Fossil shows how penguins' wings evolved

A tiny fossil penguin plays a huge role in the evolutionary history of the bird, an international study shows.

Published in the Journal of the Royal Society of New Zealand, the study describes a new species of fossil penguin which lived in Otago about 24 million years ago.

Named Pakudyptes hakataramea, the penguin was very small -- about the same size as the little blue penguin, the smallest in the world -- with anatomical adaptations that allowed it to dive.

Lead author Dr Tatsuro Ando, formerly a PhD candidate at the University of Otago -- Ōtākou Whakaihu Waka and now at the Ashoro Museum of Palentology in Japan, collaborated with researchers from Otago, Okayama University of Science and Osaka University.

Dr Ando's inspiration for the paper came from discussions with the late Professor Ewan Fordyce, his supervisor and mentor at Otago.

Researchers analysed three bones -- a humerus, femur and ulna -- found by Professor Fordyce in the Hakataramea Valley, South Canterbury.

Dr Ando says Pakudyptes fills a morphological gap between modern and fossil penguins.

"In particular, the shape of the wing bones differed greatly, and the process by which penguin wings came to have their present form and function remained unclear," he says.

The humerus and ulna highlight how penguins' wings have evolved.

"Surprisingly, while the shoulder joints of the wing of Pakudyptes were very close to the condition of the present-day penguin, the elbow joints were very similar to those of older types of fossil penguins.

"Pakudyptes is the first fossil penguin ever found with this combination, and it is the 'key' fossil to unlocking the evolution of penguin wings."

Co-author Dr Carolina Loch, from Otago's Faculty of Dentistry, says analysis of the internal bone structure conducted at the Faculty of Dentistry, with comparison with data on living penguins provided from the Okayama University of Science, shows these penguins had microanatomical features suggestive of diving.

Modern penguins have excellent swimming abilities, largely due to their dense, thick bones that contribute to buoyancy during diving.

In Pakudyptes, the bone cortex was reasonably thick although the medullary cavity, which contains bone marrow, was open, similar to what we see in the modern little blue penguin, which tends to swim in shallow waters.

The ability for Pakudyptes to dive and swim comes down to the distinctive combination of its bones.

Bones such as the humerus and ulna show areas for attachment of muscles and ligaments which reveal how the wings were being used to swim and manoeuvre under water.

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How did humans learn to walk? New evolutionary study offers an earful

Humans and our closest relatives, living apes, display a remarkable diversity of types of locomotion -- from walking upright on two legs to climbing in trees and walking using all four limbs.

While scientists have long been intrigued by the question of how humans' bipedal stance and movement evolved from a quadrupedal ancestor, neither past studies nor fossil records have permitted the reconstruction of a clear and definitive history of the early evolutionary stages that led to human bipedalism.

However, a new study, which centers on recently discovered evidence from skulls of a 6-million-year-old fossil ape, Lufengpithecus, offers important clues about the origins of bipedal locomotion courtesy of a novel method: analyzing its bony inner ear region using three-dimensional CT-scanning.

"The semicircular canals, located in the skull between our brains and the external ear, are critical to providing our sense of balance and position when we move, and they provide a fundamental component of our locomotion that most people are probably unaware of," explains Yinan Zhang, a doctoral student at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences (IVPP) and the lead author of the paper, which appears in the journal the Innovation. "The size and shape of the semicircular canals correlate with how mammals, including apes and humans, move around their environment. Using modern imaging technologies, we were able to visualize the internal structure of fossil skulls and study the anatomical details of the semicircular canals to reveal how extinct mammals moved."

"Our study points to a three-step evolution of human bipedalism," adds Terry Harrison, a New York University anthropologist and one of the paper's co-authors.

"First, the earliest apes moved in the trees in a style that was most similar to aspects of the way that gibbons in Asia do today. Second, the last common ancestor of apes and humans was similar in its locomotor repertoire to Lufengpithecus, using a combination of climbing and clambering, forelimb suspension, arboreal bipedalism, and terrestrial quadrupedalism. It is from this broad ancestral locomotor repertoire that human bipedalism evolved."

Most studies of the evolution of ape locomotion had focused on comparisons of the bones of the limbs, shoulders, pelvis, and spine and the way they are associated with the different types of locomotor behaviors seen in living apes and humans.

However, the diversity of locomotor behaviors in living apes and the incompleteness of the fossil record have hampered the development of a clear picture of human bipedalism's origins.

The skulls of Lufengpithecus -- originally discovered in China's Yunnan Province in the early 1980s -- have given scientists the opportunity to address, in new ways, unanswered questions about the evolution of locomotion.

However, the heavy compression and distortion of the skulls obscured the bony ear region and led previous researchers to believe that the delicate semicircular canals were not preserved.

To better explore this region, Zhang, Ni and Harrison, along with other researchers at IVPP and the Yunnan Institute of Cultural Relics and Archaeology (YICRA), used three dimensional scanning technologies to illuminate these portions of the skulls to create a virtual reconstruction of the inner ear's bony canals.

They then compared these scans to those collected from other living and fossil apes and humans from Asia, Europe, and Africa.

"Our analyses show that early apes shared a locomotor repertoire that was ancestral to human bipedalism," explains IVPP Professor Xijun Ni, who led the project.

"It appears that the inner ear provides a unique record of the evolutionary history of ape locomotion that offers an invaluable alternative to the study of the postcranial skeleton."

"Most fossil apes and their inferred ancestors are intermediate in locomotor mode between gibbons and African apes," adds Ni. "Later, the human lineage diverged from the great apes with the acquisition of bipedalism, as seen in Australopithecus, an early human relative from Africa."

By studying the rate of evolutionary change in the bony labyrinth, the international team proposed that climate change may have been an important environmental catalyst in promoting the locomotor diversification of apes and humans.

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Complex green organisms emerged a billion years ago

Of all the organisms that photosynthesize, land plants have the most complex bodies. How did this morphology emerge? A team of scientists led by the University of Göttingen has taken a deep dive into the evolutionary history of morphological complexity in streptophytes, which include land plants and many green algae. Their research allowed them to go back in time to investigate lineages that emerged long before land plants existed. Their results revise the understanding of the relationships of a group of filamentous algal land colonizers much older than land plants. Using modern gene sequencing data, researchers pinpoint the emergence of multicellularity to almost a billion years ago. The results were published in the journal Current Biology.

The study focused on Klebsormidiophyceae, a class of green algae known for its ability to colonize diverse habitats worldwide.

The team of researchers conducted extensive sampling, investigating habitats ranging from streams, rivers, and lake shores to bogs, soil, natural rocks, tree bark, acidic post-mining sites, sand dunes, urban walls, and building façades.

"It's really fascinating that these tiny robust little organisms have such a high diversity in their morphology and also are extremely well adapted to live in sometimes very harsh environments," says Dr Tatyana Darienko, University of Göttingen's Institute for Microbiology and Genetics.

This comprehensive sampling aimed to create a global distribution map for Klebsormidiophyceae, emphasizing their adaptability, ecological significance, and hidden diversity.

Based on genetic data calibrated by fossils, the researchers performed "molecular clock analyses."

While delving into the complex evolutionary history of Klebsormidiophyceae, the researchers faced challenges in resolving phylogenetic relationships using traditional markers.

To overcome this, they employed hundreds of genes obtained from the transcriptomes of 24 isolates from different continents and habitats.

"Our approach, known as phylogenomics, was to reconstruct the evolutionary history taking into account whole genomes or large fractions of genomes," explains Dr Iker Irisarri, Leibniz Institute for the Analysis of Biodiversity Change.

"This extremely powerful method can reconstruct evolutionary relationships with very high precision."

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Evolution is not as random as previously thought

A groundbreaking study has found that evolution is not as unpredictable as previously thought, which could allow scientists to explore which genes could be useful to tackle real-world issues such as antibiotic resistance, disease and climate change.

The study, which is published in the Proceedings of the National Academy of Sciences (PNAS), challenges the long-standing belief about the unpredictability of evolution, and has found that the evolutionary trajectory of a genome may be influenced by its evolutionary history, rather than determined by numerous factors and historical accidents.

The study was led by Professor James McInerney and Dr. Alan Beavan from the School of Life Sciences at the University of Nottingham, and Dr. Maria Rosa Domingo-Sananes from Nottingham Trent University.

"The implications of this research are nothing short of revolutionary," said Professor McInerney, the lead author of the study.

"By demonstrating that evolution is not as random as we once thought, we've opened the door to an array of possibilities in synthetic biology, medicine, and environmental science."

The team carried out an analysis of the pangenome -- the complete set of genes within a given species, to answer a critical question of whether evolution is predictable or whether the evolutionary paths of genomes are dependent on their history and so not predictable today.

