Genetic evidence suggests early mammals were nocturnal

Our earliest mammalian ancestors likely skulked through the dark, using their powerful night-time vision to find food and avoid reptilian predators that hunted by day. This conclusion, published by Stanford researchers in Scientific Reports, used genetic data to support existing fossil evidence suggesting that our distant relatives may have adapted to life in the dark.

Many modern mammals, like this wood rat, are nocturnal, thanks to evolutionary developments such as night vision 
in their distant ancestors, Stanford researchers say [Credit: Damian Kuzdak/Getty Images]

The team, led by Liz Hadly, professor of biology and senior author on the paper, examined genes involved in night vision in animals throughout the evolutionary tree, looking for places where those genes became enhanced.

"This method is like using the genome as a fossil record, and with it we've shown when genes involved in night vision appear," Hadly said. "It's a very powerful way of corroborating a story that has been, up to now, only hypothesized."

Mammals versus reptiles

Mammals and reptiles share a common ancestor, with the earliest mammal-like animals appearing in the Late Triassic (about 200 million years ago). Fossil evidence suggests that early mammals had excellent hearing and sense of smell and were likely also warm-blooded. All of these features are common in their descendants, the living mammals, most of whom are nocturnal. Therefore, experts have hypothesized that early mammals were also nocturnal. This study offers direct, genetic evidence for that hypothesis.

To trace the evolution of nocturnality, the researchers studied genes that the lead author, visiting scholar Yonghua Wu, had previously found associated with night vision in certain birds, such as owls. The team members examined those night-vision genes in many mammals and reptiles, including snakes, alligators, mice, platypuses and humans. Using what they know about how those animals are related, they figured out when in their evolutionary histories, if ever, the function of these genes was enhanced.

From this, they deduced that the earliest common ancestor did not have good night vision and was instead active during the day. However, soon after the split, mammals began enhancing their night vision genes, allowing them to begin to roam at night, thus avoiding the reptiles that hunted during the day.

"Early mammals coexisted with early reptiles in the Age of the Dinosaurs and somehow escaped extinction," Wu said. "This research further supports the hypothesis that diurnal reptiles, such as lizards, snakes and their relatives, competed with mammals and may have led them to better adapt to dim light conditions."

In the millions of years that have elapsed since mammals and reptiles diverged, natural selection and evolution haven't stopped. Not all mammals are still nocturnal. Some groups of mammals have reoccupied the day, adapting in various ways to daylight activity. These animals include cheetahs, pikas, camels, elephants, and, of course, humans.

"Understanding the constant pressure to get better at seeing the world at night for over 100 million years is a beautiful way of thinking about evolution," Hadly said. "We think of it as something simple -- seeing in the light or the dark -- but these genes are being constantly refined and altered by natural selection."

Filling in our history

The methods used by these researchers could be applied to different areas of the animal evolutionary tree to learn more about the evolution of vision, including how humans made the switch to bright-light vision. This study is also an example of how little information we have about the first mammals, compared to what we know about our ancient and more compelling reptile cousins, the dinosaurs.

"When people talk about the dinosaur age, even when you look at cartoons, the focus is mainly on dinosaurs," said Haifeng Wang, co-author of the paper and postdoctoral research fellow with Stanley Qi, an assistant professor of bioengineering. "This ancient period is an important piece of the story of our evolution too. We want to know better what the mammals were like then."

Author: Taylor Kubota | Source: Stanford University [April 20, 2017]

byUnknown

in Evolution, Fossils, Genetics, Ticker

April 20, 2017

Genetic evidence suggests early mammals were nocturnal

Our earliest mammalian ancestors likely skulked through the dark, using their powerful night-time vision to find food and avoid reptilian pr...

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Tracing the puzzling origins of clinging jellyfish

For such small and delicate creatures, they can pack mighty painful stings. Known as clinging jellyfish because they attach themselves to seagrasses and seaweeds, Gonionemus is found along coastlines in the Pacific and Atlantic oceans, and in particular in waters near Vladivostok, Russia. Exactly how these jellyfish, long assumed to be native to the North Pacific, became so widely distributed throughout the world has perplexed researchers for decades.

Clinging jellyfish in waters near Vladivostok, Russia (like the one above) are known to cause severe sting reactions. 
Interest in the jellies has renewed in recent years, when stings with symptoms similar to those previously 
described  off of the Russian coast suddenly started occurring in Cape Cod and nearby regions 
[Credit: Lubov Petrova, Primorsky Aquarium]

Interest in the jellyfish has renewed in recent years, when stings with symptoms similar to those previously described off of the Russian coast -- including severe pain, respiratory and neurological symptoms -- suddenly started occurring in Cape Cod and nearby regions.

Now, the first genetic study of the diversity of clinging jellyfish populations around the globe has discovered some surprising links among distant communities of jellies and also revealed there may be more than one species of the infamous stinger. The paper published in the journal Peer J.

Annette Govindarajan, a biologist at Woods Hole Oceanographic Institution (WHOI) and lead author of the paper, has studied these jellies for the past three years with the ultimate goal of tracing the species' origin off the U.S. East Coast, where it is thought to be invasive.

The clinging jellyfish first appeared in the Cape Cod area in 1894. Scientists in Woods Hole studied the clingers in the early 1900s. Following an eelgrass die-off, their numbers dwindled. Then the tiny creatures, whose sizes range from about the diameter of a dime to a quarter, nearly vanished in the 1930s. Prior to that, says Govindarajan, researchers and others who were handling the jellies in Massachusetts made no reports of stings.

The clinging jellyfish first appeared in Cape Cod in 1894. Following an eelgrass die-off, the tiny creatures
 nearly vanished in the 1930s. It wasn't until 1990 that the jellies reappeared in the region and painful 
stings were first reported [Credit: Mary Carman, Woods Hole Oceanographic Institution]

"The Cape Cod populations were assumed to be a variety that didn't cause severe stings," Govindarajan adds. It wasn't until 1990 that the clinging jellyfish re-appeared in Cape Cod and painful stings were first reported. These observations lead Govindarajan and her colleague, WHOI researcher Mary Carman to suggest in a previous paper that an invasion from a toxic population had occurred.

The new study shows that the story is much more complex than previously thought. The researchers uncovered a genetic match between populations of clinging jellyfish in the Vladivostok, Russia-area -- specifically the area well known to cause severe sting reactions -- and those found along the U.S. East Coast in the Northwest Atlantic.

"We know the two regions share one genetic variant or haplotype," Govindarajan says. "In the Northwest Atlantic, this variant was actually most frequently found in eastern Long Island Sound. The details about how and when an invasion, or possibly multiple invasions, occurred aren't clear. Interestingly, we also found evidence that both regions may contain native forms."

Working with Carman and colleagues Marat Khaidarov and Alexander Semenchenko from the A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch, Russian Academy of Sciences in Vladivostok, Russia, and John Wares from the University of Georgia, Govindarajan obtained tissue samples for DNA sequencing. The jellyfish samples came from several Atlantic and Pacific locations. Their analysis identified seven variants, some of which were specific to only one location, and others that were shared among communities in distant locations. Interestingly, jellies from the Northeast Pacific and Northeast Atlantic locations shared a haplotype that was sufficiently different from Northwest Atlantic and Northwest Pacific jellyfish, which suggests the possibility that the two related groups may represent different species of Gonionemus.

The researchers uncovered a genetic match between populations of clinging jellyfish in the Vladivostok,
Russia-area and those found along the U.S. East Coast (above) in the Northwest Atlantic 
[Credit: Annette Govindarajan, Woods Hole Oceanographic Institution]

"In the past, some people have suggested that the Atlantic and the Pacific jellies were different forms," Govindarajan says. "Others have suggested that jellies in the Atlantic were introduced from the Pacific. But what we found doesn't correspond exactly to either hypothesis. And it could be that what we have in the Northwest Atlantic and Northwest Pacific is not Gonionemus 'vertens' at all, as it has been called, but some other species of Gonionemus."

