Playing both ends: Amphibian adapted to varied evolutionary pressures

Caecilians are serpent-like creatures, but they're not snakes or giant worms. The limbless amphibians, related to frogs and salamanders, favor tropical climates of Africa, Asia and the Americas. Most live in burrows of their own making; some are aquatic.

A limbless amphibian, known as Caecilian, Siphonops annulatus, widely distributed in Brazil. Scientists from Utah State
University in the United States and Brazil’s Butantan Institute report skin gland concentrations adapted
to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

With colleagues from Brazil, Utah State University ecologist Edmund "Butch" Brodie, Jr. reports caecilians feature greatly enlarged poison glands at each end of their bodies, which appear to have evolved from different selective pressures - the ability to tunnel into the ground and to defend oneself from predators.

Brodie, along with Carlos Jared, Pedro Luiz Mailho-Fontana, Rafael Marques-Porto, Juliana Mozer Sciani, Daniel Carvalho Pimenta, and Marta Maria Antoniazzi of São Paulo's Butantan Institute, published the findings in Scientific Reports.

The team's research, supported by the Brazilian National Council for Scientific and Technological Development, focuses on Siphonops annulatus, a caecilian species found throughout Brazil.

"My Brazilian colleagues noticed the burrows made by this species were lined with a shiny, slick substance," says Brodie, professor in USU's Department of Biology and the USU Ecology Center. "We didn't think it was a secretion from the poison glands, so we decided to investigate."

The Brazilian caecilian, grayish in color and measuring about 18 inches in length, is a surprisingly rapid burrower, he says.

Magnified image of connective tissue matrix forming honeycomb structure surrounding glands on the head of Caecilian,
Siphonops annulatus. Scientists from Utah State University in the United States and Brazil’s Butantan Institute report skin
gland concentrations adapted to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

"When caecilians burrow, they force their snouts into the ground and essentially dive into the soil," Brodie says.

As suspected, the team discovered all the skin glands in the serpentine creatures' head region were greatly enlarged, tightly packed mucous glands - not poison ones. The slippery lubrication enables the caecilians' rapid, subterranean escape from predators, especially coral snakes.

"We know of no other amphibian with this high concentration of mucous glands," Brodie says. "In other terrestrial amphibians, mucous is mainly related to the uptake of oxygen. Here, in caecilians, it's obviously used in locomotion."

Examination of the caecilians revealed further information. The mucous glands extend throughout the amphibians' body, in gradually reduced concentration, and give way to poison glands concentrated in the tail.

"The poison glands, resulting from a different selective pressure, provide another defense from predators," Brodie says. "In addition to chemical defense, the tail acts as a 'plug,' blocking the tunnel and further deterring predators."

The eccentric amphibian, Brodie and colleagues write, is "really a box of surprises."

Author: Mary-Ann Muffoletto | Source: Utah State University [February 23, 2018]

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First 3D models reveal development of Tasmanian tiger from joey to adulthood

Researchers from the University of Melbourne and Museums Victoria have CT scanned all 13 known Tasmanian tiger joey specimens to create 3D digital models, allowing them to study their skeletons and internal organs, and reconstruct their growth and development.

Internal structures of Thylacine joeys [Credit: University of Melbourne]

This has revealed important new information about how this unique extinct marsupial evolved to look so similar to the dingo, despite being very distantly related.

The digital scans show that when first born the Tasmanian tiger or thylacine (Thylacinus cynocephalus) looked like any other marsupial. But three months later, when they left the pouch, they had taken on the appearance of a puppy and continued to grow with a dog-like appearance.

The research, led by the University of Melbourne and Museums Victoria and in conjunction with an international team of scientists, is published in Royal Society Open Science.

The Tasmanian tiger was a marsupial, which raised its young in a pouch. Its resemblance to the dingo is one of the best examples of convergent evolution in mammals. This is where two species, despite not being closely related, evolve to look very similar. The Tasmanian tiger would have last shared a common ancestor with the canids (dogs and wolves) around 160 million years ago.

The specimens cover ages from two to 12 weeks. The white scalebar is 10mm [Credit: University of Melbourne]

Dr Christy Hipsley, Research Associate at the University of Melbourne and Museums Victoria, said after sequencing the Tasmanian tiger genome in 2017, this research fills one more piece of the puzzle on why they have evolved to look so similar to dogs. 

"This is the first digital development series of the Tasmanian tiger, Australia’s most iconic extinct marsupial predator.

"Using CT technology we have been able to garner new information on the biology of this iconic species, and its growth and development."

These scans show in incredible detail how the Tasmanian tiger started its journey in life as a joey that looked very much like any other marsupial, with robust forearms so that it could climb into its mothers pouch. But by the time it left the pouch around 12 weeks to start independent life, it looked more like a dog or wolf, with longer hind limbs than forelimbs.

Once ranging throughout Australian and New Guinea, the Tasmanian tiger disappeared from the mainland around 3000 years ago, likely due to competition with humans and dingos.

The remaining Tasmanian tiger population, isolated on Tasmania, was hunted to extinction in the early 20th century, with the last known individual dying at Hobart Zoo in 1936.

Axel Newton, PhD student and Lead Author on the paper notes, until now there have only been limited details on its growth and development. For the very first time we have been able to look inside these remarkably rare and precious specimens.

