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Rapid genetic evolution linked to lighter skin pigmentation
Dezember 10, 2018
Anthropology
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Genetics
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Human Evolution
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Indigenous Cultures
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South Africa
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Populations of indigenous people in southern Africa carry a gene that causes lighter skin, and scientists have now identified the rapid evolution of this gene in recent human history.
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| San man of Namibia [Credit: Ian Beatty/WikiCommons] |
UC Davis anthropologist Brenna Henn and colleagues have shown that a gene for lighter skin spread rapidly among people in southern Africa in the last 2,000 years.
This is a "rare example of intense, ongoing adaptation in recent human history and is the first known example of adaptive gene flow at a pigmentation locus in humans," according to the paper published online in the Proceedings of the National Academy of Sciences.
The findings are based on research by multiple scientists. The primary author, Meng Lin, conducted the research as a graduate student at Stony Brook University, working with anthropologist Brenna Henn, now of the University of California, Davis, Genome Center and Department of Anthropology. Lin is now a post-doctoral researcher in genetics at the University of Southern California.
In previous work, the researchers looked at pigmentation variation in two KhoeSan populations from South Africa by performing a genome-wide association analysis in about 450 individuals. They followed up on the top associated gene, SLC24A5, by simulating population histories with and without positive selection. The DNA and pigmentation sampling took place in the Northern Cape of South Africa in the southern Kalahari Desert and Richtersveld regions.
Gene plays a role in lighter skin pigmentation
Individuals who carry two copies of the lighter pigmentation gene are 14 percent lighter-skinned than the population average, the researchers said. The gene SLC24A5 plays a key role in the genetic basis of light skin pigmentation.
While light skin is often associated with European ancestry, even in South Africa, the present-day Khoekhoe and San did not experience enough recent migration to account for the frequency of the gene. Rather, strong positive selection during the past 2,000 years was the only way to explain the current distribution. The gene, which is also present in people from the Near East and eastern Africa, was probably initially brought into the region by only a small number of individuals.
The actual source of the positive selection is not clear. The researchers theorize that a shift from consuming vitamin D-rich marine animals to consuming pasture animals, or a reduction in exposure to ultraviolent rays, might have changed skin pigmentation over time.
"While the biological cause of the selective event merits further investigation, we have demonstrated an unusual rapid case of selection for lighter skin pigmentation based on a recently introduced allele less that 2,000 years ago, the first case of pigmentation adaptation from migration in humans," the paper concludes.
Author: Karen Nikos-Rose | Source: UC Davis [December 10, 2018]
South African skeleton shows humans learnt to walk upright in the trees
Dezember 10, 2018
Anthropology
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Fossils
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Human Evolution
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South Africa
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Ticker
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The analysis of the world’s most complete skeleton of an early human ancestor, conducted by a research collaboration involving the University of Liverpool, offers conclusive evidence that human ancestors became efficient upright walkers while they were still substantially tree dwelling animals.
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| Professor Ronald Clarke with Little Foot [Credit: University of Liverpool] |
Limbs intact
The over 90% complete skeleton of an old female, much more than twice as complete as the famous Lucy, and considerably older as well, Little Foot is a member of the genus Australopithecus, a widespread and varied genus of hominins to which Lucy belonged, and which was an early precursor to modern-day Homo sapiens which appeared roughly 300,000 years ago. Little Foot is the first fossil of Australopithecus ever to have been discovered with its limbs intact.
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| Little Foot’s fossil bones [Credit: Patrick Landmann/Science Photo Library] |
Important finding
As part of the study, which has been reported in Nature Science, Professor Robin Crompton, Honorary University of Liverpool Research Associate in Musculoskeletal Biology, and his colleagues analysed how she would have walked.
Professor Crompton, states: “This hominin, for the first time in the fossil record, had longer lower limbs than upper limbs, like ourselves. This is an important finding, as the slightly older hominin Ardipithecus, which came before Australopithecus, had longer arms than legs – more like other great apes such as the gorilla.
“That means she was being selected for long stride length in bipedalism. Moreover, unlike Lucy, ‘Littlefoot’ had a hip joint like our own, able to transmit large forces from the trunk to the leg and vice versa. Although Little Foot’s legs were longer than her arms, they had not yet achieved the great relative leg length found in humans. Thus, she would not have been as good at carrying objects as we are. However, she would have been much better at climbing trees than modern humans.