Using a machine learning approach known as Random Forest, along with a dataset of 2,500 complete genomes from a single bacterial species, the team carried out several hundred thousand hours of computer processing to address the question.

After feeding the data into their high-performance computer, the team first made "gene families" from each of the gene of each genome.

"In this way, we could compare like-with-like across the genomes," said Dr. Domingo-Sananes.

Once the families had been identified, the team analysed the pattern of how these families were present in some genomes and absent in others.

"We found that some gene families never turned up in a genome when a particular other gene family was already there, and on other occasions, some genes were very much dependent on a different gene family being present."

In effect, the researchers discovered an invisible ecosystem where genes can cooperate or can be in conflict with one another.

"These interactions between genes make aspects of evolution somewhat predictable and furthermore, we now have a tool that allows us to make those predictions," adds Dr. Domingo-Sananes.

Dr Beavan said: "From this work, we can begin to explore which genes "support" an antibiotic resistance gene, for example. Therefore, if we are trying to eliminate antibiotic resistance, we can target not just the focal gene, but we can also target its supporting genes.

"We can use this approach to synthesise new kinds of genetic constructs that could be used to develop new drugs or vaccines. Knowing what we now know has opened the door to a whole host of other discoveries."

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Artificial cells demonstrate that 'life finds a way'

"Listen, if there's one thing the history of evolution has taught us is that life will not be contained. Life breaks free. It expands to new territories, and it crashes through barriers painfully, maybe even dangerously, but . . . life finds a way," said Ian Malcolm, Jeff Goldblum's character in Jurassic Park, the 1993 science fiction film about a park with living dinosaurs.

You won't find any Velociraptors lurking around evolutionary biologist Jay T. Lennon's lab; however, Lennon, a professor in the College of Arts and Sciences Department of Biology at Indiana University Bloomington, and his colleagues have found that life does indeed find a way. Lennon's research team has been studying a synthetically constructed minimal cell that has been stripped of all but its essential genes. The team found that the streamlined cell can evolve just as fast as a normal cell -- demonstrating the capacity for organisms to adapt, even with an unnatural genome that would seemingly provide little flexibility.

"It appears there's something about life that's really robust," says Lennon. "We can simplify it down to just the bare essentials, but that doesn't stop evolution from going to work."

For their study, Lennon's team used the synthetic organism, Mycoplasma mycoides JCVI-syn3B -- a minimized version of the bacterium M. mycoides commonly found in the guts of goats and similar animals. Over millennia, the parasitic bacterium has naturally lost many of its genes as it evolved to depend on its host for nutrition. Researchers at the J. Craig Venter Institute in California took this one step further. In 2016, they eliminated 45 percent of the 901 genes from the natural M. mycoides genome -- reducing it to the smallest set of genes required for autonomous cellular life. At 493 genes, the minimal genome of M. mycoides JCVI-syn3B is the smallest of any known free-living organism. In comparison, many animal and plant genomes contain more than 20,000 genes.

In principle, the simplest organism would have no functional redundancies and possess only the minimum number of genes essential for life. Any mutation in such an organism could lethally disrupt one or more cellular functions, placing constraints on evolution. Organisms with streamlined genomes have fewer targets upon which positive selection can act, thus limiting opportunities for adaptation.

Although M. mycoides JCVI-syn3B could grow and divide in laboratory conditions, Lennon and colleagues wanted to know how a minimal cell would respond to the forces of evolution over time, particularly given the limited raw materials upon which natural selection could operate as well as the uncharacterized input of new mutations.

"Every single gene in its genome is essential," says Lennon in reference to M. mycoides JCVI-syn3B. "One could hypothesize that there is no wiggle room for mutations, which could constrain its potential to evolve."

The researchers established that M. mycoides JCVI-syn3B, in fact, has an exceptionally high mutation rate. They then grew it in the lab where it was allowed to evolve freely for 300 days, equivalent to 2000 bacterial generations or about 40,000 years of human evolution.

The next step was to set up experiments to determine how the minimal cells that had evolved for 300 days performed in comparison to the original, non-minimal M. mycoides as well as to a strain of minimal cells that hadn't evolved for 300 days. In the comparison tests, the researchers put equal amounts of the strains being assessed together in a test tube. The strain better suited to its environment became the more common strain.

They found that the non-minimal version of the bacterium easily outcompeted the unevolved minimal version. The minimal bacterium that had evolved for 300 days, however, did much better, effectively recovering all of the fitness that it had lost due to genome streamlining. The researchers identified the genes that changed the most during evolution. Some of these genes were involved in constructing the surface of the cell, while the functions of several others remain unknown.

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Scientists present evidence for a billion-years arms race between viruses and their hosts

Researchers have proposed a new evolutionary model for the origin of a kingdom of viruses called Bamfordvirae, suggesting a billion-years evolutionary arms race between two groups within this kingdom and their hosts.

Their study, published today as a Reviewed Preprint in eLife, provides what the editors say are convincing analyses that advance our understanding of the deep evolutionary history of viruses, the interaction between viruses and the first eukaryotes (organisms with cells that include a nucleus), and the diversification of viral lineages.

Viruses in the kingdom Bamfordvirae make up one of the most diverse groups that infect living organisms. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs; the largest viruses characterised to date), virophages (viral parasites of other viruses), adenoviruses (common viruses that cause cold and flu-like symptoms), and Mavericks and Polinton-like viruses (both virus-like mobile genetic elements that colonise the genomes of their hosts).

There are two main hypotheses for the origins of these viruses: the 'nuclear-escape' and 'virophage-first' hypotheses. The nuclear-escape hypothesis says that a Maverick-like ancestor originated with hosts (endogenous), escaped from the host cell nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis suggests that NCLDVs co-evolved with early virophages. Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the host nucleus at a later stage.

"Despite these proposed scenarios, the diversification of viruses in the Bamfordvirae kingdom remains a major open question in virus evolution. To gain a better understanding of their history, we wanted to test the predictions made by both the nuclear-escape and virophage-first models, and consider alternative scenarios regarding the origin of different lineages," says José Gabriel Niño Barreat, Postdoctoral Research Assistant at the University of Oxford, UK. Barreat is a co-author of the study alongside Aris Katzourakis, Professor of Evolution and Genomics at the University of Oxford's Department of Biology.

Barreat and Katzourakis used two hypothesis-testing methods (maximum-likelihood and Bayesian frameworks) to compare the plausibility of the nuclear-escape versus alternative evolutionary scenarios. They focused on four key proteins shared by viruses in this lineage which are involved in the formation of viral capsids: major and minor capsid proteins, DNA-packaging ATPase, and protease. They applied another two methods that use genetic data to estimate rooted phylogenies, to infer the evolutionary trajectory of the different lineages. Then, they assessed whether adenoviruses and NCLDVs descended from a common ancestor, as predicted by the nuclear-escape scenario.

Their analyses revealed strong evidence against a sister relationship between adenoviruses and NCLDVs, as suggested by the nuclear-escape hypothesis. Instead, the findings suggest that adenoviruses descended from a common ancestor with Mavericks, to the exclusion of NCLDVs. At odds with a virophage-first scenario, the researchers found that the most recent common ancestor of Mavericks and adenoviruses was not a virophage. However, their work does not rule out the virophage-first hypothesis completely, making it the one best supported by current phylogenetic analyses.

Additionally, their work provides support for the positioning of the Bamfordvirae ancestral root between virophages and the other viral lineages. This positioning pointed the team towards a new model for the evolutionary origins of these viruses.

"The model proposes that the Bamfordvirae ancestor did not originate from an invasion of the eukaryotic cell nucleus, and that it was a non-virophage DNA virus with a small genome," says co-author Aris Katzourakis. "The lifestyle of virophages would have evolved at a later stage as these became specialised parasites of the ancestral NCLDVs." Katzourakis adds that the relative timing of events suggests the most recent common ancestor of the Bamfordvirae kingdom existed more than a billion years ago, extending to the initial stages of eukaryotic life. However, an absolute timescale for the precise dating of these events is not currently available.

Another limitation of the study is that the phylogenetic signal in the protein data analysed may have been obscured by the deep divergences and extreme diversity in this lineage. However, the authors were able to robustly distinguish between alternative scenarios, and the focus on the origin and development of the viral capsid provides a simple way to explain the available data.

"This work contributes to our knowledge on how viruses evolve different evolutionary strategies, for example to become parasites of other viruses like virophages, or viral giants like NCLDVs," Barreat says. "As well as playing important roles in Earth's ecosystems, it is becoming increasingly clear that viruses may have contributed to major evolutionary transitions during the history of life. Therefore, understanding the deep evolutionary history of viruses provides more context for these ancient interactions and the actors involved."

