds than their counterparts, much to the team's surprise. They began combing through their observations, searching for an explanation.

"The first time we really realized the pattern was at the airport on the way home," Cabin recalled. He was reading off data as Hodges entered it into the computer. "Scott could see the pattern developing, because he had all the data in front of him, and was getting more and more excited."

The team had recorded herbivory from caterpillars, aphids and deer on the different morphs. Damage from caterpillars and aphids can hamper seed production, Cabin explained, while deer can devastate an entire plant. And as the data built up, a clear trend emerged: Deer and aphids preferred flowers with nectar spurs.

Shifts in floral morphology are usually driven by pollinators, but spurlessness seems to be driven by herbivory. "Natural selection can come from very surprising sources," Hodges said. "It's not always what you'd expect it to be."

Timing it right

Now that they've identified their hopeful monster, Cabin and Hodges plan to investigate the DNA around APETALA3-3 to build a timeline of when the mutations may have occurred. When the gene first mutated, only one of the plant's chromosomes was affected. That means that every descendant with that mutation would have the same genetic code around APETALA3-3 for many generations, Hodges explained.

However, chromosomes do swap alleles occasionally in a process called recombination. By tracking the amount of recombination that has accumulated around the different versions of APETALA3-3, the scientists can estimate how long ago each mutation occurred. More variation requires more time to accumulate. And the closer this variation is to APETALA3-3 itself, the more recombination events there have been since a mutation first appeared.

Read more at Science Daily

Natural selection favors cheaters

Acmispon strigosus is an annual herb that is native to California.

Mutualisms, which are interactions between members of different species that benefit both parties, are found everywhere -- from exchanges between pollinators and the plants they pollinate, to symbiotic interactions between us and our beneficial microbes.

Natural selection -- the process whereby organisms better adapted to their environment tend to survive and produce more offspring -- predicts, however, that mutualisms should fall apart. Individuals that gain from the cooperation of others but do not reciprocate (so-called cheaters) should arise and destabilize mutualisms. Yet to date, surprisingly little evidence of such cheating or destabilization exists.

A team of biologists at the University of California, Riverside, has now found strong evidence of this cheating. Focusing on the interaction between nitrogen-fixing bacteria, or rhizobia, and their legume hosts spanning about 530 miles of California habitat, the researchers found that natural selection in their study populations favors cheating rhizobia.

The study, appearing in Ecology Letters, is the first to uncover cheater strains in natural populations and show how natural selection favors them.

The researchers used a previously published database to quantify the landscape abundance of different rhizobial strains. They focused on naturally occurring populations of rhizobia in the genus Bradyrhizobium and the native annual plants, Acmispon strigosus, that these bacteria inhabit. Within these datasets they found that the fewer benefits the rhizobia provide to their host plants, the more common the rhizobia are.

"Our data show that natural selection favors cheating rhizobia, and support predictions that rhizobia can often subvert plant defenses and evolve to exploit hosts," said Joel Sachs, a professor of biology in the Department of Evolution, Ecology & Organismal Biology, who led the research team.

Sachs explained that beneficial bacteria are increasingly appreciated to be key for human health as well as the productivity of crops and livestock. Little is understood, however, about how much these bacterial services vary in natural systems and the forces that modulate them.

"In crop plants, in particular, agronomists have attempted -- and failed -- for several decades to design crop biofertilizers based on beneficial bacteria," he said. "Similar challenges have been faced in applying bacteria in other host systems -- probiotics, for example, which rarely affect host microbes. Our dataset suggests a potential flaw in these approaches; the bacteria, with their own evolutionary interests, can destabilize these interactions."

In their paper, the researchers show how benefits of bacterial symbionts vary over space and time, and how rapidly these systems can evolve.

"We often view the services of bacteria as fixed, but this is not at all true," Sachs said. "Just as each human varies a great deal in almost any trait we can measure, bacterial populations are even more highly variable. Understanding this variation and its drivers will be key to usefully harnessing these bacteria for our own purposes."

Already, his team is actively working to better understand how beneficial bacteria can be applied to improve plant growth. Preliminary data show that it is crucial to carefully select among bacterial variants to avoid using harmful strains.

"Simply applying beneficial bacteria to a crop is often not going to be sufficient since exploitative strains are expected to be lurking within these populations," Sachs said.

Read more at Science Daily

How new species arise in the sea

A barred Hamlet (Hypoplectrus puella) off the coast of Panama.

For a new species to evolve, two things are essential: a characteristic -- such as a colour -- unique to one species and a mating preference for this characteristic. For example, individuals from a blue fish species prefer blue mates and individuals from a red fish species prefer red mates. If the two species interbreed, the process of sexual recombination is expected to destroy the coupling between colour and mate preferences and form red individuals with a preference for blue mates and vice versa. This will prevent the two species from diverging, and this is one of the reasons why it has been thought for a long time that new species can only evolve in absolute isolation, without interbreeding.