Unable to study the living species, the team had to look to the 13 Tasmanian tiger joey specimens that exist in museum collections worldwide, including three from the collection of Museums Victoria. These joey specimens, representing five stages of postnatal development, were scanned using non-invasive X-ray micro-CT scanning technology to create high resolution 3D digital models, in which all their internal structures such as skeleton and organs could be studied.

Associate Professor Andrew Pask from the University of Melbourne explains this was an incredibly effective technique to study the skeletal anatomy of the specimens without causing any damage to them.

"This research clearly demonstrates the power of CT technology. It has allowed us to scan all the known Thylacine joey specimens in the world, and study their internal structures in high resolution without having to dissect or cause damage to the specimen. By examining their bone development, we’ve been able to illustrate how the Tasmanian tiger matured and identify when they took on the appearance of a dog."

The study has also revealed the incorrect classification of two specimens held in the collection of the Tasmanian Museums and Art Gallery (TMAG). Instead, they are most likely to be quolls or Tasmanian devils, based on the number of vertebrate and presence of large epipubic bones (specialised bones that support the pouch in modern marsupials).

Tasmanian tiger [Credit: Tasmanian Museum and Art Gallery, Hobart, Tasmania]

Senior Curator of Vertebrate Zoology at TMAG, Ms Kathryn Medlock, said that the museum had received many requests to dissect its pouch young over the years but requests were always refused.

"One of the major advantages of this new technology is that it has enabled us to do research and answer many questions without destruction of the sample specimens. This is a significant advancement that also has an additional benefit of helping us to learn more about the identity of these specimens that have been in the TMAG collection for many years."

An exciting outcome of the research is that the 3D digital Tasmanian tiger models are to be made publicly available as a resource for current and future researchers.

Source: The University of Melbourne [February 21, 2018]

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The conflict between males and females could replace the evolution of new species

New research shows that males and females of the same species can evolve to be so different that they prevent other species from evolving or colonising habitats, challenging long-held theories on the way natural selection drives the evolution of biodiversity.

Image showing variations between male and female Liolaemus nigriceps [Credit: Dr Daniel Pincheira-Donoso,
School of Life Sciences, University of Lincoln]

According to Darwin's theory of natural selection, first introduced in his book On the Origin of Species (1859), new environments such as mountains and islands with abundant food and habitats, offer species the 'ecological opportunity' to colonise an area using those resources.

New research from the UK has shown that exactly the same mechanism of evolution that creates new species also operates within the same species when males and females compete for the ecological resources available in different habitats, such as bushy areas or stony patches with abundant food. The conflict between the sexes can lead to one sex becoming bigger, more colourful or adapting to eat different food, just like a traditional process of evolution by natural selection can lead an ancestor to split into two different species.

This process of evolution between the sexes expands the biodiversity of the area - a development that evolutionary biologists previously thought only occurred when the number of different species using different resources or 'niches' increases. This new research challenges that assumption, showing that different species and different sexes of the same species can occupy these niches.

Image showing variations between male and female Liolaemus tenuis [Credit: Dr Daniel Pincheira-Donoso,
School of Life Sciences, University of Lincoln]

This new research which explored the evolution of lizards in the Chilean Andes Mountains and Argentinean Patagonia, shows that different sexes of the same species can fill niches as well, meaning new species are actively prevented from evolving. This is because there is no new environment for them to occupy - a necessary condition for new species to evolve under Darwin's theory of natural selection.

Conducted by academics from the Universities of Lincoln, Exeter and Sheffield, the study demonstrated that biodiversity can now be seen as the formation of new, different species, or, as the formation of different sexes which are distinct enough to be equivalent to different species in the way they 'saturate' ecological niches.

Dr Daniel Pincheira-Donoso, Senior Lecturer in Evolutionary Biology at the School of Life Sciences at the University of Lincoln and lead researcher on the study, said: "Our research reveals evidence for this intriguing phenomenon that the evolution of sexes within a species could replace the evolution of new species, which begins to add a new layer to our understanding of the evolution of biodiversity.

"It is important to stress that the diversity of life on our planet applies not only to the evolution of different species, but also to the independent evolution of males and females within the same species, which potentially has very important implications."

The findings have been published in the scientific journal Global Ecology and Biogeography.

Source: University of Lincoln [February 21, 2018]

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Theory suggests root efficiency, independence drove global spread of flora

A new theory of plant evolution suggests that the 400 million-year drive of flora across the globe may not have been propelled by the above-ground traits we can see easily, but by underground adaptations that allowed plants to become more efficient and independent.

Researchers from Princeton University and the Chinese Academy of Sciences have posed a theory of plant evolution based
on root adaptations that allowed plants to become more efficient and independent. The cross sections above show that the
roots of plants such as the subtropical oak species Lithocarpus chintungensis (largest cross section, center left) and the
tropical species Parashorea chinensis (lower-right of largest cross section) retained their ancestral thickness and reliance
on the symbiotic fungi (purple ring) that surround the root to help it obtain nutrients. As plant species spread from their
nutrient-rich tropical origins, however, the root tips of plants such as the desert shrub species Tamarix ramosissima
(left of largest cross section) evolved to be thinner so they could more efficiently explore soil for nutrients, and they
have less dependence on symbiotic fungi [Credit: Zeqing Ma, Chinese Academy of Sciences]

As plant species spread north and south from their nutrient-rich tropical beginnings, the fine tips of their roots became narrower and more widespread to help them explore increasingly poor soil for vital nutrients, according to a study in the journal Nature led by researchers from Princeton University and the Chinese Academy of Sciences (CAS) in Beijing. In addition, as plants spread into unpredictable environments such as arid deserts they grew less dependent on the symbiotic fungi -- or mycorrhiza -- that colonize roots and help host plants obtain the essential plant nutrients nitrogen and phosphorous.