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Information 'deleted' from the human genome may be what made us human

What the human genome is lacking compared with the genomes of other primates might have been as crucial to the development of humankind as what has been added during our evolutionary history, according to a new study led by researchers at Yale and the Broad Institute of MIT and Harvard.

The new findings, published April 28 in the journal Science, fill an important gap in what is known about historical changes to the human genome. While a revolution in the capacity to collect data from genomes of different species has allowed scientists to identify additions that are specific to the human genome -- such as a gene that was critical for humans to develop the ability to speak -- less attention has been paid to what's missing in the human genome.

For the new study researchers used an even deeper genomic dive into primate DNA to show that the loss of about 10,000 bits of genetic information -- most as small as a few base pairs of DNA -- over the course of our evolutionary history differentiate humans from chimpanzees, our closest primate relative. Some of those "deleted" pieces of genetic information are closely related to genes involved in neuronal and cognitive functions, including one associated with the formation of cells in the developing brain.

These 10,000 missing pieces of DNA -- which are present in the genomes of other mammals -- are common to all humans, the Yale team found.

The fact that these genetic deletions became conserved in all humans, the authors say, attests to their evolutionary importance, suggesting that they conferred some biological advantage.

"Often we think new biological functions must require new pieces of DNA, but this work shows us that deleting genetic code can result in profound consequences for traits make us unique as a species," said Steven Reilly, an assistant professor of genetics at Yale School of Medicine and senior author of the paper.

The paper was one of several published in Science from the Zoonomia Project, an international research collaboration that is cataloging the diversity in mammalian genomes by comparing DNA sequences from 240 species of mammals that exist today.

In their study, the Yale team found that some genetic sequences found in the genomes of most other mammal species, from mice to whales, vanished in humans. But rather than disrupt human biology, they say, some of these deletions created new genetic encodings that eliminated elements that would normally turn genes off.

The deletion of this genetic information, Reilly said, had an effect that was the equivalent of removing three characters -- "n't" -- from the word "isn't" to create a new word, "is."

"[Such deletions] can tweak the meaning of the instructions of how to make a human slightly, helping explain our bigger brains and complex cognition," he said.

The researchers used a technology called Massively Parallel Reporter Assays (MPRA), which can simultaneously screen and measure the function of thousands of genetic changes among species.

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Colorado's spicy ancient history of chili peppers

Botanists and paleontologists, led by researchers from the University of Colorado Boulder, have identified a fossil chili pepper that may rewrite the geography and evolutionary timeline of the tomato plant family.

The team's findings, published last month in the journal New Phytologist, show that the chili pepper tribe (Capsiceae) within the tomato, or nightshade (Solanaceae), family is much older and was much more widespread than previously thought. Scientists previously believed that chili peppers evolved in South America at most 15 million years ago, but the new research pushes that date to at least 50 million years ago -- and suggests that chili peppers were in fact present in North America at that time.

Rocío Deanna, a postdoctoral researcher in ecology and evolutionary biology, and Abel Campos, an undergraduate double majoring in evolutionary biology and molecular, cellular and developmental biology, weren't planning to rewrite history when they met up one afternoon at the CU Boulder Museum of Natural History in 2021. Yet among a group of specimens in its collections gathered from the Green River Formation -- geological treasure trove in northwestern Colorado and southwestern Wyoming -- Deanna spotted a specific, solanaceous trait embedded in one fossil: little spikes on the end of a fruiting stem.

"At first, I thought 'No way! This can't be true,'" said Rocío Deanna, lead author of the study. "But it was so characteristic of the chili pepper."

After they discovered two of these fossils in the CU Boulder collections, Deanna and Campos, a co-author of the study, found one more from the chili pepper tribe in collections at the Denver Museum of Nature and Science. All three fossils are from the Green River Formation in Colorado: the CU specimens from Garfield County and the DMNS fossil from Rio Blanco County.

These chili pepper fossils from the Eocene geological epoch (34 to 56 million years ago) match the timeline of another nightshade fossil found in the Esmeraldas Formation in Colombia, revealing that the family was already distributed across all of the Americas by as early as 50 million years ago.

"The family is way older than we thought," said Deanna, also a faculty member at the National University of Cordoba.

A fruit-fossil history

The nightshade family comprises 3,000 species and almost 100 different genera, including chili peppers. The ancient chili pepper was technically a fruit -- and a berry, at that. While tomatoes and peppers are commonly associated with vegetables, they have seeds on the inside, which officially categorizes them as fruits.

The researchers cannot be sure of the chili's exact shape or color, but it was probably on the smaller end compared to modern day chili peppers. And like its relatives, it could have been quite spicy, according to Deanna.

Deanna and Campos identified the fossil by the unique shape of its calyx teeth: spikes on the end of the fruiting stem that hold on to the pepper, like those which hold a gemstone in a ring.

"The world has maybe 300,000 plant species. The only plants with that kind of calyx is this group of 80 or 90 species," said Stacey Smith, senior author of the paper and associate professor of evolutionary biology at CU Boulder.

Paleontologists collected the CU Boulder fossil from the Green River Formation in the 1990s. But its exact identity remained a mystery for years, in part because there are only a handful of "solanologists," botanists who study the nightshade family, in the world. When Deanna found these Colorado-based fossils, she had just returned from a global search for tomato family fossil specimens, only to find some "just ripe for the picking" right on campus.

"A lot of discoveries happen decades after the specimens have been collected," said Smith. "Who knows how many other new fossil species are sitting in any of these museums? They're just waiting for the right eyes to look at them."

Trickle-down evolution

These chili pepper fossils were around during the Eocene, a geologic epoch that lasted from about 34 to 56 million years ago as the continents drifted toward their present positions. During this balmy time in Earth's history, carbon dioxide levels ranged between 700 and 900 parts per million (twice as high as they are today), and palm trees grew as far north as Alaska. Because little to no ice was present on Earth, sea level was as much as 500 feet higher than it is today.

Scientists had assumed that the origins of chili peppers began in South America roughly 10 to 15 million years ago, where they then dispersed over land and water to the other continents. While Colorado today is home to very few native nightshades and no chili peppers, this new discovery hints that a plethora of plants from the tomato plant family may have existed in North America 40 to 50 million years ago, which have since largely disappeared.

But how did these peppers first get to North America? It's now a case of "the chicken or the chili pepper?"

Experts have theorized that fruit-eating birds, which existed as early as 60 million years ago, may have carried seeds and plants around the world with them in their guts, stuck to their feathers or in the mud on their feet. But these birds also had to be eating something to fuel their journeys -- and fleshy berries, or peppers, make the perfect fuel. Birds may have distributed peppers from continent to continent, but peppers may also have been crucial to the success of those same birds.

So the nightshade family could have easily started in North America instead of South America, then dispersed in the other direction -- and with this discovery, scientists can no longer say for sure, said Smith.

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Hunter-gatherer childhoods may offer clues to improving education and wellbeing in developed countries

Hunter-gatherers can help us understand the conditions that children may be psychologically adapted to because we lived as hunter-gatherers for 95% of our evolutionary history. And paying greater attention to hunter-gatherer childhoods may help economically developed countries improve education and wellbeing.

Published today in the Journal of Child Psychology and Psychiatry, a new study by Dr Nikhil Chaudhary, an evolutionary anthropologist at the University of Cambridge, and Dr Annie Swanepoel, a child psychiatrist, calls for new research into child mental health in hunter-gatherer societies. They explore the possibility that some common aspects of hunter-gatherer childhoods could help families in economically developed countries. Eventually, hunter-gatherer behaviours could inform 'experimental intervention trials' in homes, schools and nurseries.

The authors acknowledge that children living in hunter-gatherer societies live in very different environments and circumstances than those in developed countries. They also stress that hunter-gatherer children invariably face many difficulties that are not experienced in developed countries and, therefore, caution that these childhoods should not be idealised.

Drawing on his own observations of the BaYaka people in Congo and the extensive research of anthropologists studying other hunter-gatherer societies, Dr Chaudhary highlights major differences in the ways in which hunter-gatherer children are cared for compared to their peers in developed countries. He stresses that "contemporary hunter-gatherers must not be thought of as 'living fossils', and while their ways of life may offer some clues about our prehistory, they are still very much modern populations each with a unique cultural and demographic history."

Physical contact and attentiveness

Despite increasing uptake of baby carriers and baby massage in developed countries, levels of physical contact with infants remain far higher in hunter-gatherer societies. In Botswana, for instance, 10-20 week old !Kung infants are in physical contact with someone for around 90% of daylight hours, and almost 100% of crying bouts are responded to, almost always with comforting or nursing -- scolding is extremely rare.