“It is most likely that she would have resided in an area that was a mix of tropical rainforest, broken woodland and grassland, through which she would roam around. She would have lived primarily on forest fruits and leaves”
Source: University of Liverpool [December 10, 2018]
Researchers discover information about a gene that helps define us as humans
Dezember 06, 2018
Biology
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Evolution
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Genetics
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Human Evolution
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Neuroscience
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University of Otago researchers have discovered information about a gene that sets primates—great apes and humans—apart from other mammals, through the study of a rare developmental brain disorder.
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| Brain organoids, or "mini-brains" growing in culture [Credit: Dr Adam O'Neill] |
"Broadly speaking, this gene can be thought of as one of the genetic factors that make us human in a neurological sense," Dr. O'Neill who now works in the Department of Physiological Genomics at Ludwig Maximilian Universität in Munich, Germany, explains.
Professor Robertson says the research, just published in international journal Cell Reports, aimed to address the idea that there must be genes that humans have that have made our brains bigger and better functioning in some respects than other animals. However, that increased complexity could come at a cost, potentially predisposing humans to the development of a whole suite of neurological or psychiatric conditions.
"Such genes have been hard to find, but using an approach where we studied children with a certain brain malformation called periventricular nodular heterotopia, we found a 'damaged' genomic element in a child that had the attributes of such a primate specific genetic factor," he explains. In this particular condition a subset of neurons in the developing brain fail to take up their correct position resulting in a variety of symptoms including epilepsy and delayed development.
Dr. O'Neill and research collaborators from Max Planck Institute of Psychiatry, Germany, then set forth to test the point that the gene drives aspects of brain development that are unique to primates. Some amazing data was found using a novel approach through studying human "mini-brains" in culture. It is now possible to take a skin cell and transform it using a set of genetic tricks, so that it can be triggered to form a tiny brain-like structure in culture in the lab.
Their results showed that the particular genetic change that disabled a component of this gene (PLEKHG6) altered its ability to support the growth and proliferation of specialised stem cells in the developing brain. In addition, some of these cells also failed to migrate to their correct position in the growing "mini-brain" during the first few weeks of brain development.
Professor Robertson says it has been known for a while that these stem cells behave differently between primates/humans and other animals, but understanding what genes regulate these differences has been a mystery.
"Adam's achievement has been to show that this particular component of the PLEKHG6 gene is one such regulator that humans have 'acquired' very recently in their evolution to make their brains 'exceptional'."
Dr. O'Neill says there are very few genetic elements that are primate specific in our genome, so this discovery adds to a very short list of genetic factors that, at least in one sense, make us human.
"Such an understanding positions us to better understand how a brain builds itself- knowledge that will add to our ability to design strategies to repair the damaged brain, especially early in infancy where there are still lots of stem cells around," Dr. O'Neill says.
The work also helps provide more information about the list of genes that are altered to cause this particular type of brain malformation.
"Personally, I also think it does underscore how it is very subtle nuanced differences that separate us from other animals. Our anthropocentrism could be a whole lot more humble," Dr. O'Neill says.
Source: University of Otago [December 06, 2018]
Life has a new ingredient
Our prehistoric Earth, bombarded with asteroids and lightening, rife with bubbling geothermal pools, may not seem hospitable today. But somewhere in the chemical chaos of our early planet, life did form. How? For decades, scientists have attempted to create miniature replicas of infant Earth in the lab. There, they hunt for the primordial ingredients that created the essential building blocks for life.
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| Somewhere in the hostile environment of early Earth, life was born [Credit: Harvard University] |
Today, much of the origin-of-life research focuses on one specific building block: RNA. While some scientists believe that life formed from simpler molecules and only later evolved RNA, others look for evidence to prove (or disprove) that RNA formed first. A complex but versatile molecule, RNA stores and transmits genetic information and helps synthesize proteins, making it a capable candidate for the backbone of the first cells.
To verify this "RNA World Hypothesis," researchers face two challenges. First, they need to identify which ingredients reacted to create RNA's four nucleotides--adenine, guanine, cytosine, and uracil (A, G, C, and U). And, second, they need to determine how RNA stored and copied genetic information in order to replicate itself.
So far, scientists have made significant progress finding precursors to C and U. But A and G remain elusive. Now, in a paper published in the Proceedings of the National Academy of Sciences, Jack W. Szostak, Professor of Chemistry and Chemical Biology at Harvard University, along with first-author and graduate student Seohyun (Chris) Kim suggest that RNA could have started with a different set of nucleotide bases. In place of guanine, RNA could have relied on a surrogate--inosine.