The findings reconsider how plants adapted to new environments as they evolved, said corresponding author Lars Hedin, the George M. Moffett Professor of Biology and chair and professor of ecology and evolutionary biology and the Princeton Environmental Institute. Scientists have in the past focused on above-ground characteristics, primarily leaf traits and the efficiency with which plants absorb sunlight for photosynthesis, he said.

Instead, Hedin said, he and his colleagues have found for the first time that root diameter and reliance on fungi -- or the lack thereof -- are the traits that most consistently characterize the plant community across entire biomes, which are large distinct communities of animals and plants such as a desert, temperate forest or savanna.

"These are the secret strategies that plants have used over time to take over the world," Hedin said. "Our goal was to unlock the understanding of those strategies, and our findings offer a new global theory for plant evolution. Hidden underground there has been a tremendous game of survival-of-the-fittest and we are fortunate to have the first-ever view of the science of that game.

"This work has major implications for conservation and our stewardship of the plant world," Hedin continued. "It provides some of the hidden, below-ground rules by which plants survive and spread. It's a global view of plant evolution at a time when global rules are essential for building climate models and understanding the biosphere."

Mingzhen Lu, first Princeton author and a graduate student in Hedin's research group, said that if root traits do in fact determine a plant's ability to withstand a particular environment, these findings could be valuable in conserving endangered species or projecting how plants might adapt to climate change.

"Our findings simplify how we can practically characterize a plant's strategy for obtaining nutrients," Lu said. "Knowing their underlying nutrient strategy will help us know how to preserve them, or know the conditions under which they could or could not survive."

Kurt Pregitzer, the Thomas Reveley Professor and dean of the College of Natural Resources at the University of Idaho, said this work could be especially useful in combating invasive species, which, in a highly mobile world, increasingly threaten biodiversity. Pregitzer is familiar with the research but had no role in it.

"Invasive species cause widespread displacement of native plants and tremendous economic impacts across the globe," Pregitzer said. "This study may open entirely new lines of scientific investigation that help us better understand how invasive-plant root systems help these exotic species outcompete native plants."

The researchers spent two years examining a database of root traits consisting of 369 species from seven biomes (above):
desert, grassland, Mediterranean, boreal, temperate, subtropical and tropical. Woody biomes are identified as shades
of tan-to-yellow and non-woody biomes are in shades of green. The researchers found that plants in tropical (light orange)
and subtropical biomes (beige) exhibited the largest range of root-tip diameters, from less than 0.25 millimeters up to
1 millimeter. These plants rely on soil fungi to provide nutrients, a similar strategy to that of Earth's earliest land plants.
Plants in biomes characterized by poor soil, cold winters and/or infrequent precipitation have a narrow root-diameter
range ideal for that environment. The desert (light green) and grassland (green) species studied all had root
diameters of less than 0.25 millimeters [Credit: Lars Hedin and Mingzhen Lu, Department
of Ecology and Evolutionary Biology]

The Nature paper is unique for its scale and careful application of scientific methods, Pregitzer said. "This study is the first conducted across a wide range of terrestrial environments and it demonstrates that plant species have evolved root strategies that are conserved within corresponding families, genera and species," he said. "These root traits likely facilitate plant success in highly competitive natural ecosystems."

The researchers spent two years examining a uniquely large database of root traits consisting of 369 species from seven biomes: desert, grassland, Mediterranean, boreal, temperate, subtropical and tropical.

These data were compiled over the course of a decade in the lab of late co-corresponding author Dali Guo, a professor at CAS' Institute of Geographic Sciences and Natural Resources Research. First author Zeqing Ma is a research associate in Guo's lab and co-author Xiangliang Xu is a colleague of Guo's. The paper's co-authors also included root experts Richard Bardgett, professor of ecology at the University of Manchester in the UK; David Eissenstat, professor of woody plant physiology at Pennsylvania State University; and M. Luke McCormack, a research associate at the University of Minnesota.

The researchers found that plants in tropical and subtropical biomes exhibited the largest diameter range for the finest root tips that forage for nutrients, from less than 0.25 millimeters up to 1 millimeter. These thicker-rooted plants employ what the authors call a "conservative" strategy -- similar to that of Earth's earliest land plants -- that relies on the soil fungi prevalent in wet, warm tropical and subtropical soils to provide nutrients. The researchers refer to nutrient-rich soil in consistently sultry environs as "predictable."

Meanwhile, fine-root diameters in "unpredictable" biomes characterized by poor soil, cold winters and/or infrequent precipitation fall within a narrower range ideal for that environment. For instance, the desert and grassland species studied all had root diameters of less than 0.25 millimeters. Root tips in these biomes evolved to be thinner so they could more efficiently explore soil for every unit of carbon the plant expends, and they have less dependence on symbiotic fungi.