The study points out that this exceptionally attentive childcare is made possible because of the major role played by non-parental caregivers, or 'alloparents', which is far rarer in developed countries.

Non-parental caregivers

In many hunter-gatherer societies, alloparents provide almost half of a child's care. A previous study found that in the DRC, Efe infants have 14 alloparents a day by the time they are 18 weeks old, and are passed between caregivers eight times an hour.

Dr Chaudhary said: "Parents now have much less childcare support from their familial and social networks than would likely have been the case during most of our evolutionary history. Such differences seem likely to create the kind of evolutionary mismatches that could be harmful to both caregivers and children."

"The availability of other caregivers can reduce the negative impacts of stress within the nuclear family, and the risk of maternal depression, which has knock-on effects for child wellbeing and cognitive development."

The study emphasises that alloparenting is a core human adaptation, contradicting 'intensive mothering' narratives which emphasise that mothers should use their maternal instincts to manage childcare alone. Dr Chaudhary and Dr Swanepoel write that 'such narratives can lead to maternal exhaustion and have dangerous consequences'.

Care-giving ratios

The study points out that communal living in hunter-gatherer societies results in a very high ratio of available caregivers to infants/toddlers, which can even exceed 10:1.

This contrasts starkly with the nuclear family unit, and even more so with nursery settings, in developed countries. According to the UK's Department of Education regulations, nurseries require ratios of 1 carer to 3 children aged under 2 years, or 1 carer to 4 children aged 2-3.

Dr Chaudhary said: "Almost all day, hunter-gatherer infants and toddlers have a capable caregiver within a couple of metres of them. From the infant's perspective, that proximity and responsiveness, is very different from what is experienced in many nursery settings in the UK."

"If that ratio is stretched even thinner, we need to consider the possibility that this could have impacts on children's wellbeing."

Children providing care and mixed-age active learning

In hunter-gatherer societies, children play a significantly bigger role in providing care to infants and toddlers than is the case in developed countries. In some communities they begin providing some childcare from the age of four and are capable of sensitive caregiving; and it is common to see older, but still pre-adolescent children looking after infants.

By contrast, the NSPCC in the UK recommends that when leaving pre-adolescent children at home, babysitters should be in their late teens at least.

Dr Chaudhary said: "In developed countries, children are busy with schooling and may have less opportunity to develop caregiving competence. However, we should at least explore the possibility that older siblings could play a greater role in supporting their parents, which might also enhance their own social development."

The study also points out that instructive teaching is rare in hunter-gatherer societies and that infants primarily learn via observation and imitation. From around the age of two, hunter-gatherer children spend large portions of the day in mixed-age (2-16) 'playgroups' without adult supervision. There, they learn from one another, acquiring skills and knowledge collaboratively via highly active play practice and exploration.

Learning and play are two sides of the same coin, which contrasts with the lesson-time / play-time dichotomy of schooling in the UK and other developed countries.

Dr Chaudhary and Dr Swanepoel note that "Classroom schooling is often at odds with the modes of learning typical of human evolutionary history." The study acknowledges that children living in hunter-gather societies live in very different environments and circumstances than those in developed countries:

"Foraging skills are very different to those required to make a living in market-economies, and classroom teaching is certainly necessary to learn the latter. But children may possess certain psychological learning adaptations that can be practically harnessed in some aspects of their schooling. When peer and active learning can be incorporated, they have been shown to improve motivation and performance, and reduce stress." The authors also highlight that physical activity interventions have been shown to aid performance among students diagnosed with ADHD.

The study calls for more research into children's mental health in hunter-gatherer societies to test whether the hypothesised evolutionary mismatches actually exist. If they do, such insights could then be used to direct experimental intervention trials in developed countries.

Read more at Science Daily

How pandas survive solely on bamboo: Evolutionary history

When is a thumb not a thumb? When it's an elongated wrist bone of the giant panda used to grasp bamboo. Through its long evolutionary history, the panda's hand has never developed a truly opposable thumb and instead evolved a thumb-like digit from a wrist bone, the radial sesamoid. This unique adaptation helps these bears subsist entirely on bamboo despite being bears (members of the order Carnivora, or meat-eaters). In a new paper published in Scientific Reports, the Natural History Museum of Los Angeles County's Curator of Vertebrate Paleontology Xiaoming Wang and colleagues report on the discovery of the earliest bamboo-eating ancestral panda to have this "thumb." Surprisingly, it's longer than its modern descendants.

While the celebrated false thumb in living giant pandas (Ailuropoda melanoleuca) has been known for more than 100 years, how this wrist bone evolved was not understood due to a near-total absence of fossil records. Uncovered at the Shuitangba site in the City of Zhaotong, Yunnan Province in south China and dating back 6-7 million years ago, a fossil false thumb from an ancestral giant panda, Ailurarctos, gives scientists a first look at the early use of this extra (sixth) digit-and the earliest evidence of a bamboo diet in ancestral pandas-helping us better understanding the evolution of this unique structure.

"Deep in the bamboo forest, giant pandas traded an omnivorous diet of meat and berries to quietly consuming bamboos, a plant plentiful in the subtropical forest but of low nutrient value," says NHM Vertebrate Paleontology Curator Dr. Xiaoming Wang. "Tightly holding bamboo stems in order to crush them into bite sizes is perhaps the most crucial adaptation to consuming a prodigious quantity of bamboo."

How to Walk and Chew Bamboo at the Same Time

This discovery could also help solve an enduring panda mystery: why are their false thumbs so seemingly underdeveloped? As an ancestor to modern pandas, Ailurarctos might be expected to have even less well-developed false"thumbs," but the fossil Wang and his colleagues discovered revealed a longer false thumb with a straighter end than its modern descendants' shorter, hooked digit. So why did pandas' false thumbs stop growing to achieve a longer digit?

"Panda's false thumb must walk and 'chew'," says Wang. "Such a dual function serves as the limit on how big this 'thumb' can become."

Wang and his colleagues think that modern panda's shorter false thumbs are an evolutionary compromise between the need to manipulate bamboo and the need to walk. The hooked tip of a modern panda's second thumb lets them manipulate bamboo while letting them carry their impressive weight to the next bamboo meal. After all, the "thumb" is doing double duty as the radial sesamoid-a bone in the animal's wrist.

"Five to six million years should be enough time for the panda to develop longer false thumbs, but it seems that the evolutionary pressure of needing to travel and bear its weight kept the 'thumb' short-strong enough to be useful without being big enough to get in the way," says Denise Su, associate professor at the School of Human Evolution and Social Change and research scientist at the Institute of Human Origins at Arizona State University, and co-leader of the project that recovered the panda specimens.

"Evolving from a carnivorous ancestor and becoming a pure bamboo-feeder, pandas must overcome many obstacles," Wang says. "An opposable 'thumb' from a wrist bone may be the most amazing development against these hurdles."

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How species form: What the tangled history of polar bear and brown bear relations tells us

A new study is providing an enhanced look at the intertwined evolutionary histories of polar bears and brown bears.

Becoming separate species did not completely stop these animals from mating with each other. Scientists have known this for some time, but the new research draws on an expanded dataset -- including DNA from an ancient polar bear tooth -- to tease out more detail.

The story that emerges reveals complexities similar to those that complicate human evolutionary history.

"The formation and maintenance of species can be a messy process," says Charlotte Lindqvist, PhD, associate professor of biological sciences in the University at Buffalo College of Arts and Sciences, and an expert on bear genetics. "What's happened with polar bears and brown bears is a neat analog to what we're learning about human evolution: that the splitting of species can be incomplete. As more and more ancient genomes have been recovered from ancient human populations, including Neanderthals and Denisovans, we're seeing that there was multidirectional genetic mixing going on as different groups of archaic humans mated with ancestors of modern humans. Polar bears and brown bears are another system where you see this happening."

"We find evidence for interbreeding between polar bears and brown bears that predates an ancient polar bear we studied," she says. "And, moreover, our results demonstrate a complicated, intertwined evolutionary history among brown and polar bears, with the main direction of gene flow going into polar bears from brown bears. This inverts a hypothesis suggested by other researchers that gene flow has been unidirectional and going into brown bears around the peak of the last ice age."

The study will be published the week of June 6 in the Proceedings of the National Academy of Sciences. It was led by Lindqvist at UB in the U.S.; Luis Herrera-Estrella at the National Laboratory of Genomics for Biodiversity (LANGEBIO) in Mexico and Texas Tech University in the U.S.; and Kalle Leppälä at the University of Oulu in Finland. Tianying Lan, PhD, a former UB postdoctoral researcher now at Daicel Arbor Biosciences, was co-first author with Leppälä.