"Our study suggests that the earliest forms of life (with A, U, C, and I) may have arisen from a different set of nucleobases than those found in modern life (A, U, C, and G)," said Kim. How did he and his team arrive at this conclusion? Lab attempts to craft A and G, purine-based nucleotides, produced too many undesired side products. Recently, however, researchers discovered a way to make versions of adenosine and inosine--8-oxo-adenosine and 8-oxo-inosine--from materials available on primeval Earth. So, Kim and his colleagues set out to investigate whether RNA constructed with these analogs could replicate efficiently.
But, the substitutes failed to perform. Like a cake baked with honey instead of sugar, the final product may look and taste similar, but it doesn't function as well. The honey-cake burns and drowns in liquid. The 8-oxo-purine RNA still performs, but it loses both the speed and accuracy needed to copy itself. If it replicates too slowly, it falls apart before completing the process. If it makes too many errors, it cannot serve as a faithful tool for propagation and evolution.
Despite their inadequate performance, the 8-oxo-purines brought an unexpected surprise. As part of the test, the team compared 8-oxo-inosine's abilities against a control, inosine. Unlike its 8-oxo counterpart, inosine enabled RNA to replicate with high speed and few errors. It "turns out to exhibit reasonable rates and fidelities in RNA copying reactions," the team concluded. "We propose that inosine could have served as a surrogate for guanosine in the early emergence of life."
Szostak and Kim's discovery could help substantiate the RNA world hypothesis. In time, their work might confirm RNA's primary role in our origin story. Or, scientists might find that early Earth offered multiple paths for life to grow. Eventually, armed with this knowledge, scientists could identify other planets that have the essential ingredients and determine whether we share this universe or are, indeed, alone.
Source: Harvard University [December 03, 2018]
The hominins of Sima de los Huesos are drawing ever closer to the Neanderthals
Dezember 01, 2018
Anthropology
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Croatia
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Early Humans
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Fossils
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Human Evolution
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Spain
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The Dental Anthropology Group of the Centro Nacional de Investigación sobre la Evolución Humana (CENIEH) has just published a paper on dental histology in the journal Comptes Rendus PALEVOL, in which a comparison is made for the first time between the sample from the Sima de los Huesos site, in Atapuerca (Burgos), and dental samples from the Neanderthal site of Krapina, in Croatia, as well as with different modern human populations.
“The teeth from Sima de los Huesos exhibit large coronal and root dentine dimensions, as well as thin enamel. This histological pattern has traditionally been considered a distinctive trait of the Neanderthals, and it has allowed them to be distinguished both from other groups and from modern humans”, according to Cecilia García Campos, lead author of the paper.
Further, the results of this study might support an early appearance of this highly characteristic dental trait, which had been observed as early as 800,000 years ago in Homo antecessor, and maintained in later groups during the Middle Pleistocene.
The fossils found at Sima de los Huesos were initially considered to belong to the taxon Homo heidelbergensis, a species which populated Europe before the Neanderthals, so named from the mandible found in the locality of Heidelberg (Germany).
Nevertheless, a study led by Juan Luis Arsuaga, Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos de Madrid, published in 2014 in the journal Science, raised doubts about this assignment, and suggested removing the population at Sima from this taxon because of its evident similarities to Homo neanderthalensis.
Later, two genetic studies of Sima de los Huesos, published in the journal Nature in 2014 and 2016, underpinned this decision by showing that these hominins belonged to the Neanderthal evolutionary lineage because of their close relationship to the ancestors of the Neanderthals.
“The dental histology results obtained for the individuals at la Sima de los Huesos support the close relationship there must have been between the Middle Pleistocene hominins at Atapuerca and the later Neanderthal groups living in Europe”, adds García Campos.
Source: CENIEH - Centro Nacional de Investigación sobre la Evolución Humana [December 01, 2018]
A bastard seal from the past reveals the potential for human hybrids
Almost ninety years ago on a freezing January morning, the keepers of the Stockholm Zoo in Sweden discovered a dead seal pup in their seal pond. The pup was immediately recognized as a bastard; a hybrid between species that should not interbreed. Only two grey seal males and one ringed seal female, species belonging to different mammalian genera, were housed in the pond. The hybrid appeared to carry a mixture of features of both the parent species.
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| Credit: Jukka Jernvall |
They also examined new genomic data from wild Baltic Sea grey and ringed seals. By comparing these genomic sequences with that of the Saimaa ringed seal, it was possible to examine whether the grey and the ringed seals could have interbred also in the wild.
Just like has been found to be the case between many mammalian species, including early humans, the analyses revealed genetic traces of hybridization between the seal species in the Baltic.