The extensive data the researchers used allowed them to explore the evolution of plant roots to an extent never before possible, Lu said. "Below-ground plant ecology has been understudied, limited by a paucity of data," he said. "Because of that, the governing rule of what's going on below ground has been very poorly known."

"Thus far," Hedin added, "everybody has quite naturally tried to understand how plants are organized by looking at above-ground traits. But our findings do not follow the above-ground theories -- that was a surprise."

The study reveals that root and leaf evolution have followed different paths, Pregitzer said. Plant ecologists have known that the form and function of leaves are essential to a plant species' success, but "we did not understand if this was true across the tremendous diversity of plant root systems," he said.

"Interestingly, little was known about how plant roots have evolved to facilitate success in their native habitats," Pregitzer said. "Now we know that leaves and roots have responded to different evolutionary selective pressures, and we can start building a better understanding of how root form and function drive plant success within the tremendous biological diversity we see on Earth."

The findings align with ideas explored at Princeton that suggest that plants -- rather than being passive features of their environment -- have actively adapted to and shaped their environments, Hedin said. He was senior author of a 2015 paper in Nature Plants that suggested that ecosystems take their various forms because plants behave in ways that not only benefit themselves but also determine the productivity and composition of their habitats.

"Over evolutionary time, it's as if plants have actively explored the best strategies to safeguard their own survival," Hedin said. He and Lu brought this perspective to the database put together by their colleagues at CAS.

"We understood from a plant perspective how to bring evolutionary questions to their unique global dataset," Hedin said. "It was this great collaboration where we combined new ideas with years of painstaking fieldwork to produce this great result. It couldn't have happened without both sides."

Source: Princeton University [February 21, 2018]

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Scientists create 'Evolutionwatch' for plants

Using a hitchhiking weed, scientists from the Max Planck Institute for Developmental Biology reveal for the first time the mutation rate of a plant growing in the wild.

Scientists created an 'Evolutionwatch' for plants [Credit: Moises Exposito-Alonso,
Claude Becker and colleagues]

They compared 100 historic and modern genomes of the tiny plant Arabidopsis to measure precisely the rate at which it evolves in nature. The oldest plant, preserved in a herbarium, was from 1863. At this time, the scientists estimate the species had already more than 200 years in the New World behind it. Two different methods gave the same result, that Arabidopsis had been introduced by Europeans who arrived on the US East Coast around the year 1600. It was almost certainly introduced there by chance, perhaps carried on the boots of Europeans, or mixed in with the seeds of edible plants.

The team focused on samples from North America, because they knew that one particular genetic family of Arabidopsis was very widespread, presenting an opportunity to observe newly-acquired mutations. The comparison of 100 complete genomes revealed 5000 new mutations, some of which could have given the plant an adaptive advantage as it colonised its new environment. The plant moved inland alongside human settlers, gradually diverging from the European ancestor from which it originated. Samples of the species along the same path today reveal increasingly deep and fast-growing roots, perhaps evidence that it adapted during its hitchhiking trip.

"Collections of invasive populations sampled from different times in history enable us to observe the 'live' process of evolution in action," says Moises Exposito-Alonso, first author of the paper published in PLOS Genetics.

They sequenced the genomes of 100 plants collected by botanists between 1863 and 2006. All samples from before 1990 came from museum collections of dried plants. The oldest dried plants, preserved in time 150 years ago, show how much they had evolved by that time. The youngest plants continued to change and evolve. By comparing genomes of plants that had diverged from a common ancestor for different amounts of times, the scientists calculated how many mutations the plant acquires a year.

This in turn enabled the team to deduce that the last common ancestor of the lineage must have lived at the end of the 16th or beginning of the 17th century, coinciding with the time that many people were arriving by boat from Europe, particularly the southern UK, west coast of France and the Netherlands. This was very surprising, since a previous estimate, which had not made use of genetic information from dried herbarium samples, suggested that the colonizing Arabidopsis plants had only arrived in the 19th century.

Arabidopsis is not a harmful weed, but the findings help reveal some of the fundamental evolutionary processes behind the ability of invasive species to colonise new environments. In particular, they unlock some of the secrets of the "genetic paradox of invasion". This occurs when a colonizer with low genetic diversity is nevertheless surprisingly successful in a new environment.

To determine the effect of new mutations, the scientists grew some of the plants in the lab to identify any differences in growth. The fact that such differences were found suggests that some of the mutations that appeared during the past 400 years conferred an advantage during colonisation.

"We were very surprised, since scientific dogma suggests that evolution normally proceeds at a much slower pace," said Hernan Burbano, one of the supervisors of this study.

"Accurate evolutionary rates for plants and animals will be fundamental to reconstruct their past history and to predict the opportunity of novel advantageous traits to arise. Our results show that herbarium and animal specimens can be the source of a great new branch of genetics in future," Exposito says.

Source: Public Library of Science [February 21, 2018]

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Extreme-altitude birds evolved same trait via different mutations

On the Himalayan-enveloped Tibetan Plateau and the Altiplano plateau of South America - the world's two highest tabletops - a select few bird species survive on 35 to 40 percent less oxygen than at sea level.