"The study documents what we suspected, that there are different types of Gonionemus jellies and some of these types co-occur in New England," says coauthor Carman. "Some types seem to have a toxic sting to people and some do not." Understanding the relationship between the genetic variants and toxicity is something the researchers would like to pursue in the future. "It could very well be that the toxicity is a function of both genetics and the environment, perhaps something in the environment is triggering the toxicity," Govindarajan says.

While the animals bloom in the summer months, beginning in June through September, Govindarajan says swimmers and beachgoers shouldn't be overly concerned as the fragile stingers are not found along sandy beaches in high-energy areas where there are waves.

"Unlike other jellies, it is unlikely that these would be in open water," she says. "We only see them in areas with eelgrass or seaweeds since they're able to cling to these surfaces with the sticky pads found on their tentacles." The lack of movement in open waters also makes the mystery of how the different varieties have become so widespread even more intriguing. The jellyfish are produced by microscopic polyps that are only about a millimeter or less in size, which Govindarajan says is a stage where they could easily hitchhike on a blade of eelgrass, an oyster shell or even a boat hull.

"At that stage, they're so tiny," she adds. "To find them is like finding a needle in a haystack."

Govindarajan and her coauthors hope to obtain funding to do additional genomic analyses that will give greater resolution and suggest genetic markers to help reveal more about the species and its toxicity. They hope this will lead to a better understanding of how invasive forms of the jellyfish are dispersing, so that further spread can be prevented. "With this study, we answered some questions, but it also opened up many others," says Govindarajan. "That's part of the scientific process. It's what makes it for me, personally, very interesting. I feel like I'm solving a mystery."

Source: Woods Hole Oceanographic Institution [April 18, 2017]

byUnknown

in Biology, Evolution, Genetics, Wildlife

April 18, 2017

Tracing the puzzling origins of clinging jellyfish

For such small and delicate creatures, they can pack mighty painful stings. Known as clinging jellyfish because they attach themselves to se...

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Ant agricultural revolution began 30 million years ago in dry, desert-like climate

Millions of years before humans discovered agriculture, vast farming systems were thriving beneath the surface of the Earth. The subterranean farms, which produced various types of fungi, were cultivated and maintained by colonies of ants, whose descendants continue practicing agriculture today.

Left panel: Ted Schultz (left) and Jeffrey Sosa-Calvo (right) excavate a primitive, lower fungus-farming ant nest in the 
seasonally dry Brazilian Cerrado (savanna) near Brasilia in 2009. Center and right panel: The underground garden 
chamber of a primitive, lower fungus-farming ant colony revealed by excavation. Lower, primitive fungus-farming ant 
colonies and agricultural behaviors are comparably smaller-scale and simpler than the colonies of higher
 fungus-farming ants [Credit: Caue Lopes. Ted Schultz, Smithsonian]

By tracing the evolutionary history of these fungus-farming ants, scientists at the Smithsonian's National Museum of Natural History have learned about a key transition in the insects' agricultural evolution. This transition allowed the ants to achieve higher levels of complexity in farming, rivaling the agricultural practices of humans: the domestication of crops that became permanently isolated from their wild habitats and thereby grew dependent on their farmers for their evolution and survival.

In the Proceedings of Royal Society B, scientists led by entomologist Ted Schultz, the museum's curator of ants, report that the transition likely occurred when farming ants began living in dry climates, where moisture-loving fungi could not survive on their own. The finding comes from a genetic analysis that charts the evolutionary relationships of farming and non-farming ants from wet and dry habitats throughout the Neotropics.

About 250 species of fungus-farming ants have been found in tropical forests, deserts and grasslands in the Americas and the Caribbean, and these species fall into two different groups based on the level of complexity of their farming societies: lower and higher agriculture. All farming ants start new fungal gardens when a queen's daughter leaves her mother's nest to go off and found her own nest, taking with her a piece of the original colony's fungus to start the next colony's farm.

In the lower, primitive forms of ant agriculture -- which largely occur in wet rain forests -- fungal crops occasionally escape from their ant colonies and return to the wild. Lower ants also occasionally regather their farmed fungi from the wild and bring them back to their nests to replace faltering crops. These processes allow wild and cultivated fungi to interbreed and limit the degree of influence the lower ants have over the evolution of their crops.

Ted Schultz is the curator of ants at the Smithsonian's National Museum of Natural History. He studies ants 
that began farming millions of years before the evolution of humans. 'These higher agricultural-ant societies
 have been practicing sustainable, industrial-scale agriculture for millions of years,' Schultz said. 'Studying their
 dynamics and how their relationships with their fungal partners have evolved may offer important lessons 
to inform our own challenges with our agricultural practices. Ants have established a form of agriculture that 
provides all the nourishment needed for their societies using a single crop that is resistant to disease,
pests and droughts at a scale and level of efficiency that rivals human agriculture' 
[Credit: Paul Fetters for the Smithsonian Institution]

vBut, as with certain crops that have been so heavily modified by human breeders that they can no longer reproduce and live on their own in the wild, some fungal species have become so completely dependent on their relationship with farming ants that they are never found living independent of their farmers. These higher agricultural ants cultivate highly "domesticated" crops, enabling them to live in vast communities and to work together through division of labor to fertilize their fungal crops, haul away waste, keep pathogens at bay and maintain ideal growing conditions.

"These higher agricultural-ant societies have been practicing sustainable, industrial-scale agriculture for millions of years," Schultz said. "Studying their dynamics and how their relationships with their fungal partners have evolved may offer important lessons to inform our own challenges with our agricultural practices. Ants have established a form of agriculture that provides all the nourishment needed for their societies using a single crop that is resistant to disease, pests and droughts at a scale and level of efficiency that rivals human agriculture."

Today, many agricultural ant species are threatened by habitat destruction, and as part of his studies, Schultz has been collecting specimens from the field and preserving them in the museum's cryogenic biorepository for future genomic studies. In the current study, he and his colleagues compared the genomes of 119 modern ant species, most of which were collected during his decades of field expeditions.

Using powerful new genomic tools, the scientists compared DNA sequences at each of more than 1,500 genome sites for 78 fungus-farming species and 41 non-fungus-farming species. Their data-rich analysis gave the team a great deal of confidence in the evolutionary relationships they were able to map, Schultz said.

Ted Schultz surveys the gigantic mound of a higher agricultural ant colony in the seasonally dry Brazilian Cerrado 
(savanna) near Brasilia in 2009. Higher fungus-farming ant colonies and agricultural behaviours are 
comparably larger-scale and more complex than the colonies of lower fungus-farming ants 
[Credit: Jeffrey Sosa-Calvo, Smithsonian]

Their analysis clarifies the closest living non-farming relative of today's fungus-growing ants and allows Schultz and his team to begin to look at the geographic backgrounds of these species and deduce when, where and under what conditions particular traits emerged. In this study, the team was interested in learning when ants began practicing higher agriculture -- that is, when some fungal crops came to be dependent on the ant-fungus relationship for survival.

According to the evolutionary tree they constructed, the first ants to transition to higher agriculture likely lived in a dry or seasonally dry climate. The transition appears to have occurred around 30 million years ago -- a time when the planet was cooling, and dry areas were becoming more prevalent.

Fungi that had evolved to live in wet forests would have been poorly equipped to survive independently in this changing climate. "But if your ant farmer evolves to be better at living in a dry habitat, and it brings you along and it sees to all your needs, then you're going to be doing okay," Schultz said.