However, the dynamics of this process depend on the exact number and location of genes underlying species characteristics and mate preferences, the strength of natural selection acting on these genes, and the amount of interbreeding between species. In a new study, Professor Oscar Puebla from GEOMAR Helmholtz Centre for Ocean Research Kiel in Germany together with colleagues from the Smithsonian Tropical Research Institute in Panama have found that natural selection can couple the evolution of genes for colour pattern and mate preferences when species still interbreed. The study has been published today in the international journal Nature Ecology and Evolution.

"To address this question, the first challenge was to identify an animal group in which species are still young and interbreed, with clear species characteristics, and in which the bases of reproductive isolation are well understood," Oscar Puebla explains. The hamlets, a group of closely related reef fishes from the wider Caribbean, constitute exactly such a group. The hamlets are extremely close genetically, differ essentially in terms of colour pattern, and are reproductively isolated through strong visually-based mate preferences.

A second difficulty consists in identifying the genes that underlie species differences and mate preferences. The authors of the new study have assembled a reference genome for the hamlets and sequenced the whole genomes of 110 individuals from three species in Panama, Belize and Honduras. "This powerful dataset allowed us to identify four narrow regions of the genome that are highly and consistently differentiated among species in a backdrop of almost no genetic differentiation in the rest of the genome," co-author Kosmas Hench from GEOMAR says. In line with the ecology and reproductive biology of the hamlets, these four intervals include genes involved in vision and colour pattern.

The data also show that vision and colour pattern genes remain coupled despite the fact that they are located on three different chromosomes and that species still interbreed. Such a coupling had been previously reported when the two sets of genes are very close to each other on chromosomes, in which case they are protected from sexual recombination, but not when they are on different chromosomes. By capturing the very earliest stages of speciation in hamlets, the team shows how selection can contribute to the creation of new species.

Read more at Science Daily

Social isolation: Animals that break away from the pack can influence evolution

This photo shows a cane toad. Cane toads (Rhinella marina) at the leading edge of their range expansion in Australia are more cut off from other individuals. Males from these peripheral populations display stronger social attraction than do toads from longstanding populations. Their enhanced social behavior might give them an advantage in conditions of relative social isolation by increasing the chances that they will transfer useful information, be protected against predators, and mate.

For some animals -- such as beetles, ants, toads, and primates -- short-term social isolation can be just as vital as social interaction to development and long-term evolution. In a review published July 17 in the journal Trends in Ecology & Evolution, two evolutionary biologists describe approaches for testing how an animal's isolation might impact natural selection and evolution. This framework can help design more effective breeding, reintroduction, and conservation strategies.

Research on evolution typically focuses on the importance of social interactions, including parent-offspring bonding, competition for resources, and courtship and mating rituals. But Nathan Bailey at the University of St Andrews in Scotland and his colleague Allen Moore at the University of Georgia realized that isolation must then be an extreme condition worthy of equal attention.

"The environment an animal experiences can influence which genes it expresses, when, and how much, so conditions of social isolation might cause expression of different traits," says Bailey. "This in turn could affect responses to natural selection in terms of survival and reproduction, which has evolutionary consequences. For some species, it might even mean that temporary social isolation is favorable."

The invasive cane toad Rhinella marina of Australia, for instance, will venture off on its own to expand into new territory, but the isolation this causes drives an uncharacteristically strong attraction to members of the opposite sex upon the toad's return to a social environment. This boosts the likelihood of both communication and successful mating, which are necessary for survival as the toads expand into new regions. This means that social isolation itself provides the conditions for natural selection to favor adaptations to cope with it.

Likewise, when poisoned, the European ant Temnothorax unifasciatus secludes itself from its kin until death. This eliminates contact with its nestmates, protecting them from the infection, ensuring its relatives' survival, and overall lessening some of the costs associated with social living, such as spreading disease.

"Traits expressed during social interactions might exist because they've been shaped by selection, but at the same time, social interactions themselves represent a type of environment that can select and shape how individuals behave," says Bailey.

This duality of social interaction as both trait and environment merits further study, and Bailey and Moore propose gaining a more complete understanding of social isolation's effects using a measurement termed the "index of social isolation." The index would allow researchers to compare an animal's ideal amount of isolation with how much it is actually experiencing.

To do this, researchers must first measure the optimal balance of interaction and isolation by testing individuals with different levels of each to find the best possible outcome in terms of survival and reproduction. Comparing this ideal to real observations will help determine whether animals are more or less isolated than they should be and ultimately allow for more effective designs for conservation strategies, reintroduction models, and breeding programs.