A rendering of avian hemoglobin, the blood protein that captures and delivers oxygen
throughout the body [Credit: PNAS]

All extreme-altitude birds have evolved especially efficient systems for delivering that precious oxygen to their tissues. But a new study led by the University of Nebraska-Lincoln and Chinese Academy of Sciences has found that these birds often evolved different blueprints for assembling the proteins - hemoglobins - that actually capture oxygen.

Published in the Proceedings of the National Academy of Sciences, the study found that many species from the two plateaus underwent different mutations to produce the same result: hemoglobins more adept at snaring oxygen from the lungs before sharing it with the other organs that depend on it.

Those mutational differences often emerged even among closely related species residing on the same plateau, the study reported.

"You could imagine, just because of the different ancestral starting points, that the Tibetan birds maybe all went one (mutational) route, and the Andean birds typically did things a different way," said co-author Jay Storz, Susan J. Rosowski Professor of biological sciences at Nebraska. "But that's not what we saw. Across the board, there weren't really any region-specific patterns.

"In both cases, it seems like there were many different ways of evolving a similar alteration of protein function."

Jay Storz stands on the Tibetan Plateau, more than 15,000 feet above sea level. Storz and his colleagues have shown that
many high-altitude bird species underwent different mutations to develop the same adaptation: hemoglobin better at
capturing and distributing scarce oxygen [Credit: University of Nebraska-Lincoln]

Like all proteins, hemoglobin consists of intricately folded chains of amino acids. The interactions among those amino acids dictate the structure of a protein, which in turn determines its properties - how readily it binds with and releases oxygen, for instance. But a mutation can effectively swap out an amino acid for a chemically distinct version at the same site in the protein, potentially modifying its behavior in the process.

After comparing the ancestral vs. modern hemoglobin proteins of nine species that inhabit the Tibetan Plateau, the team did identify two cases in which distantly related species underwent identical, functionally important mutations. Yet in the other instances, species evolved different ways to build a better hemoglobin.

The latest findings reinforce a 2016 Storz-led study published in the journal Science, which was the first to establish that vertebrate species can follow different molecular-level paths to reach the same adaptation. That study, which investigated birds only from the Andes, inspired the team to follow up with its comparison of Andean and Himalayan species.

"Birds that have adapted to high-altitude conditions from all these different mountain ranges have repeatedly evolved hemoglobin with elevated oxygen affinities," Storz said. "At that (functional) level, everything is highly repeatable, and there's a very striking pattern of convergent evolution. But in terms of the actual molecular underpinnings, there's far less predictability, and it's clear that there are many possible changes that can produce the same functional outcome."

Source: University of Nebraska-Lincoln [February 20, 2018]

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Finches from remote corners of New Guinea help solve an evolutionary puzzle

Tucked away in an unassuming gray metal file cabinet in a graduate student office at Boston University is an evolutionary puzzle that would leave even Charles Darwin scratching his head. Inside the cabinet, 18 clear Tupperware containers house 301 estrildid finch specimens from New Guinea, carefully laid out in rows by population and species. Each of the 11 species’ plumage is splashed with its own distinct pattern of black, brown, gray, and white.

Credit: Cydney Scott

Michael Sorenson, a professor of biology, explains that the birds are an evolutionary anomaly: Despite their striking coloration differences, all 11 species are extremely closely related, suggesting that they evolved quickly and recently (evolutionarily speaking), even faster than the famous Darwin’s finches of the Galapagos.

But how and why did these close relatives end up looking so different? And how did they evolve so quickly into different species? Biologists have long wondered exactly how new species form, but generally assume that new genetic mutations account for the changes in form and function that ultimately make each species unique. However, that may not always be the case, and studying unusual groups like the finches of New Guinea helps biologists better understand other ways new species emerge, revealing more about evolution as a whole.

“Speciation is the process by which the incredible diversity of life on earth came into being—including humans,” Sorenson says. “It is not only one of the most fundamental processes in evolutionary biology, but is central to understanding the history of life on earth.”

To understand how this extraordinary group of finches evolved, Katie Stryjewski (GRS’15) collected birds throughout New Guinea and carefully preserved blood, feather, and tissue samples, with Sorenson joining her on the last of four trips. Then Stryjewski used genome sequencing to peer deep inside the birds’ genetic codes.

Credit: Katie Stryjewski

Sorenson first became interested in the estrildid finches of New Guinea during the late 1990s, when his research on the indigobirds of Africa snowballed into an ambitious effort to build a family tree of all 145 estrildid finch species in the world.

“My career has been a somewhat less-than-coherent series of studies on out-of-the-ordinary examples of behavior and evolution in birds,” he says. “The unifying theme, however, is an interest in understanding not only the evolution of new species, but also the diversity of behavior and morphology observed in different species.”

Sorenson’s project on estrildid finches started in the hallowed halls of natural history museums around the world.

“Because many of these species occur in remote and far-flung corners of the globe, we often had to use old museum specimens, taking a little feather or a bit of skin from the foot as a source of DNA that would allow us to figure out how all these birds were related,” he explains. “This group of species in New Guinea popped out as very, very closely related.”

Credit: Katie Stryjewski

Sorenson discovered that the entire group of New Guinea finch species was more genetically similar than is typical for the birds within a single African finch species. This points to an “extraordinarily recent and rapid radiation” occurring over tens or hundreds of thousands of years (compared to millions of years for most bird species).