Just as humans living in a dry or temperate climate might raise tropical plants in a greenhouse, agricultural ants carefully maintain the humidity within their fungal gardens. "If things are getting a little too dry, the ants go out and get water and they add it," Schultz said. "If they're too wet, they do the opposite." So even when conditions above the surface become inhospitable, fungi can thrive inside the underground, climate-controlled chambers of an agricultural ant colony.

In this situation, fungi can become dependent on their ant farmers -- unable to escape the nest and return to the wild. "If you've been carried into a dry habitat, your fate is going to match the fate of the colony you're in," Schultz said. "At that point, you're bound in a relationship with those ants that you were not bound in when you were in a wet forest."

Schultz said the conditions present during this evolutionary transition illustrate how an organism can become domesticated even if its farmers are not consciously selecting for desirable traits as human breeders might do. Ants that moved their fungi into new habitats would have isolated the organism from its wild relatives, just as humans do when they domesticate a crop. This isolation creates an opportunity for the farmed species to evolve independently from species in the wild, adopting new traits.

Funding for this study was provided by the Smithsonian and the National Science Foundation.

Source: Smithsonian [April 11, 2017]

byUnknown

in Biology, Evolution, Genetics

April 11, 2017

Ant agricultural revolution began 30 million years ago in dry, desert-like climate

Millions of years before humans discovered agriculture, vast farming systems were thriving beneath the surface of the Earth. The subterranea...

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Humans and sponges share gene regulation mechanisms

Humans have a lot in common with the humble sea sponge, according to research that changes the way we think about animal evolution.

The study used Great Barrier Reef sponge Amphimedon queenslandica 
[Credit: University of Queensland]

University of Queensland School of Biological Sciences researcher Dr Milos Tanurdzic said a collaborative study found sponges use a complex gene regulation toolkit similar to much more complex organisms such as humans.

Gene regulation refers to how and when a gene is activated.

"The research implies this complex mechanism was present at the evolutionary dawn of multicellular animals and across animal species as far apart as sponges and humans," Dr Tanurdzic said.

"Until very recently we thought increasing complexity in the animal kingdom was due to an ever-increasing number of genes that encode information about animal development and growth.

"However, the genomics explosion of the last decade taught us most animals have a similar number of genes encoded in their DNA.

"The alternative, and today the prevailing explanation, is that gene regulation is responsible for the evolution of animal diversity."

The study was largely undertaken by former UQ PhD student Dr Federico Gaiti, now at Weill Cornell Medicine in New York City, USA.

Dr Tanurdzic said a key mechanism responsible for regulating genes in multi-celled organisms was how the DNA was packaged within the genetic material, or genome.

"DNA associates with special proteins -- called histones -- in the nucleus," he said.

"Histones can bear certain chemical marks, which in turn determine if the DNA associated with them is going to be turned on or off."

Histone marking gone awry is also responsible for some of the more insidious genetic errors, such as when a normal cell becomes cancerous.

"Our study, which used a Great Barrier Reef sponge, Amphimedon queenslandica, set out to discover if this particular mechanism of gene regulation is present in the oldest multicellular animal lineage -- the sponges," he said.

"Through analysis of DNA with certain histone marks we determined that histone-based gene regulation is part of the sponge gene regulatory tool kit.

"As the common ancestor of humans and sponges probably lived 700 million years ago, this implies that gene regulatory complexity relying on histone marks was fundamental for the evolution of animal multicellularity and diverse animal forms and functions."

The study is published in eLife.

Source: University of Queensland [April 11, 2017]

byUnknown

in Evolution, Genetics

April 11, 2017

Humans and sponges share gene regulation mechanisms

Humans have a lot in common with the humble sea sponge, according to research that changes the way we think about animal evolution. The stud...

Read More

Distantly related fish find same evolutionary solution to dark water

Changes in a single color-vision gene demonstrate convergent evolutionary adaptations in widely separated species and across vastly different time scales, according to a study in the open access journal PLOS Biology by David Marques of the University of Victoria, British Columbia, and colleagues. The study, which combined genetic analysis with a 19-year-long selection experiment, supports the idea that the mechanisms of adaptive evolution may be more predictable than previously suspected.

Threespine sticklebacks on Haida Gwaii have repeatedly colonized tannin-stained blackwater lakes with a strongly 
red-shifted light spectrum. Here a male is near its nest at Drizzle lake [Credit: Thomas E. Reimchen]

Over the past 12,000 years or more, species of three-spined stickleback fish have colonized hundreds of freshwater lakes in the Haida Gwaii archipelago off the coast of British Columbia, forming independently evolving populations. The lakes can be broadly classified as "clearwater," in which full-spectrum light passes relatively unimpeded, or "blackwater," in which most of the visible light is absorbed by dissolved tannins, creating an almost nocturnal environment with only dim, red-shifted light filtering in from above.

Cone cells responsible for color vision in the stickleback retina contain SWS2, an opsin protein sensitive to blue light. Amino acid changes in SWS2 have been previously shown to "tune" this opsin to make it more sensitive to either the blue or red end of the spectrum. In the current study, the authors compared genetic sequences of SWS2 from marine, clearwater, and blackwater sticklebacks, including a group of blackwater fish that they had transplanted to an empty clearwater lake 19 years previously and left there to evolve.

The researchers found that the pattern of genetic changes in SWS2 seen in blackwater sticklebacks implied there had been very strong selection for red-shift tuning, maximizing the opsin's sensitivity in the dark water; no such pattern was seen in clearwater sticklebacks. In blackwater fish transplanted to a clearwater lake, after only 13 generations, many members of the population contained alternative versions of SWS2 that were more sensitive to the more abundant blue light of their new habitat, demonstrating the rapid effect of this selective pressure.

Next, the authors compared their stickleback results to previously published opsin genes in two related species of fish (bluefin killifish and black bream), separated from sticklebacks by millions of years, that had also adapted to blackwater and clearwater habitats. These fish have two distinct copies of the SWS2 gene -- SWS2A and SWS2B, which arose from an ancient gene duplication event 198 million years ago in the ancestor of all spiny-finned fish. Remarkably, two of the same genetic changes seen in stickleback SWS2 also distinguish SWS2A (red-shifted) and SWS2B (blue-shifted) of these fish species, with whom they last shared a common ancestor many million years ago. Since the same genetic changes arose separately in their ancestor and in the sticklebacks, they demonstrate convergent evolution, but over vastly different time scales.

"These data support the emerging view in evolutionary biology that mechanisms underlying adaptive evolution are often highly repeatable and thus may be predictable," said Marques. "They show that evolutionary 'tinkering' with a limited set of tools can lead to convergent 'solutions' to common problems both within species and between widely separated groups."

Source: PLOS [April 11, 2017]

byUnknown

in Biology, Ecosystems, Evolution, Genetics

April 11, 2017

Distantly related fish find same evolutionary solution to dark water

Changes in a single color-vision gene demonstrate convergent evolutionary adaptations in widely separated species and across vastly differen...

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As fins evolve to help fish swim, so does the nervous system

The sensory system in fish fins evolves in parallel to fin shape and mechanics, and is specifically tuned to work with the fish's swimming behavior, according to new research from the University of Chicago. The researchers found these parallels across a wide range of fish species, suggesting that it may occur in other animals as well.

A parrotfish, a common Labrid species [Credit: Brett Aiello, University of Chicago]

The study, published in the Proceedings of the National Academy of Sciences, combined measurements of fin shape from hundreds of specimens of the Labridae family with fin mechanical properties and neural responses recorded from eight different Labrid species, commonly known as wrasses. These measurements were then mapped on an evolutionary tree of 340 wrasses to determine how the mechanical properties and nervous systems of the fins evolved over time.

"As pectoral fins evolve different shapes, behaviors, and mechanical properties, we've shown that the sensory system is also evolving with them," said Brett Aiello, a PhD student in the Department of Organismal Biology and Anatomy, and the lead author of the study. "This allows the sensory system to be tuned to the different stimuli relevant to the locomotor behaviors and fin mechanics of different species."