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| The seal hybrid from 1929 (right) carries a mixture of features of both the parent species, Baltic Sea grey and ringed seal [Credit: Jukka Jernvall] |
Compared to Neanderthals and modern humans, grey and ringed seals are genetically and dentally at least twice as different, suggesting that there may be more fossil human hybrids to be discovered. The analyses also revealed that landlocked species, such as the Saimaa ringed seals found only in Lake Saimaa, can be genetically quite distinct as they have had no mates other than their own kin.
The study is published in Royal Society Open Science.
Source: University of Helsinki [November 30, 2018]
Oldest-known ancestor of modern primates may have come from North America, not Asia
About 56 million years ago, on an Earth so warm that palm trees graced the Arctic Circle, a mouse-sized primate known as Teilhardina first curled its fingers around a branch.
Teilhardina species quickly spread across the forests of Asia, Europe and North America, a range unparalleled by all other primates except humans. But where did its journey begin?
New research shows that Teilhardina brandti, a species found in Wyoming, is as old or older than its Asian and European relatives, upending the prevailing hypothesis that Teilhardina first appeared in China. Teilhardina's origins, however, remain a riddle.
"The scientific conclusion is 'We just don't know,'" said Paul Morse, the study's lead author and a recent University of Florida doctoral graduate. "While the fossils we've found potentially overturn past hypotheses of where Teilhardina came from and where it migrated, they definitely don't offer a clearer scenario."
What is clear, Morse said, is that T. brandti had a wide variety of features, some of which are as primitive as those found in Teilhardina asiatica, its Asian cousin, previously thought to be the oldest species in the genus.
To make this determination, Morse studied 163 teeth and jaws in the most comprehensive analysis of T. brandti to date.
Teeth contain a treasure-trove of information and often preserve better than bone, thanks to their tough enamel. They can reveal clues about an animal's evolutionary past, its size, diet and age as an individual and in geological time.
"Identifying differences between primate teeth is not so different from a biker recognizing that a Harley is different from a scooter or an art critic evaluating whether an image was created by Picasso or Banksy," he said. "In detail, they are very different from each other in specific, predictable ways."
While Teilhardina bones are very rare in the fossil record, its teeth are more plentiful - if you know how to find them. Bloch's team of paleontologists, Morse included, have spent years combing the surface of Wyoming's Bighorn Basin on hands and knees and then packing out 50-pound bags of soil to a river to screen wash. The remaining bits of bones and teeth - which can be smaller than a flea - are examined under a microscope back at the museum.
This painstaking search has built up the dental record of T. brandti from a single molar - used to first describe the species in 1993 - to hundreds of teeth, providing a broad look at the primate's population-level variation.
Still, Morse and Bloch were unprepared for the peculiar variation exhibited by specimen UF 333700, a jagged piece of jaw with T. brandti teeth.
"Jon and I started arguing about the alveoli" - empty tooth sockets - "and how they didn't look right at all," said Morse, now a postdoctoral researcher at Duke University. "By the end of the day, we realized that specimen completely overturned both the species definition of T. asiatica and part of the rationale for why it is the oldest Teilhardina species."
Studies based on a small number of teeth simply missed the diversity in Teilhardina's physical characteristics, Morse said.
"There's likely a tremendous amount of variation in the fossil record, but it's extremely difficult to capture and measure when you have a small sample size," he said. "That's one of the reasons collecting additional fossils is so important."
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| Teilhardina americana, whose jaw is pictured here, has been reclassified as a new genus, Bownonomys, as a result of Morse’s analysis [Credit: Florida Museum/Zach Randall & Rose Roberts] |
But the precise ages of Teilhardina species are still impossible to pinpoint and may remain that way.
Teilhardina appeared during the geological equivalent of a flash in the pan, a brief 200,000-year period known as the Paleocene-Eocene Thermal Maximum, or PETM. This era was characterized by a massive injection of carbon into the Earth's atmosphere, which sent global temperatures soaring. Sea levels surged by 220 feet, ecosystems were overhauled and the waters at the North Pole warmed to 74 degrees.
Scientists can use the distinct carbon signature of the PETM to locate this period in the rock record, and carbon isotopes in teeth can also be used to identify fossil animals from the era.
But among Teilhardina fossil sites across the globe, only Wyoming has the uninterrupted, neatly demarcated layers of rock that allow paleontologists to hone in on more precise dates.