Today, clusters of two to three New Guinea estrildid finch species live in overlapping geographic regions, yet somehow have remained separate species with distinct plumage patterns. For example, both Lonchura grandis and Lonchura castaneothorax (below) live in the same central region of New Guinea, yet look very different.

Sorenson was intrigued. “Which genes are involved? And how many genes does it take to build this species versus that species?” he says. “The profound genetic similarity of these species provided the perfect opportunity to answer these questions.”

To investigate further, he needed higher-quality DNA samples, which meant he had to find a PhD student willing to travel to New Guinea to collect finches in the field. He found Stryjewski, who had developed an interest in tropical birds, and top-notch skills in field research, genetic analyses, and bird taxidermy, as an undergraduate student at Louisiana State University.

Credit: Cydney Scott

“Bird taxidermy is my favorite special skill to mention during icebreaker activities,” Stryjewski says with a laugh. “It’s really more art than science, it’s very delicate, and it takes a lot of practice to do it well. Making specimens, says Stryjewski, allows scientists to create a perfect, permanent record of how a bird looked, and the tissues removed in the process are better for DNA analysis.

Stryjewski made four multiweek trips to New Guinea, traveling throughout the country with the help of local guides, looking for clusters of two or three estrildid finch species living in overlapping geographic areas. Once she found a population of finches, which often live by human settlements, she would set up a mist net.

“I would watch them flying and see what their regular patterns were,” she explains. “And the next morning I would go back before sunrise and set up the net, and they fly right into it.” On their final trip, the hunt for two elusive finch species sent Stryjewski and Sorenson nine hours down the Fly River in the remote Trans-Fly region of Papua, New Guinea, where they and their guides deployed mist nets boatside.

Stryjewski took 20 birds from each population (such as the Chestnut-breasted Munia, Lonchura castaneothorax ramsayi) to make taxidermied specimens.

Credit: Katie Stryjewski (top) and Michael Sorenson (bottom)

She set up a station wherever she was staying (often in the village guest house) and preserved muscle, heart, and liver tissue from each bird in a buffer solution for later DNA sequencing. She also recorded as much additional information as she could, including body measurements, stomach contents, fat content, and the size of internal organs. And she collected blood and feather samples from up to 30 more birds in each population.

Back at BU, Stryjewski used the tissue samples to sequence the birds’ DNA. First, she sampled thousands of tiny DNA snippets from across each bird’s genome, and confirmed that the finch species are “remarkably similar.” This suggests that rather than requiring many changes across the entire genome—how biologists usually think about speciation—it only takes differences in a small number of genes to form a completely new species.

Moreover, different finch species living in the same place, such as the Grey-crowned Munia, Lonchura nevermanni (below, top) and the Black Munia, Lonchura stygia (below, bottom), are often more genetically similar than populations of the same species living in different places.

To pinpoint the genetic differences between species, Stryjewski turned to whole genome sequencing, pooling results from 10 birds in a single population. “Basically you take two different species and you compare their genomes,” Stryjewski explains. “Since they’re really similar all across, anything that’s different should pop out.”

Credit: Katie Stryjewski (top) and Tommy Stryjewski (bottom)

Stryjewski and Sorenson identified about 20 genes that differed among finch species, half a dozen of which are known to control coloration in other organisms, including humans. Different combinations of genes were mixed and matched among species, “as opposed to new mutations cropping up,” Stryjewski says. “Each version of a gene is like a different little thing you could put on a Mr. Potato Head doll, and each bird is collecting a different set of them, and so they all end up looking different.” She and Sorenson published their findings in Nature Ecology & Evolution. The research was supported by the National Geographic Society, the National Science Foundation, and others.

Sorenson adds that “the birds’ genes likely interact with each other in complex ways, making the plumage that results from a particular combination of genes something more than the sum of the parts.” Sorenson thinks that occasional interbreeding between species that live in the same area like the Grey-headed Munia, Lonchura caniceps (below, top) and the Grand Munia, Lonchura grandis (below, bottom) is likely how different versions of genes moved from population to population over time.

Darren Irwin, a zoologist at the University of British Columbia, praises the research for its “elegant analysis of a particularly interesting recent and rapid avian radiation.” He adds that scientists usually think of new species as arising from a single species splitting into two, but “this study provides a great example of how new forms arise in part through mixing genes from other populations.”

Credit: Cydney Scott

Sorenson’s broader goal for the research is to advance general understanding of how evolution works.

“Hopefully it will expand the boundaries of what we know is possible in the process of speciation, and will change scientists’ understanding and perspectives on what exactly species are, and what the minimum requirements are to get the evolution of new species,” he says.

As for the finch specimens, after traveling thousands of miles from New Guinea to BU, they have one more short leg left to their journey: they will cross the Charles River and join the collection at the Harvard Museum of Comparative Zoology.

“I’m pretty excited to donate to Harvard because some of these species they don’t even have, and they’ve only got one or two of the others. They’ll just be preserved there forever,” Stryjewski says. “It’s like the same thing people were doing during the age of exploration, but now we can add this additional layer of the tissue samples and the blood, so their genomes will be preserved as well. It’s a very exciting time to be a zoologist.”

Author: Catherine Caruso | Source: Boston University [February 16, 2018]

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Plants are given a new family tree

A new genealogy of plant evolution, led by researchers at the University of Bristol, shows that the first plants to conquer land were a complex species, challenging long-held assumptions about plant evolution.