When animals use appendages for movement, they rely on sensory feedback from those limbs to control motion. Nerves in the pectoral fins of fish detect the fin rays' position and how much they bend as they move through the water, which helps the fish sense speed and the relative position of their fins.

The shape of the fin affects how the fish will move too. Scientists use a number called aspect ratio (AR) to measure this shape. High AR means the fin is long and narrow, or more wing-like; low AR means the fin is broad or round, and more paddle-like. Wrasses with high AR, wing-like fins flap them to maximize efficiency and thrust as they propel themselves forward, while those with the broader, low AR, paddle-like fins use rowing movements to maneuver close to reef bottoms.

Cheilinus fasciatus, or red-breasted wrasse, on a coral reef in Palau [Credit: Mark Westneat, University of Chicago]

Aiello and his colleagues collected fin aspect ratio measurements from hundreds of Labrid species at the Field Museum, and combined that data with a genetic phylogeny of 340 Labrids developed by Mark Westneat, PhD, professor of Organismal Biology and Anatomy and co-author on the study. Using DNA from living fishes, Westneat constructed a family tree of relationships between these species, tracing how they evolved through time. The researchers then mapped the fin shape of each species on the phylogeny, allowing them to track fin evolution from their ancestral state to living species. The ancestral state reconstruction revealed patterns of convergent evolution, with high AR fins originating independently at least 22 times.

With this history of fin evolution in place, the researchers also tested the mechanical properties and sensory system sensitivity in the pectoral fins of four pairs of closely related Labrid species, one with low AR fins and one with independently evolved high AR fins. The team tested the sensory response by measuring the neural response from the pectoral fin nerves as they bent the fin, and then repeated the process, bending the fins a different amount each time.

What they found gave more clues about the utility of each kind of fin. The low AR, paddle-like fins tended to be more flexible, and the high AR fins were more stiff or rigid. But the sensory system of the wing-like, high AR fins was also more sensitive, meaning the fins were more responsive to a smaller magnitude of bending. Aiello said he believes that a more sensitive nervous system evolved in the high AR fins because it needed to be more responsive to smaller movements as the fish use these stiff, less flexible fins to swim.

The work is the product of collaboration across disciplines, a hallmark of the Organismal Biology and Anatomy program at UChicago. The resulting PNAS study could have been three separate papers: the archival research of specimens from the Field Museum, the genetic phylogeny, and the neurobiological study of the living species.

Gomphosus varius, or bird wrasse, on a coral reef in Palau [Credit: Mark Westneat, University of Chicago]

"Collaboration among scientists with different perspectives and expertise can take research in whole new directions," said Melina Hale, the William Rainey Harper Professor of Organismal Biology and Anatomy and senior author of the study. "It is also a lot of fun because we learn about each other's fields. For experimentalists, like us, working with colleagues and natural history collections at the Field Museum has been particularly important as they bring key insights on evolution and biodiversity."

Besides giving biologists a better understanding of how fish have optimized their swimming mechanics, the results of the study could also be useful to engineers developing underwater autonomous vehicles. The propulsion systems of these devices need to be both efficient and responsive, and there are perhaps no better designs to copy than those perfected through evolution over millions of years.

"A lot of the problems that engineers run into are similar to the type of things that animals have already evolved solutions to over time," Aiello said. "If we start to look more towards bio-inspired technology and incorporating some of the things we see in nature in our engineered devices, I think it will help advance and solve some of these problems more quickly."

Source: University of Chicago Medical Center [April 10, 2017]

byUnknown

in Biology, Evolution, Genetics

April 10, 2017

As fins evolve to help fish swim, so does the nervous system

The sensory system in fish fins evolves in parallel to fin shape and mechanics, and is specifically tuned to work with the fish's swimmi...

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How domestication can change animals' facial features

Domesticated animals, compared to their wild counterparts, have undergone numerous changes in physiology, behavior and morphology. These changes are commonly referred to as the domestication syndrome and include behavioral changes, such as increased docility as well as genetic alterations in size, color and facial characteristics.

The researchers found a clear distinction in facial morphology between the tame and aggressive strains of rats 
[Credit: Nandini Singh et al., PLOS ONE]

In attempting to find whether these changes have a single cause, Russian zoologist Dmitry Belyaev conducted a series of selection experiments with silver foxes, hypothesizing that behavior, specifically tameness, was the key driving factor behind the changes brought about by domestication. After generations of selecting foxes for tameness, they were found to display phenotypes similar to those observed in domesticated species.

Since then, it has been further hypothesized that selection for social tolerance and reduced aggression may also have played an important role in shaping the modern human anatomy, which is remarkable for the reduced face and gracile overall features.

In parallel to his fox experiment, Belyaev also selected rats over 64 generations for their behavior: either tameness or defensive aggression towards humans.

In the first ever quantitative study on the facial anatomy of Belyaev's selected rats, an international team of researchers from the Senckenberg Center for Human Evolution and Paleoenvironment at the University of Tübingen and Pennsylvania State University collected 3-D measurements on the skulls of both tame- and aggressive-selected rats, in order to evaluate Belyaev's hypothesis that tame behavior correlates with the facial changes similar to those seen in domesticated animals.

The study found that rats selected for tame behavior show some -- though not all -- traits present in domesticated animals and the tame silver foxes. The findings are published in PLOS ONE.

Senior author, Tübinger palaeoanthropologist Professor Katerina Harvati and Dr. Nandini Singh from Pennsylvania State University conceived the project, in collaboration with Dr. Frank Albert from the University of Minnesota.

Quantitative analyses of cranial measurements revealed clear differences, including a smaller and retracted snout, but no difference in overall size, between rats selected for either tameness or defensive aggression.

However, unlike Belyaev who found a kind of "feminization" and sexual dimorphism in the tame silver foxes -- traits also seen in domesticated animals -- Harvati and colleagues did not see this trend among the tame rats.

Professor Harvati says this shows that not all elements of the domestication syndrome might appear in domesticated animals, depending on the species. However, this study con-firms the wide-ranging effect of behavioral changes on the phenotype over generations.

Experimental animal models can provide novel ways to test and address a number of questions regarding the developmental origins of animal domestication not otherwise possible with archaeological samples.

Source: Universitaet Tübingen [April 10, 2017]

byUnknown

in Biology, Evolution, Genetics

April 10, 2017

How domestication can change animals' facial features

Domesticated animals, compared to their wild counterparts, have undergone numerous changes in physiology, behavior and morphology. These cha...

Read More

Forget sponges: The earliest animals were marine jellies

For the last decade, zoologists have been battling over the question, "What was the oldest branch of the animal family tree?" Was it the sponges, as they had long thought, or was it a distinctly different set of creatures, the delicate marine predators called comb jellies? The answer to this question could have a major impact on scientists' thinking about how the nervous system, digestive tract and other basic organs in modern animals evolved.

Comb jellies, aka Ctenophores, similar to this may have been the earliest form of animal 
[Credit: WikiCommons]

Now, a team of evolutionary biologists from Vanderbilt University and the University of Wisconsin-Madison have devised a new approach designed specifically to settle contentious phylogenetic tree-of-life issues like this. The new approach comes down squarely on the side of comb jellies.

The method and its application to this and 17 other controversial phylogenetic relationships was published by the journal Nature Ecology & Evolution.

For nearly a century, scientists organized the animal family tree based in large part on their judgement of the relative complexity of various organisms. Because of their comparative simplicity, sponges were considered to be the earliest members of the animal lineage. This paradigm began to shift when the revolution in genomics began providing vast quantities of information about the DNA of an increasing number of species. Evolutionary biologists started to apply this wealth of information to refine and redefine evolutionary relationships, creating a new field called phylogenomics. In most cases, the DNA data helped clarify these relationships. In a number of instances, however, it gave rise to controversies that intensified as more and more data accumulated.