"The humblest statement would be to say that these species are essentially equivalent in age," Bloch said. "Determining which came earlier in the PETM probably surpasses the level of resolution we have in the rock record. But what we can say is that the only place where you can really establish where Teilhardina appears in this climate event with confidence is in the Bighorn Basin."
As the Earth warmed, plants and animals expanded their ranges northward, returning south as temperatures cooled at the end of the PETM.
"This dance of plants and animals with climate change happened over vast landscapes, with forests moving from the Gulf Coast to the Rocky Mountains in just a few thousand years," Bloch said.
Teilhardina likely tracked the shifts in its forest habitats across the land bridges that then connected North America, Greenland and Eurasia, he said.
"Teilhardina is not throwing its bag over its shoulder and walking," he said. "Its range is shifting from one generation to the next. Over 1,000 years, you get a lot of movement, and over 2,000-3,000 years, you could easily cover continental distances."
While it was well-suited to Earth's hothouse environment, Teilhardina disappeared with the PETM, replaced by new and physically distinct primates. It's a sobering reminder of what can happen to species - including humans - during periods of swift climatic changes, Bloch said.
"A changing planet has dramatic effects on biology, ecosystems and evolution. It's part of the process that has produced the diversity of life we see today and mass extinctions of life that have happened periodically in Earth's history," Bloch said. "One of the unexpected results of global warming 56 million years ago is that it marks the origin of the group that ultimately led to us. How we will fare under future warming scenarios is less certain."
The findings were published in the Journal of Human Evolution.
Source: Florida Museum of Natural History [November 29, 2018]
Study shows mitochondrial DNA can be passed through fathers – what does this mean for genetics?
Some things you learn in school turn out not to be true, for example that there are just five senses or three states of matter. Now cutting-edge research has added to the list by proving the mitochondria (the power sources in our cells) comes from both our parents and not – as biology students are taught – just from our mothers.
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| Mitochondria are tiny, free-floating organelles inside cells [Credit: Northwestern University] |
Mitochondria convert the sugars, fats and proteins that we eat into the molecules our cells use to power themselves. So when they go wrong, the result is often catastrophic, resulting in lifelong problems or even the death of an affected baby in the womb.
MELAS syndrome, for example, begins in early childhood and results in seizures and dementia. Kearns-Sayre syndrome causes problems with sight and hearing, potentially leaving the sufferer blind and deaf.
Most of a cell's DNA is contained in its nucleus but mitochondria sit separately inside the cell and have their own DNA. This is because mitochondria are thought to have started as separate organisms, which entered early cells about 1.45 billion years ago and never left. They reproduce themselves and move from one generation to another by "hitching a lift" in the egg.
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| Mitochondria are the power sources of a cell [Credit: Sebastian Kaulitzk/Shutterstock] |
There's a chance that previous research may have also found examples of mitochondria being passed on from fathers but that these results were discounted and assumed to be the result of sample contamination. But with ever-increasing technological advances, cheaper and more in-depth DNA analysis is possible. So it's likely that more and more cases will now be reported.
This work could affect scientists studying the movement of humans around the planet. Human mitochondrial DNA tends to alter very little over time because even tiny changes are often fatal so aren't passed on to future generations. This means a person's mitochondrial DNA is likely to be very similar to that of their distant ancestors and other people from their ethnic group.
So by studying mitochondrial DNA in different populations, scientists have also been able to follow how these groups have moved around the world and even to identify a potential common female ancestor for all humans, known as "mitochondrial Eve". All of this work has, however, been based on the "fact" that mitochondria pass down the female line only, something we now know to be wrong.
The most significant implications of these findings are staggering, because a better understanding of how mitochondria are passed on gives us a much better chance of developing treatments for mitochondrial disorders. It may even be possible to encourage properly functioning mitochondria to multiply inside a fertilised egg at the expense of the broken ones.
Any treatment would likely be controversial, because it would involve influencing someone's DNA in a way that would be inherited by subsequent generations. But the only other current treatment is equally controversial and involves inserting the nucleus from a fertilised egg into a donor egg containing normal mitochondria. This is often described as producing "three-parent babies" and is not permitted in most countries, although the first such baby was born in April 2016. So manipulating the parent's mitochondria instead may be seen as more preferable.
When it comes to our use of mitochondrial DNA to study human evolution and migration, the rarity of the cases identified by the new study means it won't significantly impact our understanding in this area. But if further research suggests that the inheritance of fathers' mitochondrial DNA is more common, our whole understanding of human migration may need to be adjusted.
Author: Michael J Porter | Source: The Conversation [November 29, 2018]
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