Early life on land resembled cryptogamic ground covers like this lava field in Iceland. Co-author Sylvia Pressel
appears in the right of the picture [Credit: Paul Kenrick]

Earth scientists had assumed that the first plants to become land-based around half a billion years ago were simple structures. This new research indicates that they were already more complex than some of the most primitive of living land plants and have been given a new name – ‘Setaphyta’.

Before the first land plants, Earth would have looked unrecognisable with no grass, trees, or even mosses.  Mosses, and their relatives the hornworts and liverworts are regarded as the first true plants on dry land.  These groups, collectively known as the bryophytes, are small and inconspicuous, damp-loving plants.  The simplest of these are liverworts and were believed to be the first on land.

By modelling the molecular sequences of modern plants the researchers have shown that liverworts are more closely related to mosses than hornworts. The liverworts and mosses are now united in a new group, which the team named ‘Setaphyta’.

The new family tree of plants with the Setaphyta group shows that liverworts were not the first group to conquer land, and liverwort simplicity reflects the loss of features, not ancestral simplicity.

University of Bristol Earth Sciences Research Associate Dr Mark Puttick explained: “Land plants are of fundamental importance to the planet and to us. Everything from coal to the food we eat comes from land plants, so it is vital we understand the origin of this group. In order to understand their evolution we need to know how groups are related to one another.”

The group used an extensive molecular dataset and sophisticated models for evolution to understand which plant group was the first to conquer the land from their algal ancestry.

Research Associate Dr Jennifer Morris added: “In order to produce this family tree we analysed a large molecular dataset representative all major groups of land plants and their algal relatives. In none of our analyses do we see liverworts as the earliest group of land plants, so their relative simplicity represents loss rather than the primitive state”.

For scientists this change in the family tree is particularly important as modern liverworts were taken to be the exemplar of the first plant species, but this is shown not to be the case.

Overall leaders of the study Professors Philip Donoghue and Harald Schneider said: “Scientists use ‘model organisms’ to understand the evolution of life. For plants, we typically use modern liverworts as a proxy for the earliest forms and then build on this to understand long-term evolution. As our new tree of plant relationships indicates that the first land plants were more complex than liverworts, we will have to re-evaluate our assumptions on the evolution of land plants.

“Building on this research, our next steps are to reconstruct where the setaphyta grew to help us understand more fully how plants evolved and how they were influenced by changes in climate.”

The study is published in Current Biology.

Source: University of Bristol [February 16, 2018]

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At last, butterflies get a bigger, better evolutionary tree

For hundreds of years, butterfly collecting has often inspired a special kind of fanaticism, spurring lengthy expeditions, sparking rivalries and prompting some collectors to risk their fortunes and skins in their quest for the next elusive specimen.

Researchers have produced a bigger, better butterfly evolutionary tree with a 35-fold increase in genetic data 
and three times as many taxa as previous studies [Credit: Espeland et al. Current Biology]

The result is a treasure trove of scientific information stored in the form of millions of butterfly specimens, offering insights into community ecology, how species originate and evolve, climate change and interactions between plants and insects.

But a comprehensive map of how butterflies are related to each other has been lacking -- until now.

Lepidopterists Akito Kawahara and Marianne Espeland led a team effort to produce a bigger, better butterfly evolutionary tree with a 35-fold increase in genetic data and three times as many taxa -- classification units of organisms -- as previous studies. They then calibrated the tree based on the fossil record, assigning dates to certain developmental milestones.

"We still have a long way to go, but this is the first comprehensive map of butterfly evolution," said Kawahara, associate professor and curator at the Florida Museum of Natural History's McGuire Center for Lepidoptera and Biodiversity on the University of Florida campus. "Lots of previous studies cover butterfly evolution on smaller scales -- by locality or taxon -- but surprisingly few have reached across the breadth of butterfly diversity."

Shake-ups and surprises

The team analyzed a dataset of 352 genetic markers from 207 butterfly species representing 98 percent of tribes, which are a rank above genus but below family and subfamily. Their findings paint a detailed picture of relationships between butterflies and point to some name changes.

The data confirm that swallowtails are a sister group to all other butterflies, meaning they were the first family on the butterfly family tree to branch off. But while previous literature groups swallowtails, birdwings, zebra swallowtails and swordtails together, this study shows they do not share a common ancestor, a finding supported by the fact that these butterflies feed on different host plants.

"That tells us that butterflies and plants may have evolved together," Kawahara said.

A finding that surprised Espeland, the study's lead author, is that the blues are nested within the hairstreaks.

"Both of these groups have remained quite stable through time, but our study shows that a substantial rearrangement of the classification is necessary," said Espeland, who started the project as a postdoctoral researcher at the Florida Museum and is now curator and head of the Lepidoptera section at the Zoological Research Museum Alexander Koenig in Germany.

Most blues and hairstreaks and some metalmarks have mutually beneficial relationships with ants: Butterfly larvae provide sugary nectar in exchange for the ants' protection from predators. The researchers found this association evolved once in blues and hairstreaks and twice in metalmarks.

Previous studies suggest the first butterflies date back more than 100 million years, a date this study supports. But most of the lineages that exist today originated after the mass extinction event that killed off non-avian dinosaurs about 65 million years ago.