Read more at Science Daily

Natural selection gave a freediving people in Southeast Asia bigger spleens

This image shows a Bajau diver hunting fish underwater using a traditional spear.

The Bajau people of Southeast Asia, known as Sea Nomads, spend their whole lives at sea, working eight-hour diving shifts with traditional equipment and short breaks to catch fish and shellfish for their families. In a study published April 19 in the journal Cell, researchers report that the extraordinary diving abilities of the Bajau may be thanks in part to their unusually large spleens. The adaptation, the researchers say, is a rare example of natural selection in modern humans -- and one that could provide medically relevant insight into how humans manage acute hypoxia.

"Humans are pretty plastic beings. We can adapt to a number of different extreme environments just through our lifestyle changes or our behavioral changes, so it wasn't necessarily likely that we would find an actual genetic adaptation to diving," says first author Melissa Ilardo, a doctoral student at the University of Copenhagen working with co-senior researchers Rasmus Nielsen (@ras_nielsen) of the University of California, Berkeley, and Eske Willerslev of the University of Copenhagen and the University of Cambridge. "The first sign that we were maybe onto something was when we saw that both the Bajau divers and non-divers had larger spleens than the Saluan, a nearby, non-diving population."

Spleen size is significant because of the organ's role in the human dive response, which occurs when our faces are submerged in water and we hold our breath. As our heart rate slows and blood vessels in our extremities constrict, the spleen contracts, releasing oxygenated red blood cells and making more oxygen available in the bloodstream. A larger spleen means that more oxygen gets released. Perhaps for this reason, large spleens have also been documented in diving seals.

The Bajau having larger spleens than their non-diving neighbors suggested that their diving culture had shaped their physiology. But the fact that non-divers and divers both had larger spleens suggested that it wasn't just a plastic response to spending so much time under water. There was likely something different about the Sea Nomads' DNA.

When the researchers scanned the genomes of the Bajau, they identified 25 sites that differed significantly from two comparison populations, the Saluan and the Han Chinese. Of these, one site on a gene known as PDE10A was found to be correlated with the Bajau's larger spleen size, even after accounting for confounding factors like age, sex, and height. In mice, PDE10A is known for regulating a thyroid hormone that controls spleen size, lending support for the idea that the Bajau might have evolved the spleen size necessary to sustain their long and frequent dives.

"The chance of finding evidence of population-specific natural selection, even in a population as extreme as the Bajau, was pretty slim. It was very exciting to find, and it just opens up so many possibilities," says Ilardo.

Understanding how the human body responds to a lack of oxygen, for instance, is important in a lot of medical contexts, from chronic obstructive pulmonary disease to surgery. Hypoxia has been well studied in populations living at high altitudes, where the lack of oxygen is much more chronic. But not as much research has been done on diving populations. "Here it's more of an acute hypoxia, almost similar to what's experienced with sleep apnea," she says. By making their data freely available to other researchers, she and her co-authors hope that some of what they've learned from the Bajau can be applied in medical contexts.

For the Bajau, Ilardo believes that the decision to participate in this research is about better understanding themselves. "I basically just showed up at the house of the chief of the village, this bizarre, foreign girl with an ultrasound machine asking about spleens," she says. "They're the most welcoming people I've ever met, but I wanted to make sure that they understood the science behind what I was doing, so that it wasn't just me taking measurements from them without giving back. And we do have a trip planned to return to the community to explain the results to them."

"They're explorers, so I think they're inherently curious and want to know more about the world, including about their own biology," she says.

Read more at Science Daily

New algorithm can pinpoint mutations favored by natural selection in large sections of the human genome

It is hypothesized that natural selection favors lighter skin in northern latitudes to compensate for vitamin D deficiency due to lower UV radiation. iSAFE identified identical mutations in multiple non-African populations in 5 regions associated with skin pigmentation, suggesting an early response to the onset of selection as humans migrated out of Africa. Blue is derived and red is ancestral.

A team of scientists has developed an algorithm that can accurately pinpoint, in large regions of the human genome, mutations favored by natural selection. The finding provides deeper insight into how evolution works, and ultimately could lead to better treatments for genetic disorders. For example, adaptation to chronic hypoxia at high altitude can suggest targets for cardiovascular and other ischemic diseases.

The sequenced genome of a single individual yields about half a terabyte of data of information -- that's about as much information as you'll find on 106 DVDs. A population sample of size 1000 individuals contains 1000 times as much information. So to examine such a massive amount of data, researchers turned to computational techniques.