In 2008, one of the early phylogenomic studies fingered the comb jellies (aka ctenophores) as the earliest members of the animal kingdom, rather than sponges. This triggered an ongoing controversy with the latest round being a massive study published last month that marshalled an unprecedented array of genetic data to support the sponges' position as the first animal offshoot.

"The current method that scientists use in phylogenomic studies is to collect large amounts of genetic data, analyze the data, build a set of relationships and then argue that their conclusions are correct because of various improvements they have made in their analysis," said Antonis Rokas, Cornelius Vanderbilt Professor of Biological Sciences, who devised the new approach with Vanderbilt postdoctoral scholar Xing-Xing Shen and Assistant Professor Chris Todd Hittinger from the University of Wisconsin-Madison. "This has worked extremely well in 95 percent of the cases, but it has led to apparently irreconcilable differences in the remaining 5 percent."

Rokas and his collaborators decided to focus on 18 of these controversial relationships (seven from animals, five from plants and six from fungi) in an attempt to figure out why the studies have produced such strongly contradictory results. To do so, they got down into the weeds, genetically speaking, and began comparing the individual genes of the leading contenders in each relationship.

"In these analyses, we only use genes that are shared across all organisms," Rokas said. "The trick is to examine the gene sequences from different organisms to figure out who they identify as their closest relatives. When you look at a particular gene in an organism, let's call it A, we ask if it is most closely related to its counterpart in organism B? Or to its counterpart in organism C? And by how much?"

These analyses typically involve hundreds to thousands of genes. The researchers determined how much support each gene provides to one hypothesis (comb-jellies first) over another (sponges first). They labeled the resulting difference a "phylogenetic signal." The correct hypothesis is the one that the phylogenetic signals from the most genes consistently favor.

In this fashion, they determined that comb jellies have considerably more genes which support their "first to diverge" status in the animal lineage than do sponges.

Another contentious relationship the researchers addressed was whether crocodiles are more closely related to birds or turtles. They found that 74 percent of the shared genes favor the hypothesis that crocodiles and turtles are sister lineages while birds are close cousins.

In the course of their study, they also discovered that in a number of contentious cases one or two "strongly opinionated genes" among all the genes being analyzed appear to be causing the problem because the statistical methods that evolutionary biologists have been using are highly susceptible to their influence.

In some cases, such as the controversies over the origins of flowering plants and modern birds, they determined that the removal of even a single opinionated gene can flip the results of an analysis from one candidate to another. In cases like this, the researchers were forced to conclude that the available data is either inadequate to support a definitive conclusion or it indicates that the diversification occurred too rapidly to resolve.

"We believe that our approach can help resolve many of these long-standing controversies and raise the game of phylogenetic reconstruction to a new level," Rokas said.

Author: David F Salisbury | Source: Vanderbilt University [April 10, 2017]

byUnknown

in Biology, Evolution, Genetics

April 10, 2017

Forget sponges: The earliest animals were marine jellies

For the last decade, zoologists have been battling over the question, "What was the oldest branch of the animal family tree?" Was...

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Promiscuity slows down evolution of new species

Promiscuity mixes up the gene pool and dilutes genetic differences between populations, slowing down the evolution of new species, says new research by an international team led by the University of Bath's Milner Centre for Evolution.

Researchers found that promiscuous species are less likely to diversify into new species 
[Credit: Clemens Kuepper]

Darwin's theory of evolution showed that new species evolve when natural selection favours individuals with particular characteristics, allowing them to survive, breed and pass on their genes more successfully than their peers. Over time, a group of individuals can evolve to adapt to their local environment and form a new species.

Previously it was thought that sexual selection, when one sex prefers to mate with individuals with specific characteristics, was a strong driver of the formation of new species. One of these processes is the Fisherian runaway selection whereby arbitrary traits such as conspicuous feathers or fancy songs attract female's attention and hence improve the mating success of the bearer. Due to local variations in female preferences, nearby populations can rapidly differentiate and over time evolve into new species.

However new research in birds, published in the leading academic journal Evolution, overturns the conventional wisdom and suggests that promiscuity actually slows down the evolution of new species.

A research team led by the University of Bath, Cardiff University and the Max Planck Institute for Ornithology analysed the genetic structure of shorebird populations to track how they had evolved over time.

The team found that polygamous bird species, which breed with several partners during a season, are less diverse genetically within the species compared to monogamous species that only pair with one mate per season. This contradicts contemporary theories that predict rapid diversification and thus higher genetic differences between populations of polygamous shorebirds.

First author on the paper, Josie D'Urban Jackson, who is jointly supervised at University of Bath and Cardiff University, analysed the data, she said: "Our findings suggest that because of the pressure to find more than one mate, polygamous shorebirds may search large areas and therefore spread their genes as they go."

"This means they effectively mix up the gene pool by diluting any genetic differences between geographically distant locations, so that populations are less likely to diversify into new species over time."

"In contrast, monogamous species only have to find one partner to pair with each season and tend to come back to the same breeding sites over time. This means they can gradually adapt to their local environment which increases the chance that they will split off and form a new species."

Her supervisor, Professor Tamás Székely from the University of Bath's Milner Centre for Evolution, added: "We're very excited about these findings as this theory completely overturns conventional wisdom.

"You might think that birds choose mates arbitrarily if they are promiscuous, but most individuals prefer a certain type, just as some humans might prefer blonde or dark hair in a partner.

"Our study is consistent with previous findings that polygamous birds sometimes travel hundreds of kilometres to find a suitable partner.

"For example, in Madagascar, we found that the polygamous plovers were similar across the whole island, whereas the monogamous plovers have distinct genetic composition between nearby locations -- showing the same pattern that our larger scale study just confirmed."

The research is published in Evolution.

Source: University of Bath [April 10, 2017]

byUnknown

in Biology, Evolution, Genetics

April 10, 2017

Promiscuity slows down evolution of new species

Promiscuity mixes up the gene pool and dilutes genetic differences between populations, slowing down the evolution of new species, says new ...

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'Smart' cephalopods trade off genome evolution for prolific RNA editing

Octopus, squid, and cuttlefish are famous for engaging in complex behavior, from unlocking an aquarium tank and escaping to instantaneous skin camouflage to hide from predators. A new study suggests their evolutionary path to neural sophistication includes a novel mechanism: Prolific RNA editing at the expense of evolution in their genomic DNA.

California two-spot octopus (Octopus bimaculoides) with one if its namesake blue eye spots visible below its eye 
[Credit: Tom Kleindinst/MBL]

The study, led by Joshua J.C. Rosenthal of the Marine Biological Laboratory (MBL), Woods Hole and Eli Eisenberg and Noa Liscovitch-Brauer of Tel Aviv University, is published in Cell.

The research builds on the scientists' prior discovery that squid display an extraordinarily high rate of editing in coding regions of their RNA -- particularly in nervous system cells -- which has the effect of diversifying the proteins that the cells can produce. (More than 60 percent of RNA transcripts in the squid brain are recoded by editing, while in humans or fruit flies, only a fraction of 1 percent of their RNAs have a recoding event.)

In the present study, the scientists found similarly high levels of RNA editing in three other "smart" cephalopod species (two octopus and one cuttlefish) and identified tens of thousands of evolutionarily conserved RNA recoding sites in this class of cephalopods, called coleoid. Editing is especially enriched in the coleoid nervous system, they found, affecting proteins that are the key players in neural excitability and neuronal morphology.