"It is actually quite nice that the ages inferred in this study are relatively similar to those found in previous studies since this means that we are gradually converging towards a consensus, which should be close to the correct ages," Espeland said.

One curious finding, Kawahara said, is that the phylogeny suggests butterfly-moths -- the only butterflies known to be nocturnal -- developed hearing organs before bats, their primary predator, appeared.

"I'm fascinated by the timing of when these hearing organs developed and why," Kawahara said. "There's a lot of mystery and uncertainty here."

He pointed to the value of the McGuire Center, home to one of the world's largest collections of butterflies and moths, in providing the data necessary -- especially from rare specimens -- for the study.

"The collections at the McGuire Center made this possible," he said. "There are probably only a few other research institutions in the world that would be able to carry this project."

Childhood dream

Like many butterfly enthusiasts, Kawahara developed the obsession early. By age 5, he had a tiny collection and could differentiate various groups of butterflies. He used his mother's Xerox machine to photocopy a simple butterfly phylogeny to help him identify specimens, posting it to the wall of his bedroom.

"It was a really boring-looking picture, gray with lines on it," he said. "I didn't know anything about evolutionary trees, but I was mystified by the unknown. A lot of the lines were dashed -- there were clearly discoveries to be made. I remember looking at it and just thinking, 'It would be really amazing to be able to study this one day.' "

An even bigger tree

The researchers have set their sights on an even more comprehensive phylogeny, one that accounts for every described butterfly species. Generating this tree is the main goal of the U.S. National Science Foundation-funded ButterflyNet project, which will organize all butterflies based on how they are related to one another. For each species, the project will include associated data such as its geographical distribution, host plants and life history traits.

"This tree represents 207 species out of some 18,800," Kawahara said. "So, it's a tiny, tiny fraction. But it's the first step."

The study was published in Current Biology.

Author: Natalie van Hoose | Source: Florida Museum of Natural History [Februaty 15, 2018]

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

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

A green morph of the Timema genus of stick insects [Credit: Moritz Muschick]

"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 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."

A melanistic or dark brown morph of the Timema genus of stick insects [Credit: Moritz Muschick]

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."

While we can use the past to predict change, he says, we're constrained by our lack of knowledge of the future and complex ecological processes that contribute to change.

Author: Mary-Ann Muffoletto | Source: Utah State University [February 15, 2018]

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What fluffy bunnies can tell us about domestication: It didn't go the way you think

It turns out that nobody knows when rabbits were domesticated. Despite a well-cited story of the domestic bunny's origins, a review published in Trends in Ecology and Evolution finds that historical and archaeological records and genetic methods all suggest different timeframes for its domestication. But the researchers involved in the study don't think this puzzle is a dead end. Instead, they believe it's an indication that domestication happens on a continuum.

Credit: Bunny Blossom/Facebook

The story goes like this: rabbits were domesticated by monks in 600 A.D. after an edict from Pope Gregory declared that it was acceptable to eat fetal rabbits, known as laurices, during Lent. The problem is it isn't true--something that archaeologists Evan Irving-Pease and Greger Larson of the University of Oxford accidentally discovered while trying to test how well the molecular clock method works for genetically dating domestication.

This method compares the genomes of a domestic rabbit and a modern wild one to determine how long it took for them to diverge. Larson hoped to match the domestication date indicated by the rabbits' genomes to the date suggested by the historical record: 600 A.D. But the molecular clock method indicated a date during the last ice age, before the very first domesticated animals.

His team's analysis of these results suggested that the wild rabbits they used simply don't share a recent ancestor with the domestic ones we know and love. But archaeological records, which look for changes in the skeletal structure of the domesticated rabbit, point to the 17th or 18th century, when modern pet-keeping began. And upon closer examination of historical records, the 600 A.D. story of the laurices fell apart.

"I had cited it, colleagues of mine had cited it, it's all over Wikipedia, it's all over the web... but it turns out that the modern story is a complete house of cards," Larson says. "What was really interesting to me then was why nobody's really thought about it or been critical about it."

He thinks it has to do with the way we tell stories. "We really have trouble appreciating slow, continuous change over long periods of time," Larson says, even though that's how most change happens. "Our narrative structures work much better if you have a eureka moment." Domestication that happens at a specific moment in time, due to a concrete series of events, makes intuitive sense to us.

But in the case of rabbits, Irving-Pease, Larson, and colleagues suggest in the paper, domestication is more likely the cumulative effect of hunting rabbits during the Palaeolithic era, keeping them in Roman and medieval enclosures, moving them from place to place, and eventually breeding them as pets. "For the vast majority of human existence, no one said, 'I am going to grab this wild organism and bring it into captivity and, voila, I will create a domestic one,'" Larson says. "If you want to divide the continuum into a dichotomy of wild and domestic, you can do that, but you have to know that it's necessarily going to be arbitrary."

Rather than asking when domestication occurred, Larson believes we need to reconsider what domestication is and whether humans have ever really intended to cause it. His team's next step will be to reexamine the domestication of other plants and animals our civilization relies upon. "We have been slightly arrogant," says Irving-Pease. "We know a hell of a lot less about the origins of the things that matter most to us than we think we do."

Source: Cell Press [February 14, 2018]

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