The concept of Arctic-adapted polar bears capturing genetic material from brown bears, which are adapted to life in lower latitudes, is one of several findings of possible interest for scientists concerned with climate change impacts on threatened species.

As the world warms and Arctic sea ice declines, polar bears and brown bears may run into each other more frequently in places where their ranges overlap. This makes their shared evolutionary history a particularly intriguing subject of study, Lindqvist says.

Splitting of species can be a messy process

As Lindqvist explains, scientists once thought modern humans and Neanderthals simply split into separate species after evolving from a common ancestor. Then, researchers found Neanderthal DNA in modern Eurasian people, implying that modern human populations received an influx of genes from Neanderthals at some point in their shared evolutionary history, she says.

Only later did scientists realize that this genetic intermingling also supplemented Neanderthal populations with modern human genes, Lindqvist adds. In other words, interbreeding can be complex, not necessarily a one-way street, she says.

The new study on bears reveals a remarkably similar story: The analysis finds evidence of hybridization in both polar bear and brown bear genomes, with polar bears in particular carrying a strong signature of an influx of DNA from brown bears, researchers say. Earlier research proposed the inverse pattern only, Lindqvist says.

"It's exciting how DNA can help reveal ancient life history. Gene flow direction is harder to determine than merely its presence, but these patterns are vital to understanding how past adaptations have transferred among species to give modern animals their current features," says Leppälä, PhD, postdoctoral researcher in the research unit of mathematical sciences at the University of Oulu.

"Population genomics is an increasingly powerful toolbox to study plant and animal evolution and the effects of human activity and climate change on endangered species," says Herrera-Estrella, PhD, President's Distinguished Professor of Plant Genomics and director of the Institute of Genomics for Crop Abiotic Stress Tolerance in the Texas Tech Department of Plant and Soil Science. He is also a professor emeritus at LANGEBIO. "Bears don't provide simple speciation stories any more than human evolution has. This new genomic research suggests that mammalian species groups can hide complicated evolutionary histories."

Evidence from modern bear genomes -- and DNA from an ancient tooth

The study analyzed the genomes of 64 modern polar and brown bears, including several new genomes from Alaska, a state where both species are found.

The team also produced a new, more complete genome for a polar bear that lived 115,000 to 130,000 years ago in Norway's Svalbard archipelago. DNA for the ancient polar bear was extracted from a tooth attached to a subfossil jawbone, which is now housed at the Natural History Museum at the University of Oslo.

Using this dataset, researchers estimate that polar bears and brown bears started to become distinct species about 1.3 to 1.6 million years ago, updating prior assessments made by some of the same scientists. The age of the split has been and remains a topic of scientific debate, with past interbreeding and limited fossil evidence for ancient polar bears among factors that make the timing hard to pinpoint, Lindqvist says.

In any case: After becoming their own species, polar bears endured dramatic population decline and a prolonged genetic bottleneck, leaving these bears with much less genetic diversity than brown bears, the new study concludes. The findings confirm past research pointing to the same trends, and add evidence in support of this hypothesis.

Together with the analysis of gene flow, these findings are providing new insights into the messy, intertwined evolutionary history of polar bears and brown bears.

Read more at Science Daily

Plants as cold specialists from the ice age

As cold relics in an increasingly warming world, plants of the spoonweed group time and again quickly adapted to a changing climate during the Ice Ages of the last two million years. An international team of evolutionary biologists and botanists led by Prof. Dr Marcus Koch of Heidelberg University used genomic analyses to study what factors favour adaptation to extreme climatic conditions. The evolutionary history of the Brassicaceae family provides insights into how plants may be able to cope with climate change in the future.

"With the challenges of increasing global warming, developing a basic understanding of how plants adapted to severe environmental change is increasingly urgent," stresses Prof. Koch, whose "Biodiversity and Plant Systematics" working group conducts research at the Centre for Organismal Studies (COS). In many cases, their evolutionary past also strongly determines the future adaptability of plants as well as their ability to develop into new forms and types, he continues. The spoonweed genus, or Latin Cochlearia, from the Brassicaceae family separated from its Mediterranean relatives more than ten million years ago. While their direct descendants specialised in response to drought stress, the spoonweeds conquered the cold and arctic habitats at the beginning of the Ice Age 2.5 million years ago.

In controlled lab experiments, the researchers studied cultivated species from both groups to determine how they repeatedly adapted during the relatively rapidly alternating cold and warm periods over the last two million years. A "cold training" indicates that the physiological adaptations to drought and salt stress during their early evolution later helped the plants develop a high tolerance to cold. Although the researchers expected that both groups would show a pronounced response to this "cold training," there appeared to be no significant difference in response to cold stress between the cold specialists of the Arctic and Alpine regions and the dry specialists or species adapted to salt water from the Mediterranean.

Furthermore, the newly emerged plants adapted to cold developed separate gene pools that frequently came into contact with one another in the cold regions. Because spoonweeds have hardly any genetic barriers to contact between species, populations with multiple sets of chromosomes developed that, subsequently, were continually reduced in their size. "Time after time, these species were then able to occupy cold ecological niches," explains Marcus Koch.

While the gene pool of the cold specialists from the Arctic expanded, the European spoonweed population has shrunk since the last Ice Age. Cold habitats in Europe are disappearing in the face of significant global warming, thus seriously endangering all spoonweed species. Only the Danish spoonweed, with its abundant sets of chromosomes, remains unscathed and in some cases is even spreading. "It is the only species of spoonweed that changed its life cycle and flourishes in salt and sand locations. In some of its ecological features, it resembles its faraway Mediterranean cousins," adds Prof. Koch. For the researchers, the physiological adaptability of the spoonweeds makes them a promising model system to simultaneously study adaptations to drought, cold, and salt stress.

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Advanced analysis of Apollo sample illuminates Moon’s evolution

Sophisticated analysis of a rock sample taken from the Moon during the Apollo 17 mission revealed new information about the complex cooling and evolutionary history of the Moon. The findings, from University of Hawai'i (UH) at Manoa researchers, were published today in Nature Communications.

Apollo 17 astronauts collected the rock sample troctolite 76535 from the Moon's surface in 1972, and it remains one of the most scientifically valuable samples of the Moon due to its pristine nature. Further, the rock type is widespread on the Moon and likely contains important clues to understanding lunar formation.

William Nelson, lead author of the study and Earth Sciences graduate student in the UH Manoa School of Ocean and Earth Science and Technology (SOEST), and co-authors used a specialized electron microprobe to perform high-resolution analysis of troctolite 76535.

"Previous reports suggest the minerals in the Apollo 17 sample were chemically homogeneous," said Nelson. "Surprisingly, we found chemical variations within crystals of olivine and plagioclase. These heterogeneities allow us to constrain the earliest, high-temperature cooling histories of these minerals using numerical models."

SOEST researchers used the UH High-Performance Computing facilities, Mana, to consider the effects of a variety of computer-simulated cooling paths -- well over 5 million chemical diffusion models.

"The simulations revealed that these heterogeneities could only survive a relatively short period of time at high temperatures," said Nelson.

The diffusion patterns preserved in the mineral grains and observed with the microprobe were consistent with a rapid cooling history of no more than 20-million-years at high temperatures. The finding challenges previous estimates of a 100-million-year cooling duration and supports initial rapid cooling of magmas within the lunar crust.

"This is changing our outlook on how an important suite of lunar rocks formed," said Nelson.

To reconcile high-temperature cooling rates with the generally accepted view of the way in which these rocks formed, the research team proposed that perhaps this rock type is formed by a process called reactive infiltration wherein a melt interacts with rock -- changing its chemical and physical makeup.

The study also demonstrates the value of re-examining previously analyzed samples using modern techniques and how quickly new data can reshape our understanding of planetary evolution.

Read more at Science Daily

Visually stunning tree of all known life unveiled online

OneZoom is a one-stop site for exploring all life on Earth, its evolutionary history, and how much of it is threatened with extinction.

The OneZoom explorer -- available at onezoom.org -- maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.

OneZoom was developed by Imperial College London biodiversity researcher Dr James Rosindell and University of Oxford evolutionary biologist Dr Yan Wong. In a paper published today in Methods in Ecology and Evolution, Drs Wong and Rosindell present the result of over ten years of work, gradually creating what they regard as "the Google Earth of biology."

Dr Wong, from the Big Data Institute at the University of Oxford, said: "By developing new algorithms for visualisation and data processing, and combining them with 'big data' gathered from multiple sources, we've created something beautiful. It allows people to find their favourite living things, be they golden moles or giant sequoias, and see how evolutionary history connects them together to create a giant tree of all life on Earth."