This visual abstract depcits the findings of Liscovitch-Brauer et al., who show behaviorally complex cephalopods use 
extensive RNA editing to diversify their neural proteome at the cost of limiting genomic sequence flexibility
 and evolution [Credit: Liscovitch-Brauer et al./Cell 2017]

In contrast, RNA editing in the more primitive cephalopod Nautilus and in the mollusk Aplysia occurs at orders of magnitude lower levels than in the coleoids, they found. "This shows that high levels of RNA editing is not generally a molluscan thing; it's an invention of the coleoid cephalopods," Rosenthal says. In mammals, very few RNA editing sites are conserved; they are not thought to be under natural selection. "There is something fundamentally different going on in these cephalopods where many of the editing events are highly conserved and show clear signs of selection," Rosenthal says.

The scientists also discovered a striking trade-off between high levels of RNA recoding and genomic evolution in these cephalopods. The most common form of RNA editing is carried out by ADAR enzymes, which require large structures (dsRNA) flanking the editing sites. These structures, which can span hundreds of nucleotides, are conserved in the coleoid genome along with the editing sites themselves. The genetic mutation rate in these flanking regions is severely depressed, the team reported.

"The conclusion here is that in order to maintain this flexibility to edit RNA, the coleoids have had to give up the ability to evolve in the surrounding regions -- a lot," Rosenthal says. "Mutation is usually thought of as the currency of natural selection, and these animals are suppressing that to maintain recoding flexibility at the RNA level."

Rosenthal and colleagues at the MBL are currently developing genetically tractable cephalopod model systems to explore the mechanisms and functional consequences of their prolific RNA editing. "When do they turn it on, and under what environmental influences? It could be something as simple as temperature changes or as complicated as experience, a form of memory," he says.

Author: Diana Kenney | Source: Marine Biological Laboratory [April 06, 2017]

byUnknown

in Evolution, Genetics

April 06, 2017

'Smart' cephalopods trade off genome evolution for prolific RNA editing

Octopus, squid, and cuttlefish are famous for engaging in complex behavior, from unlocking an aquarium tank and escaping to instantaneous sk...

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Experiments test how easy life itself might be

On a lab benchtop, a handful of glass vials taped to a rocker gently sway back and forth. Inside the vials, a mixture of organic chemicals and tiny particles of fool's gold are begging a question seemingly beyond their humble appearance: Where did life come from?

UW scientists are combining theory with experiment to try to understand how life could arise from lifelike chemical 
reactions under the right conditions. “If we find many different chemistries supporting lifelike reactions, we can 
expect more origins of life elsewhere in the universe,” says botany Professor David Baum 
[Credit: Jeff Miller]

Combining theory with experiment, University of Wisconsin–Madison scientists are trying to understand how life can arise from non-life. Researchers at the UW–Madison Wisconsin Institute for Discovery are conducting experiments to test the idea that lifelike chemical reactions might develop readily under the right conditions. The work addresses some of the deepest mysteries in biology, and has implications for understanding how common life might be in the universe.

David Baum, chair and professor of botany at UW–Madison and a Discovery Fellow at WID, thinks the earliest life might have relied on a primitive metabolism that originally started on mineral surfaces. Many central reactions in modern cells rely on iron-sulfur catalysts. This reliance on iron and sulfur could be a record stamped into cells of the environments where metabolism itself first evolved. Baum is testing this idea by turning to iron pyrite, a mineral of iron and sulfur better known as fool's gold.

Together with Mike Berg, a graduate student researching the origins of life, Baum is mixing microscopic beads of iron pyrite with a source of chemical energy and simple molecular building blocks. As vials of this mixture rock back and forth in the lab, small groups of chemicals bound to the mineral surface might aggregate and start assisting one another in producing more chemicals. If so, they're likely to spread to other iron pyrite beads, colonizing new surfaces.

When Berg transfers some beads to a fresh vial, the chemical groups could continue to spread. Generation after generation, vial after vial, the most efficient and competitive chemical mixtures would colonize the most iron pyrite. This is selection. Like natural selection, which has created the diversity and complexity of life on Earth, selecting for the colonizing ability of these chemical groups may reveal lifelike chemical cycles capable of changing over time.

"The view that I've come around to is that lifelike chemistry may pop up relatively easily in many, many geological settings," says Baum. "The problem then changes. It's no longer a problem of 'will it happen,' but how will we know it happened?"

Vials containing a mixture of simple organic chemicals and microscopic beads of fool’s gold are taped
 to a rocker in the Baum lab at the UW–Madison Wisconsin Institute for Discovery 
[Credit: University of Wisconsin-Madison]

They've gone through more than 30 generations so far, and are looking for any sign of change over time, whether that is heat generation, energy consumption or the amount of material bound to the beads.

Baum and UW–Madison microbiologist and WID systems biologist Kalin Vetsigian published a paper last year that outlined the experiments, which are based in part on the principle of neighborhood selection. Normally, natural selection operates on a population of individuals. But the scientists proposed that even though no well-defined individuals exist in the chemical mixtures, the molecular communities that are best at colonizing new surfaces will prevail, and likely get better over time. Successful traits of the community as a whole can be selected for and passed on.

"This community-level selection could have taken place before there were individuals with traits that were both heritable and variable," says Vetsigian. "If you have good communities, they will persist."

The project recently received $2.5 million in funding from NASA. Baum is the lead investigator of the research, which includes Vetsigian, UW–Madison chemist Tehshik Yoon, and collaborators from seven other institutions.

Cells need the kinds of metabolic reactions that Baum studies to produce energy and the components of more complex molecules. They also need a way to store information. All living cells pass on their genetic information with DNA. But UW–Madison professor of chemical and biological engineering and WID systems biologist John Yin is exploring alternative ways to store and process information with simpler molecules in an effort to understand how information storage could evolve without cells or DNA.

Taking a cue from computer science, Yin is working with the most basic method of encoding information, binary. In place of electronic bits, his ones and zeros are the two simplest amino acids, glycine and alanine. Using a unique form of chemistry, Yin is drying out mixtures of the amino acids to encourage them to join together.

"We're seeing reproducibly different strings of alanine and glycine under different kinds of conditions," explains Yin. "So that's a first hint that in some ways the product is a way of representing a particular environment."

Yin's group is working on the technically challenging task of reading these sequences of amino acids so they can keep track of the molecular information. The Yin lab eventually hopes to discover groups of chemicals that can build off this molecular information to reproduce themselves. For both Baum and Yin, selectable systems require these cycles of chemicals able to make more of one another, what Yin calls "closing the loop."

Closing the loop in the lab is likely to be difficult. Only experimentation will tell for sure.

Yin, Baum and Vetsigian are interested not only in how life on Earth got started, but how it could get started—anywhere. If lifelike chemical reactions and molecular information are readily produced in the lab, that could change the calculus of how common life might be on other worlds.

"If we find many different chemistries supporting lifelike reactions, we can expect more origins of life elsewhere in the universe," says Baum.

Author: Eric Hamilton | Source: University of Wisconsin-Madison [April 06, 2017]

byUnknown

in Evolution, Genetics, Origin of Life

April 06, 2017

Experiments test how easy life itself might be

On a lab benchtop, a handful of glass vials taped to a rocker gently sway back and forth. Inside the vials, a mixture of organic chemicals a...

Read More

Steppe migrant thugs pacified by Stone Age farming women

In an earlier study Professor Kristian Kristiansen from the University of Gothenburg in Sweden and Lundbeck Foundation Professor Eske Willerslev from the Centre for GeoGenetics at the University of Copenhagen, and their research teams, showed that the large demographic changes during the first part of the Bronze Age happened as a result of massive migrations of Yamnaya people from the Pontic-Caspian steppes into Neolithic Europe. They were also able to show that plague was widespread in both Europe and Central Asia at this time.

Corded ware vessel, an axe and two discs made of amber from an early male grave 
[Credit: Danish National Museum]

Now Professor Kristiansen and Professor Willerslev with co-authors reveal a more detailed view of the mechanism behind the emerging culture known as the Corded Ware Culture -- the result of the encounter between the Yamnaya and the Neolithic people.