"Computer science and data science are playing a significant role to better understand the code of life and uncover the hidden patterns in our genome," said Ali Akbari, the paper's first author and a Ph.D. student in electrical and computer engineering at the University of California San Diego. "We are analyzing massively large sets of human genomic data to ultimately improve our understanding of genetic basis of diseases."

Researchers detail the algorithm, dubbed iSAFE, in the Feb. 19 issue of Nature Methods.

Many existing genomic analysis approaches can detect which regions of the human genome are evolving under selection pressure. Often, these regions are large, covering millions of base-pairs and do not shed light on the specific mutations that are responding to the selection pressure. iSAFE doesn't need to know the function of the genomic region it is analyzing or any demographic information for the human population it belongs to. Instead, the researchers used population genetic signals imprinted in the genomes of the sampled individuals and machine learning techniques to reliably identify the mutation favored by selection.

In natural selection, neighboring mutations 'hitchhike' with the mutation that is under positive selection, leading to a loss of genetic diversity near the favored mutation. iSAFE exploits signals in the neighboring sequences, the so-called "shoulder regions" to pinpoint the favored mutation.

"Finding the favored mutation among tens of thousands of other, hitchhiking, mutations was like a needle in a haystack problem," said Akbari, who works in the research group of computer science professor Vineet Bafna at the Jacobs School of Engineering at UC San Diego.

To test the algorithm, researchers ran iSAFE on regions of the genome that are home to known favored mutations. The algorithm ranked the correct mutation as the top one out of more than 21,000 possibilities in 69 percent of cases, as opposed to state of the art methods, which only did this in 10 percent of cases.

The algorithm also identified a host of previously unknown mutations, including five that involve genes related to pigmentation. In these cases, iSAFE identified identical mutations in multiple non-African populations. This suggests an early response to the onset of selection as humans migrated out of Africa.

The research was supported in part by the National Science Foundation and the National Institutes of Health.

Identifying the favored mutation in a positive selective sweep

Corresponding authors: Ali Akbari, Department of Electrical and Computer Engineering and Vineet Bafna, Department of Computer Science and Engineering, UC San Diego.

Read more at Science Daily

Comes naturally? Using stick insects, scientists explore natural selection, predictability

A green morph of the Timema genus of stick insects.

Is evolution predictable? Are changes in a species random or do they happen because of natural selection?

"Evolution often appears random, even when driven by the deterministic process of natural selection, because we just aren't aware of all the environmental fluctuations and other factors taking place that drive change," says Utah State University biologist Zach Gompert. "If we had a better understanding of the mechanisms at play, we might have a better picture of evolutionary change and its predictability."

Gompert, with colleagues Patrick Nosil, Romain Villoutreix, Clarissa de Carvalho and Victor Soria-Carracso of England's University of Sheffield, along with Timothy Farkas of the University of Connecticut, Jeffrey Feder of the University of Notre Dame and Bernard Crespi of Canada's Simon Fraser University, explored these questions and report findings in the Feb. 16, 2018, issue of the journal Science.

The research was supported by a European Research Council grant and a Canadian Natural Sciences and Engineering Research Council grant, along with computational resources from the University of Utah Center for High?Performance Computing.

Gompert and colleagues used data from the past to test their ideas of evolutionary predictability.

"We used a rare and unique data set of 25 years of field data documenting the evolution of cryptic body coloration in terms of frequencies of three 'morphs' -- flavors, if you will -- of stick insects," says Gompert, assistant professor in USU's Department of Biology and the USU Ecology Center. "Using the first 10?15 years of the data, we tried predicting, or forecasting, the changes that would occur in the subsequent years of the data."

The three morphs are green, green with a white stripe and 'melanistic' or dark brown.

"These insects are cryptic, meaning they visually blend into their surroundings to hide from hungry predators," Gompert says.

Both types of the green stick insects live on green foliage, while the brown insects live on brown stems.

How close did the team's predictions match up to the collected data? Really close for the green versus green?striped morphs, but rather poorly for the melanistic morph, he says.

Using genomic analysis, the scientists were able to show, in both cases, the deterministic process of selection was the likely cause of evolutionary change.

"With the green versus green?striped morphs, the cause of selection was simple and well understood facilitation of predictability," Gompert says. "In contrast, with the melanistic morph, natural selection was more complex and tied to variation in weather and climate, making it harder to predict from past patterns of change."

The scientists compared their results to better known studies, including Darwin's finches and the scarlet tiger moth, both of which were also not very predictable.

"Our findings support previous discoveries and suggest evolution of morph frequencies in these stick insects is indeed a result of selection," Gompert says. "They also suggest poor predictability of environmental variation and how it affects selection, rather than random evolutionary processes, might be the main limits on predicting evolution."

Read more at Science Daily