Dr Rosindell, from the Department of Life Sciences at Imperial, said: "We have worked hard to make the tree easy to explore for everyone, and we also hope to send a powerful message: that much of our biodiversity is under threat."

The 'leaves' representing each species on the tree are colour coded depending on their risk of extinction: green for not threatened, red for threatened, and black for recently extinct. However, most of the leaves on the tree are grey, meaning they have not been evaluated, or scientists don't have enough data to know their extinction risk. Even among the species described by science, only a tiny fraction have been studied or have a known risk of extinction.

Dr Wong added: "It's extraordinary how much research there is still to be done. Building the OneZoom tree of life was only possible through sophisticated methods to gather and combine existing data -- it would have been impossible to curate all this by hand."

The OneZoom explorer is configured to work with touchscreens, and the developers have made the software free to download and use by educational organisations such as museums and zoos.

Dr Rosindell commented: "Two million species can feel like a number too big to visualise, and no museum or zoo can hold all of them! But our tool can help represent all Earth's species and allow visitors to connect with their plight. We hope that now this project is complete and available, many venues will be interested in using it to complement their existing displays."

Drs Rosindell and Wong have also set up a OneZoom charity with the aim of using their tree of life to "advance the education of the public in the subjects of evolution, biodiversity and conservation of the variety of life on Earth."

Uniquely, to support this charity, each leaf on the tree is available for sponsorship, allowing anyone to 'adopt' a species and enabling OneZoom to continue their mission. More than 800 leaves have currently been sponsored by individuals and selected organisations, many with personal messages of how they feel connected to the conservation of nature.

The team have also integrated the tree with data from the Wikipedia project to reveal the 'popularity' of every species, based on how often their Wikipedia page is viewed. Dr Wong said: "Perhaps unsurprisingly, humans come out on top, but it has swapped places a few times with the second most popular: the grey wolf -- the 'species' that includes all domestic dogs."

In the plant world, cannabis comes out on top, followed by cabbage, the potato, and the coconut. The most popular ray-finned fishes are sport fishing species, particularly salmon and trout.

Now the tree is complete, the team hope to create bespoke 'tours' and experiences of species connected in imaginative new ways -- such as tours of iridescent animals, medicinal plants, or even species named after celebrities. They have created a special screen capture tool for easy saving and sharing of user-generated tours.

Read more at Science Daily

Colorblind fish show experts how vision evolved

After decades of studying color vision in mice, new research in zebrafish has allowed experts at the University of Tokyo to uncover how some animals regulate their ability to see blue light. The results, published in Science Advances, allow researchers to better understand the evolutionary history and current control mechanisms of color vision.

"In 1989 when I began studying the evolution of vision, the textbooks said that light sensitivity and color differentiation all came from the same protein. Since then, our group identified color-sensitive proteins, mapped their evolution between species, and now understand their regulation," said Emeritus Professor Yoshitaka Fukada from the University of Tokyo Graduate School of Science.

As new color-sensitive cone cells grow in the eye, controlled patterns of gene activity mean that each cell differentiates and produces one type of protein specialized to detect a specific range of light wavelengths. The ancestor of all animals with a backbone could differentiate four different color wavelengths of light: near-ultraviolet, blue, green and red.

Over millennia, some ancestor species lost the genes responsible for one or two of those color-detecting proteins. Sometimes, a descendant species eventually recreated a color-specific protein by duplicating, then mutating a remaining gene.

Genome sequencing allows researchers to study the evolution of color vision genes while gene editing tools can reveal how those genes are regulated. Studying mice has allowed experts to understand how violet- and red-wavelength sensitivity are regulated, but mice evolved without the ability to differentiate the blue and green wavelengths. Lack of convenient gene editing tools meant regulation of blue and green color sensitivity remained unknown.

In 2019, Fukada's research team, now led by Lecturer Daisuke Kojima, combined the relatively new gene editing tools and color vision studies in zebrafish, a species with all four color-sensitive proteins. Microscope images of normal zebrafish retinas, the light-sensitive membranes lining their eyeballs and connected to their brains by their optic nerves, show a vibrant arrangement of fluorescently labeled cone cells in a distinct pattern of violet-, green-, red-, blue-, red-, green- and violet-detecting cells.

Researchers first identified three genes -- six6b, six7, and foxq2 -- common only in species with all four color vision proteins. Then, they genetically modified zebrafish to reduce the activity of those genes.

Previously, the UTokyo researchers observed that reducing expression of six6b and six7 -- either in combination or individually -- eliminated both blue and green vision in zebrafish. Zebrafish without blue and green vision had difficulty finding food, indicating the importance of full-color vision for their survival.

It was their most recently published results that allowed researchers to understand how blue and green sensitivities are distinguished by different foxq2 activity. In cone cells that will detect blue light, six6b and six7 activate foxq2. Then foxq2 activates gene expression of the blue-sensitive protein and blocks expression of green-sensitive proteins. Retinas of zebrafish lacking normal foxq2 gene expression do not have cone cells sensitive to blue light, instead packing together a shorter pattern of violet-, green-, then two red-, green- and violet-detecting cone cells.

The combination of molecular genetic studies in single species with comparative genomic studies of multiple species gives researchers additional confidence in their map of color vision regulation.

Read more at Science Daily

Learning from a 'living fossil'

As we live and breathe, ancient-looking fish known as bowfin are guarding genetic secrets that that can help unravel humanity's evolutionary history and better understand its health.

Michigan State researchers Ingo Braasch and Andrew Thompson are now decoding some of those secrets. Leading a project that included more than two dozen researchers spanning three continents, the Spartans have assembled the most complete picture of the bowfin genome to date.

"For the first time, we have what's called a chromosome-level genome assembly for the bowfin," said Braasch, an assistant professor of integrative biology in the College of Natural Science. "If you think of the genome like a book, what we had in the past was like having all the pages ripped out in pieces. Now, we've put them back in the book."

"And in order," added Thompson, a postdoctoral researcher in Braasch's lab and the first author of the new research report, published Aug. 30 in the journal Nature Genetics.

This is really important information for a few reasons, the duo said, and it starts with the bowfin being what Charles Darwin referred to as a "living fossil." The bowfin, or dogfish, looks like an ancient fish.

This doesn't mean that the bowfin hasn't evolved since ancient times, but it has evolved more slowly than most fishes. This means that the bowfin has more in common with the last ancestor shared by fish and humans, hundreds of millions of years ago, than, say, today's zebrafish.

Zebrafish -- which are modern, so-called teleost fishes -- are a notable example because they're widely used by scientists as a model to test and develop theories about human health. Having more genetic information about the bowfin helps make the zebrafish a better model.

"A lot of research on human health and disease is done on model organisms, like mice and zebrafish," Thompson said. "But once you identify important genes and the elements that regulate those genes in zebrafish, it can be hard to find their equivalents in humans. It's easier to go from zebrafish to bowfin to human."

For example, one particularly interesting gene is one that's used in developing the bowfin's gas bladder, an organ the fish uses to breathe and store air. Scientists believe that the last common ancestor shared by fish and humans had air-filled organs like these that were evolutionary predecessors to human lungs.

In their new study, the Spartan researchers could see that a certain genetic process in the bowfin's gas bladder development bore striking similarities to what's known about human lung development. A similar process is also present in the modern teleost fishes, but it's been obscured by eons of evolution.

"When you looked for the human genetic elements of this organ development in zebrafish, you couldn't find it because teleost fishes have higher rates of evolution," Thompson said. "It's there in modern fishes, but it's hidden from view until you see it in bowfin and gar."

The gar is another air-breathing fish with "living fossil" status that's studied by Braasch and his team. With both the gar and bowfin genomes, the team was able to show where these genetic elements linked to gas bladder and lung formation were hiding out in the modern teleost fishes. The ancient fish enable researchers to build a better bridge between the established modern fish model organisms and human biology.

"You don't want to base that bridge on one species," said Braasch, who added this finding also strengthens the implications for evolutionary history. "This is another piece of the puzzle that suggests the common ancestor of fish and humans had an air-filled organ and used it for breathing at the water surface, quite similar to what you see in bowfin and gar."

Although these findings have insights that are pertinent to all of humanity, Spartans might feel a special affinity for the bowfin. For starters, male fish turn their fins and throats a bright shade of green during spawning season. Also, famed biologist William Ballard of Dartmouth College studied bowfin development from eggs to larval fish at Michigan State's W.K. Kellogg Biological Station during the 1980s. This was what he called his "Odyssey of Strange Fish," and Braasch's team now uses his work to guide their genomic analyses of bowfin development.