Professor Kristian Kristiansen says: "We are now for the first time able to combine results from genetics, strontium isotopes on mobility and diet, and historical linguistics on language change, to demonstrate how the integration process unfolded on the ground after the Yamnaya migrations from the steppe. In our grand synthesis we argue that Yamnaya migrants were predominantly males, who married women who came from neighbouring Stone Age farming societies"

These Stone Age Neolithic societies were based on large farming communities reflected in their collective burial ritual often in big stone chambers, so called megaliths. Very different from the traditions of the incoming migrants.

The origin of the Yamnaya

The Yamnaya people originated on the Caspian steppes where they lived as pastoralists and herders, using wagons as mobile homes. From burial pits archaeologists have found extensive use of thick plant mats and felt covers.

Their economy was based on meat, dairy products and fish, they were tall and rather healthy with little caries in their teeth. No agriculture is documented. Barrows were aligned in groups forming lines in the landscape to mark seasonal routes and after death diseased people were put into individual graves under small family barrows.

Their burial ritual thus embodied a new perception of the individual and of small monogamous family groups as the foundation of society. The continent encountered by the Yamnaya people around 3000 BC had seen a decline in the agrarian Stone Age societies, thereby allowing space for incoming migrants. This decline was probably the result of a widespread plague from Siberia to the Baltic.

"The disease dynamic here may have been comparable to the European colonization process in America after Christopher Columbus," says Kristiansen. "Perhaps Yamnaya brought plague to Europe and caused a massive collapse in the population."

Barrows in the Danish landscape [Credit: Danish National Museum]

"Black Youth" as migrating males and their marriage to Neolithic women

In the new article, Kristiansen and colleagues argue for a dominance of males during the early phase after the migrations, and correspond to the old Indo-European mythology of later times. These sources talk about war-bands of youths -- called "Black Youth" -- who were employed in pioneer migrations as a dynamic force.

Evidence from strontium isotopic analyses, published in 2016 by Kristiansen together with Douglas Price and Karl Goran Sjogren, showed that a majority of the women in Corded Ware burials in south Germany were non-locals who had married in from Neolithic societies, since they had a Neolithic diet in their childhood. These results now form part of the new synthesis.

Professor Kristian Kristiansen says: "Existing archaeological evidence of a strong 90% male dominance in the early phase of the Corded Ware/Single Grave Culture settlement in Jutland, Denmark, and elsewhere can now be explained by the old Indo-European tradition of war bands of young males who did not have any inheritance to look forward to. Therefore they were probably more willing to make a career as migrating war bands."

These Neolithic women also brought new knowledge of pottery production, and started to imitate pottery containers made of wood from the Yamnaya migrants. In this way a new pottery culture was created called Corded Ware, because of the cord impressions around the neck of the pots. They were made for beer drinking, and the new migrants also learned how to grow barley from the in-married Neolithic women in order to produce beer.

Rapid genetic changeover from Neolithic to Corded Ware cultures after 3000 BC

Eske Willerslev undertook the ancient DNA analyses together with Morten Allentoft and Martin Sikora. Professor Willerslev says:

Typical group of Danish Bronze Age barrows [Credit: Kristian Kristiansen]

"In our big Bronze Age study, published in 2015 we were astonished to see how strong and fast the genetic changeover was from the Neolithic to the Corded Ware. There was a heavy reduction of Neolithic DNA in temperate Europe, and a dramatic increase of the new Yamnaya genomic component that was only marginally present in Europe prior to 3000 BC. Moreover, the apparent abruptness with which this change occurred indicates that it was a large-scale migration event, rather than a slow periodic inflow of people."

New words and new Proto-Germanic dialect

The Yamnaya brought the Indo-European languages into Bronze Age Europe, but as herders, they did not have words for crops or cultivation, unlike the Neolithic farmers. As the Corded Ware Culture developed it adopted words related to farming from the indigenous Neolithic people, which they were admixing with.

Guus Kroonen, a historical linguist, was able to demonstrate that these new words did not belong to the original Indo-European languages. Therefore it was possible to conclude that the Neolithic people were not speaking an Indo-European language, as did the Yamnaya migrants. Thus, the process of genetic and cultural admixture was accompanied by a process of language admixture, creating the foundations for later Germanic languages, termed Proto-Germanic.

The birth of the Bronze Age

The Yamnaya migrations from the Pontic-Caspian steppe into temperate Europe changed the course of history: they brought not only a new language, but also new ideas about how society was organized around small monogamous families with individual ownership to animals and land. This new society became the foundation for the Bronze Age, and for the way European societies continued to develop to the present.

Source: Faculty of Science - University of Copenhagen [April 04, 2017]

byUnknown

in Anthropology, Central Asia, Europe, Genetics, Northern Europe

April 04, 2017

Steppe migrant thugs pacified by Stone Age farming women

In an earlier study Professor Kristian Kristiansen from the University of Gothenburg in Sweden and Lundbeck Foundation Professor Eske Willer...

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Study reveals 10,000 years of genetic continuity in northwest North America

A study of the DNA in ancient skeletal remains adds to the evidence that indigenous groups living today in southern Alaska and the western coast of British Columbia are descendants of the first humans to make their home in northwest North America more than 10,000 years ago.

Researchers are analyzing DNA from ancient individuals found in southeast Alaska, coastal British Columbia, Washington
state and Montana. A new genetic analysis of some of these human remains finds that many of today's indigenous peoples 
living in the same regions are descendants of ancient individuals dating to at least 10,300 years ago 
[Credit: Julie McMahon, University of Illinois]

"Our analysis suggests that this is the same population living in this part of the world over time, so we have genetic continuity from 10,000 years ago to the present," said University of Illinois anthropology professor Ripan Malhi, who led the study with University of Chicago postdoctoral researcher John Lindo; Penn State University biology professor Michael DeGiorgio; Rosita Worl, the director of the Sealaska Heritage Institute in Juneau, Alaska; and University of Oklahoma anthropology professor Brian M. Kemp.

The findings, reported in the Proceedings of the National Academy of Sciences, also suggest that these early American peoples had a complex population history, the researchers report.

The new work comes on the heels of earlier studies of ancient Americans that focused on mitochondrial DNA, which occurs outside the nucleus of cells and is passed only from mothers to their offspring.

"Mitochondrial DNA just traces the maternal line - your mother's mother's lineage - so, you're missing information about all of these other ancestors," said Lindo, the first author on the paper. "We wanted to analyze the nuclear genome so we could get a better assessment of the population history of this region."

The team looked at genomic data from Shuká Káa (Tlingit for "Man Before Us"), an ancient individual whose remains - found in a cave in southeastern Alaska - date to about 10,300 years ago. They also analyzed the genomes of three more individuals from the nearby coast of British Columbia whose remains date to between 6,075 and 1,750 years ago.

"Interestingly, the mitochondrial type that Shuká Káa belonged to was also observed from another ancient skeleton dated to about 6,000 years ago," Kemp said. "It seems to disappear after that. The nuclear DNA suggests that this is probably not about population replacement, but rather chance occurrence through time. If a female has no children or only sons, the mitochondrial DNA is not passed to the next generation. As a male, Shuká Káa could not have passed on his own mitochondrial DNA; he must have had some maternal relatives that did so."

The researchers turned their attention to nuclear DNA, which offers a more comprehensive record of a person's ancestry.

"DNA from the mitochondria and Y chromosome provide unique yet sometimes conflicting stories, but the nuclear genome provides a more comprehensive view of past events," DeGiorgio said.

"The data suggest that there were multiple genetic lineages in the Americas from at least 10,300 years ago," Malhi said.