Bowfins are native to Michigan. They could be in the Red Cedar River on MSU's campus now, according to Thompson, but they also can be quite elusive and, sometimes, very aggressive. This made collaborations essential for securing specimens. With colleagues at Nicholls State University in Louisiana, the team caught bowfins for genome sequencing. Amy McCune, a collaborator and professor at Cornell University, knew where to find bowfin eggs in upstate New York and had a graduate student gifted at securing these unique samples for investigating bowfin development.

The Spartans also had connections at other universities and institutions with experts in bowfin biology, chromosome evolution and more. All told, the team included researchers from six states as well as France, Japan and Switzerland. Back in East Lansing, graduate students Mauricio Losilla and Olivia Fitch, research technologist Brett Racicot, and Kevin Childs, director of the MSU Genomics Core facility, also contributed to the study, which comes with an interesting twist at the end.

Almost all vertebrate creatures that grow paired limbs or fins share a common gene.

"Humans use it, mice use it. All fishes that have been studied so far use it," Braasch said. "The naïve expectation would be that bowfin do, too."

But that's not what the team found. The bowfin, the "living fossil," has evolved a different way of growing its paired fins.

Read more at Science Daily

A common ancestor for cells involved in hearing and touch

The sensory cells in the inner ear and the touch receptors in the skin actually have a lot in common, according to a new study from the USC Stem Cell laboratory of Neil Segil published in the Proceedings of the National Academy of Sciences (PNAS).

"There are striking similarities in the development of two types of specialized sensory cells: the so-called 'hair cells' that receive sound vibrations in the inner ear, and the Merkel cells that sense light touch at the surface of the skin," said Segil, who is a Professor in the Department of Stem Cell Biology and Regenerative Medicine, and the USC Tina and Rick Caruso Department of Otolaryngology -- Head and Neck Surgery. "Ultimately, these developmental similarities are a legacy of shared evolutionary history. This demonstrates how the story of evolutionary developmental biology, or 'evo devo,' also extends to what we call the 'epigenetic level' -- or how genes are regulated."

In the study, PhD student Haoze (Vincent) Yu, postdoctoral scholar Litao Tao, and their colleagues identified a shared mechanism involved in gene regulation or epigenetics, that enables stem cells and progenitor cells to differentiate into more specialized hair cells and Merkel cells.

In order to begin the process of differentiation, the right parts of a stem cell's DNA need to be taken out of storage. Each human cell can store around six feet of DNA in its nucleus, because this DNA is wound around tiny "spools" made up of proteins called histones. These spools of DNA and histone protein are further packed together to form what are known are nucleosomes, which are stacked to create chromatin, which is the material that makes up the chromosomes.

When DNA is wound tightly into this storage configuration, the chromatin is closed and inaccessible to the protein ATOH1. This protein is a "master regulator" that can activate a network of differentiation genes in the DNA within the chromatin -- but not without first gaining access.

To this end, ATOH1 stimulates the production of a second protein known as POU4F3, an aptly named "pioneer factor" with the ability to venture into new frontiers by binding to closed and inaccessible chromatin. After POU4F3 blazes a trail by binding to the closed chromatin, ATOH1 is able to move forward with engaging and activating the network of genes that drives differentiation into hair cells and Merkel cells.

Strikingly, there is significant overlap in the specific regions of chromatin that POU4F3 makes accessible to ATOH1 in hair cells and Merkel cells.

"It's remarkable that these two cell types, which are both involved in sensing mechanical stimuli but derive from distinct parts of the embryo, both rely on the same ATOH1/POU4F3 mechanism in order to differentiate," said Segil. "Our study suggests that this mechanism is extremely ancient, and emerged before hair cells and Merkel cells diverged from a common evolutionary ancestor -- an 'ur-mechanoreceptor' cell type."

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Paleontologists find pterosaur precursors that fill a gap in early evolutionary history

 

Pterosaurs illustration.

Here's the original story of flight. Sorry, Wright Brothers, but this story began way before your time -- during the Age of the Dinosaurs.

Pterosaurs were the earliest reptiles to evolve powered flight, dominating the skies for 150 million years before their imminent extinction some 66 million years ago.

However, key details of their evolutionary origin and how they gained their ability to fly have remained a mystery; one that paleontologists have been trying to crack for the past 200 years. In order to learn more about their evolution and fill in a few gaps in the fossil record, it is imperative that their closest relatives are identified.

With the help of newly discovered skulls and skeletons that were unearthed in North America, Brazil, Argentina, and Madagascar in recent years, Virginia Tech researchers Sterling Nesbitt and Michelle Stocker from the Department of Geosciences in the College of Science have demonstrated that a group of "dinosaur precursors," called lagerpetids, are the closest relatives of pterosaurs.

"Where did pterosaurs come from?' is one of the most outstanding questions in reptile evolution; we think we now have an answer," said Sterling Nesbitt, who is an associate professor of geosciences and an affiliated faculty member of the Fralin Life Sciences Institute and the Global Change Center.

Their findings were published in Nature.

Fossils of Dromomeron gregorii, a species of lagerpetid, were first collected in Texas in the 1930s and 1940s, but they weren't properly identified until 2009. Unique to this excavation was a well-preserved partial skull and braincase, which, after further investigation, revealed that these reptiles had a good sense of equilibrium and were likely agile animals.

After finding more lagerpetid species in South America, paleontologists were able to create a pretty good picture of what the lagerpetids were; which were small, wingless reptiles that lived across Pangea during much of the Triassic Period, from 237 to 210 million years ago.

And in the past 15 years, five research groups from six different countries and three continents have come together to right some wrongs in the evolutionary history of the pterosaur, after the recent discovery of many lagerpetid skulls, forelimbs, and vertebrae from the United States, Brazil, Argentina, and Madagascar.

You may be asking yourself, what gave paleontologists the idea to take a closer look at lagerpetids as the closest relatives of pterosaurs? Well, paleontologists have been studying the bones of lagerpetids for quite some time, and they have noted that the length and shape of their bones were similar to the bones of pterosaurs and dinosaurs. But with the few fossils that they had before, it could only be assumed that lagerpetids were a bit closer to dinosaurs.

What really caused a shift in the family tree can be attributed to the recently collected lagerpetid skulls and forelimbs, which displayed features that were more similar to pterosaurs than dinosaurs. And with the help of new technological advances, researchers found that pterosaurs and lagerpetids share far more similarities than meet the eye.

Using micro-computed tomographic (?CT) scanning to reconstruct their brains and sensory systems within the recently discovered skulls, paleontologists determined that the brains and sensory systems of lagerpetids had many similarities with those of pterosaurs.

"CT data has been revolutionary for paleontology," said Stocker, who is an assistant professor of vertebrate paleontology and an affiliated faculty member of the Fralin Life Sciences Institute and the Global Change Center.

"Some of these delicate fossils were collected nearly 80 years ago, and rather than destructively cutting into this first known skull of Dromomeron, we were able to use this technology to carefully reconstruct the brain and inner ear anatomy of these small fossils to help determine the early relatives of pterosaurs."

One stark and mystifying finding was that the flightless lagerpetids had already evolved some of the neuroanatomical features that allowed the pterosaurs to fly, which brought forth even more information on the origin of flight.

"This study is a result of an international effort applying both traditional and cutting-edge techniques," said Martín D. Ezcurra, lead author of the study from the Museo Argentino de Ciencias Naturales in Buenos Aires, Argentina. "This is an example of how modern science and collaboration can shed light on long-standing questions that haunted paleontologists during more than a century."

Ultimately, the study will help bridge the anatomical and evolutionary gaps that exist between pterosaurs and other reptiles. The new evolutionary relationships that have emerged from this study will create a new paradigm, providing a completely new framework for the study of the origin of these reptiles and their flight capabilities.

With the little information that paleontologists had about early pterosaurs, they had often attributed extremely fast evolution for the acquisition of their unique body plan. But now that lagerpetids are deemed the precursors of pterosaurs, paleontologists can say that pterosaurs evolved at the same rate as other major reptile groups, thanks to the newly discovered "middle man."

"Flight is such a fascinating behaviour, and it evolved multiple times during Earth's history," said Serjoscha W. Evers, of the University of Fribourg. "Proposing a new hypothesis of their relationships with other extinct animals is a major step forward in understanding the origins of pterosaur flight."

Some questions still remain in this evolutionary mystery. Now that lagerpetids are the closest relatives of pterosaurs, why are they still lacking some of the key characteristics of pterosaurs, including the most outstanding of those -- wings?

"We are still missing lots of information about the earliest pterosaurs, and we still don't know how their skeletons transformed into an animal that was capable of flight," said Nesbitt.