The descendants of some of those lineages are still living in the same region today, and a few are co-authors on the new study. Their participation is the result of a long-term collaboration between the scientists and several native groups who are embracing genomic studies as a way to learn from their ancestors, said Worl, who is Tlingit, Ch'áak' (Eagle) moiety of the Shangukeidí­ (Thunderbird) Clan from the Kawdliyaayi Hít (House Lowered From the Sun) in Klukwan, Alaska.

"We supported DNA testing of Shuká Káa because we believed science ultimately would agree with what our oral traditions have always said - that we have lived in southeast Alaska since time immemorial. The initial analysis showed the young man was native, and now further studies are showing that our ancestral lineage stems from the first initial peopling of the region," said Worl, who also is an anthropologist. "Science is corroborating our oral histories."

Author: Diana Yates | Source: University of Illinois at Urbana-Champaign [April 04, 2017]

byUnknown

in Americas, Anthropology, Canada, Genetics, Indigenous Cultures, North America, USA

April 04, 2017

Study reveals 10,000 years of genetic continuity in northwest North America

A study of the DNA in ancient skeletal remains adds to the evidence that indigenous groups living today in southern Alaska and the western c...

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Fish study shows important genome interactions in animal cells

In a new study, researchers at the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science examined how the interaction of two genomes in animal cells—the mitochondrial and nuclear genomes—interact to affect adaptation of the Atlantic killifish to different temperatures. They showed that although these genomes are separate physical entities, the mitochondrial genome affects the evolution of the nuclear genome, the genetic material responsible for variations in most traits such as hair color and height.

A salt water marsh, where F. heteroclitus naturally occur. Individuals used in the study were collected in marshes 
in Mantoloking, NJ. Inset: a male F. heteroclitus [Credit: Douglas Crawford]

Interactions between these two genomes, which affect everything from health and physiology to fitness, have important consequences for human health and medical interventions such as mitochondrial replacement therapy in embryos.

All animal cells are made up of two genomes, the nuclear genome with 10,000s of protein coding genes and the mitochondrial genome with 13 protein-encoding genes. All 13 genes from the mitochondrial genome interact with approximately 76 nuclear genes in a single metabolic pathway—called the oxidative phosphorylation pathway—that produces nearly all the metabolic energy needed for animal cells. This study found that the interaction between these genomes and the implications on energy production is strong enough that the mitochondrial genome can alter which version of a gene is present in the nuclear genome.

Using Atlantic killifish (Fundulus heteroclitus), the researchers examined whether mitochondrial-nuclear interactions alter the frequency of alternative forms of a gene that arise by mutation, called alleles, for over 11,000 nuclear DNA sequence variations within a population of the fish with mixed ancestry. Among individuals with two divergent mitochondrial haplotypes (mt-haplotypes), the genome-wide analyses revealed significant differences in nuclear allele frequencies.

"Our results suggest that metabolic fitness is not simply a function of the mitochondria but instead is reliant on mitochondrial-nuclear interactions and therefore important for our understanding of physiology, human health and evolution," said Doug Crawford, professor of marine biology and ecology at the UM Rosenstiel School.

The study is published in the journal PLoS Genetics.

Source: University of Miami [April 04, 2017]

byUnknown

in Biology, Evolution, Genetics

April 04, 2017

Fish study shows important genome interactions in animal cells

In a new study, researchers at the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science examined how the interaction...

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Mutant Lifestyles

It's the stuff of science fiction, though there's nothing fiction about it: Researchers have discovered a multitude of previously unidentified microorganisms possess a genetic element that enables them to self-mutate.

An ultra-small bacterial cell (scale bar is 100 nanometers) is thought to be a relative of the microorganisms that encode 
diversity-generating retroelements [Credit: Birgit Luef, Norwegian University of Science and Technology]

What's more, these organisms are so great in number that they dramatically expand the diversity of the tree of life.

"These microorganisms can be 500 times smaller than bacteria like E. Coli," said UC Santa Barbara microbiologist David Valentine. "They also do unusual things to some of the key genes used for identification, like splitting them into pieces small enough to render them invisible to scientific surveillance. This combined with their ultra-small size explains why they were missed until recently."

To pinpoint these miniscule organisms -- tiny enough to pass through filters that capture traditional microbes -- the scientists turned to groundwater samples from a Colorado aquifer. Analyzing numerous genomes therein, they detected a prevalence of an unusual genetic element they had encountered once before: diversity-generating retroelements (DGRs). The new findings appear in the journal Nature Microbiology.

Co-author Valentine, a professor in UCSB's Department of Earth Science, along with postdoctoral scholar Blair Paul and co-authors from UC Berkeley, UC San Diego and UCLA, show that these DGRs are active in sprawling lineages of recently discovered phyla: two classes of archaea -- primitive, single-celled, bacteria-like microorganisms -- and among potential new bacterial candidates in the biological tree of life. These new biological classes appear to disproportionately harbor DGRs, which enable them to target their own genes for accelerated mutation.

Lead author Paul analyzed more than 500 genomes out of a pool of 2,500 and found that the majority of a certain class of archaea, as well as a yet-to-be-characterized phyla closely related to bacteria, appear to have DGRs. In fact, many possess multiple DGRs.

"These microorganisms are so small they have minimized the amount of information they can code, so they are probably not totally self-reliant," said Valentine, also a professor in UCSB's Marine Science Institute. "This means that they engage in some form of either symbiosis or parasitism. If a microorganism shrinks down its genome and its cell to this very minimal lifestyle, it has to have mechanisms that allow it to evolve new capabilities but also to shed unneeded ones."

Valentine noted that the DGR mechanism might allow these organisms to do both. Or perhaps, he posited, they optimize to the point where it's no longer beneficial to mutate and have to rid themselves of the capability.

"The finding that DGRs are relatively widespread in tiny bacteria with symbiotic lifestyles is of great interest because these elements likely contribute to the incredible diversity of protein sequences found in these organisms," said co-author Jill Banfield, a professor of earth and planetary sciences at UC Berkeley.

While very little is known about how DGRs self-regulate, scientists are finding that these elements are able to guide and target specific sites for mutation. By examining DNA sequence from the genomes, the researchers saw recent mutation activity and observed the mechanism in action by virtue of its RNA being transcribed.

"One of the reasons we were able to see the pattern of mutations in the DNA was because the data set recovered such a depth of genomes that we could see the variability within them," Paul said.

The mechanism targets only one of the four different nucleotides (A, C, G, T) that form the basic structure of nucleic acids such as DNA. Nucleic acid synthesis and degradation require enzymes to facilitate either process. In fact, a biochemical artifact of an enzyme was what first revealed this mechanism to the UCSB investigators. A distinctive signature and location as well as only A mutations are hallmarks of this mechanism.

"There are similar proteins that don't mutate only A but are error prone," Paul explained. "We think that this enzyme is similarly prone to creating mutations."

Because the scientists are dealing with new organisms, they have not yet been able to determine what the vast majority of the diversified proteins do.

"An important question is whether these mutations alter the proteins that the genes encode or are they meant to interrupt the genes themselves and target them for removal from the genome?" Paul asked. "If this mechanism forces mutations that cause some genes to go defunct, it could be associated with evolutionary benefits."

"This discovery reveals how rapid evolution happens in some of Earth's smallest and most common, yet least-known, microbes," says Mike Sieracki of National Science Foundation's Division of Ocean Sciences, and a director for the Dimensions of Biodiversity program, which sponsored the research.

"There is still so much to discover about the microbial world," said Leslie Rissler, Dimensions of Biodiversity co-director. "This research provides a glimpse into the unique mechanisms that allow adaptation and responses to environmental stress."

Author: Julie Cohen | Source: University of California - Santa Barbara [April 03, 2017]

byUnknown

in Biology, Evolution, Genetics

April 03, 2017

Mutant Lifestyles

It's the stuff of science fiction, though there's nothing fiction about it: Researchers have discovered a multitude of previously un...

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