Nesbitt, Stocker, and a team of Virginia Tech graduate and undergraduate students will continue to study animals that appeared in the Triassic Period -- a period of time in Earth history when many familiar groups of vertebrates, such as dinosaurs, turtles, mammal relatives, and amphibians, first appeared. If and when conditions are safe, they plan on going into the field to collect more fossils from the Triassic Period.

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Evolution makes the world less ragged

How does evolution impact ecological patterns? It helps smooth out the rough edges, says UConn Ecology and Evolutionary Biology Professor Mark Urban. Urban led an international team of researchers through a review of the history of ecological and evolutionary research to establish a framework to better understand evolution's impact on ecosystem patterns. The research is published as a perspective in the Proceeding of the National Academy of Sciences.

Urban says the project started years ago in the course of his field research when he encountered a trend that he had trouble explaining.

"Ever since I was a grad student I've been thinking about how evolution across landscapes happens, and then how it affects the ecology of those systems. At some point I was struggling to describe a pattern that I was seeing in the amphibian system I work in," he says.

Urban explains that historically, ecologists and evolutionary biologists have worked fairly isolated from one another. The reason is due to assumptions that evolution happens over time periods and distances that have little immediate impact on ecological systems. Ecologists and evolutionary biologists go to their own academic meetings and conferences and publish in their own journals, says Urban, and as a result, members of the fields rarely collaborate. However, Urban suspected the explanation for the puzzling pattern he was seeing relied on a merging of the disciplines.

Urban partnered with colleagues from across the globe, calling on experts from evolutionary biology and ecology, to tackle the question. The project involved an extensive review of the literature, a process that Urban says at times felt unending, yet quite fun. The process was also exciting because early on, the researchers began to notice patterns supporting their hypothesis that local adaptation alters spatial patterns.

Sean Giery, co-author and a former UConn post-doctoral researcher who's now an Eberly Research Fellow at Pennsylvania State University says, "Finding new evidence in old scientific papers was always rewarding. And collectively, these efforts show that the effects of evolution on how much communities and ecosystems vary across landscapes simply can't be overlooked."

The impetus for the undertaking, Urban says, came from a familiar figure: the salamander.

Salamander populations adapt to predators via different strategies -- from changes in body shape and size to the types and quantities of foods that they eat, which suggests a connection between evolution and ecology.

"In particular, I got excited by the evolution of foraging traits, because that could have a clear ecological impact," Urban says.

For example, Urban found that salamanders evolve to forage more in a pond with limited resources, and as a result they amplify the original ecological pattern of low resources by eating more of the already limited resources. In other cases, local adaptation of other traits dampens existing spatial patterns. Urban next turned to the existing literature to find out how general these patterns were, not just in salamanders, but in everything from bacteria to birds.

Based on a review of 500 studies, the authors found evolutionary adaptations at the local level can amplify, dampen, or even create new ecological patterns across landscapes. They identified 14 different mechanisms that affect the direction of evolution's impact, but overall the researchers found that evolution tended to dampen or smooth out variations.

"Evolution clearly plays an important role at these large scales, especially by reducing the effects of abiotic factors and biotic interactions that can limit the abundance and distribution of species. By dampening the impacts of these effects, evolution tends to reduce ecological heterogeneity across space," says Giery.

Adds Urban: "Our exhaustive review indicated that evolution usually dampens ecological spatial patterns, characterizing 85% of studies. Consequently, we do not observe the true spatial heterogeneity of nature because evolution has smoothed it out and hidden its rough edges. Evolution makes the world less ragged, which to me is a pretty cool take-home message."

An example of the smoothing can be seen again with salamanders, says Urban: "The salamanders that ate more also tended to dampen out the effect of the predator on the overall diversity of species across ponds. The prey salamander was eating different species than the predator, so in the end evolution actually maintains similar diversities of species across ponds even though, ecologically, the predator strongly decreases diversity."

Urban says these spatial patterns can be seen everywhere: "The interesting thing to me is that anyone can walk through nature and see these spatial patterns -- maybe different vegetation types. We see all of this spatial variation and we think of it as just being ecological or physical, just part of the environment and that's it. But that environmental spatial variation may be affected by the evolution of the organisms in the environment and that is what we are finding in experiments around world."

Giery says, "I'm pleased to have been a part of this project. And I'm excited to see how our efforts will influence the way people think about the role of evolution in ecological dynamics in space. This seems like one of those rare instances where a relatively simple idea is still transformative. Working on developing this idea has changed how I see and think about natural systems. I imagine our perspective will have the same impact on others."

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Tropical disease in medieval Europe revises the history of a pathogen related to syphilis

Mass burials are common remnants of the many plague outbreaks that ravaged Medieval Europe. A number of these graveyards are well documented in historical sources, but the locations of most, and the victims they contain, have been lost to the pages of time. In Vilnius, Lithuania, one such cemetery was found in a typical way: accidental discovery during a routine city construction project.

A new study published in the journal Scientific Reports details the findings of genomic analyses on these medieval skeletons, with important implications for the history of syphilis in Europe.

Just another plague pit?

"Historical information on this Vilnius graveyard is unavailable, but the burial context, along with its location outside of the medieval city limits, pointed to plague, or some other major infectious disease outbreak," comments Rimantas Jankauskas, Professor of the Faculty of Medicine, Vilnius University. "To be certain, we needed confirmation through DNA analysis."

Kirsten Bos, a group leader for Molecular Palaeopathology at the Max Planck Institute for the Science of Human History (MPI-SHH) in Jena, Germany, is frequently contacted by archaeologists requesting such analyses.

"Plague was a common disease at the time, and the information we get from all the ancient DNA work can tell us a lot about how it was spreading," says Bos, a specialist in ancient pathogen DNA recovery who led the current study.

Working in Bos's team, doctoral candidate Karen Giffin took on DNA analysis of the putative plague victims and quickly identified the pathogen's DNA in the teeth of several individuals.

"I was happy to have identified them as victims of medieval plague," says Giffin, "but we wanted to see if the new techniques we were developing in molecular detection of pathogens could allow us to learn anything more about the health of this population."

More than just plague

"The typical method for pathogen detection in archaeological bone requires that you have some idea of what you're looking for," explains Alexander Herbig, group leader of Computational Pathogenomics at the MPI-SHH. "In this case we applied a relatively new hypothesis-free DNA screening approach to search for any other pathogens we might be able to identify at the molecular level."

This process unlocked a second secret of the 15th century graveyard. One of the four plague victims, a young woman, also showed a weak signal of something that seemed related to modern syphilis.

"It was impressive to find traces of such a disease in an historical skeleton because their molecular preservation in ancient bone is known to be problematic," comments Bos.

Diseases in the syphilis family, known as the treponemal diseases, are assumed to have had a long history with humans, though their inferred history in Europe is laden with controversy. The prevailing opinion holds that the first outbreak of syphilis in Europe coincided with Charles VIII's 1495 siege of Naples, where a debilitating disease erupted amongst his infantry and quickly spread around Europe. Since this outbreak happened just after the return of Columbus and his crew from their first trans-Atlantic voyage, most discussants believe syphilis was a newcomer to Europe that originated in the New World. But support is growing for a different theory. An increasing number of specialists in bone pathology believe they have properly identified examples of pre-1493 syphilis in Europe, which has ignited on-going debates about models of its evolution.

"We were able to reconstruct an impressively well-preserved genome that, to our surprise, fell within the diversity of modern yaws," comments Giffin. Yaws is a lesser-known treponemal disease primarily of the skin that affects both humans and other primates in warm, tropical environments. "Finding it in northern Europe in the mid-15th century was unexpected," she adds.

Yaws seems much younger than we thought
Since yaws infects both humans and non-human primates, some believe it to be a very old disease, having been with humans before the massive Pleistocene migrations that spread us around the globe.

"To our surprise, the yaws genome we reconstructed was just a few genetic steps away from the ancestor of all yaws varieties known in humans and non-human primates," says Bos. "Given the age of our medieval skeletons, it seems that all strains of yaws that we know today appeared on the scene only about 1000 years ago."

"This has important implications for the history of treponemal disease in Europe," Bos adds. "We can now confirm that yaws was circulating in medieval Europe, and given its similarity to syphilis and its recent emergence, it's possible that yaws contributed in some way to the famous late 15th to 16th century outbreak that we normally ascribe only to syphilis."

One possibility is that yaws emerged in either humans or other primates in West Africa within the last millennium and made its way to Europe in the mid-15th century. European presence in West Africa increased in the 15th century, as did the forced relocations of Africans to Europe through establishment of the transatlantic slave trade. These activities would have rapidly disseminated a new and highly contagious disease such as yaws.

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