Category Archives: Transhuman News

Credit: Oliver Uberti

The tales of humanitys distant past were once revealed only by digging up ancient settlements, bones, and artifacts or by reading ancient texts, from the cuneiform clay tablets of the Hittites to the vivid chronicles of Herodotus.

In the past decade, however, a powerful new window has opened into humanitys past, in the stories written in the genes of our distant ancestors. Since 2014, the number of individuals from thousands of years ago whose DNA has been analyzed has leapt from a mere handful to more than 8,000. That has ushered in what Kristian Kristiansen, professor of archaeology at University of Gothenburg in Sweden, calls a major scientific revolution. It has created a new kind of independent evidence to answer questions in archeology that had never before been resolved, Kristiansen explains.

Indeed, the first results were quite shocking, Kristiansen says. For 50 years, scientists had assumed that our ancestors were mostly homebodies, so that recent populations in many countries were largely the descendants of those who had lived in the same general areas for thousands of years. Wrong. Beginning in 2015, ancient DNA pioneer David Reich, a Howard Hughes Medical Institute Investigator at Harvard Medical School, and others published genetic data showing that the story of humanity is actually one of vast and frequent migrations. About 5,300 years ago, Reich and others showed in detail, nomadic herders called the Yamnaya used newly invented horse-drawn carts to journey from the steppes for far eastern Europe (present-day Ukraine and western Russia) westward across Europeeven to Britainand eastward to India. As they roamed, they carried with them the seeds of the Indo-European languages spoken by billions of people around the world today. The DNA evidence was a breakthrough, showing how the languages trace the path of the migration, explains Reich.

Yet the evidence for the wandering Yamnaya raised deeper mysteries. Where did the closely related languages in ancient Anatolia (modern-day Turkey), such as Hittite, come from? And where was the origin of the parent language to Indo-European and these Anatolian languages? The leading theory was that the steppe population had travelled southeast through the Balkans into Anatolia, bringing an early version of Indo-European. Finding genetic evidence, however, was challenging, says Reich. The region is hot, and DNA does not do well in a warm environment.

But then in 2018, geneticists at the University of Copenhagen reported that theyd been able to sample the genes of a few individuals from ancient Anatolia. They found no trace of steppe ancestry, says Guus Kroonen, professor of linguistics at the University of Copenhagen and University Lecturer at the Leiden University Centre for Linguistics. That was unexpected evidence for another theorythat the Anatolian languages came not from the steppe but could rather be traced back to people who lived in the Caucasus highlands, north of the Fertile Crescent.

Now comes a far more complete and detailed answer to that question and others in a trio of papers (and cover image) in the 26 August issue of Science from Reich and a huge team of co-authors. Using advanced techniques for extracting and studying ancient DNA from bones found in the warm climate, the researchers analyzed the genes of 727 individuals across the entire Southern Arc (including modern-day Cyprus, Greece, the Balkans, Turkey, and Armenia), representing a sweeping 11,000 years of human history.

The new results demolish the previous leading theorythe idea of migrations into Anatolia from the north and westwhile providing overwhelming evidence for what the Copenhagen team had suggested. Our data show almost no DNA from the steppe in Anatolia, explains Reich. Instead, the genetic analysis points like an arrow to the Caucasus as the origin of movements that spread populations and languages both north into the steppe and west into Anatolia, he says. It also reveals that the Caucasus has been a place that has harbored a lot of diversity for a long time, says Reich, bolstering the idea that the region has been a crucible for languages and cultures.

With the DNA, we can see things, like the Anatolian influx in Rome, that that text writers might not have known about or chosen to record due to the biases of the time.

David Reich, HHMI Investigator at Harvard Medical School

Despite the large number of samples, the genetic signatures in the region dont provide absolute proof of the origins and spread of languages, linguists caution. They point out that the linguistic evidence doesnt correlate with the genetic evidence, because the reconstructed Proto-Indo-European lexicon does not reflect the predominantly farming lifestyle that was dominant in the East Mediterranean, including the Caucasus, from an early stage. Its still conceivable that a small group from the steppe might have traveled to Anatolia, bringing their language, before their genetic signal was lost as they mixed into the existing populations, says Kroonen. But the massive new evidence from Reichs team for the Caucasus origin of both Hittite (and related languages) in Anatolia and Indo-European in the steppe makes that scenario increasingly unlikely. It makes a lot of sense, and to me it looks convincing, says Kristiansen.

The new solutions to major mysteries like the origin and spread of languages is just one of the findings in Reichs three Science papers, however. The new data also are full of nuggets that fill other gaps in our stories of the past. Some 10,000-12,000 years ago, for example, the first evidence for farming appears in Anatolia. DNA extracted from those farmers shows that their genes are similar to those of contemporary people from Mesopotamia, suggesting a common ancestry. But a bit later, pottery appears in archeological sites in Anatolia for the first time. Thats when new DNA appears in the Anatolian farmers as well, a genetic signature thats more like that from farmers in the Levant (modern-day Israel and Jordan) rather than Mesopotamia. The conclusion: There is a migration associated with the arrival of pottery that is really connected to the Levant, explains Reich.

Another result sheds new light on Roman history, thousands of years after the stories of Anatolian farmers and the steppe migrations. During the heyday of the Roman Empire, Rome was a huge, diverse city. But where did most of the people and their ancestors hail from? Previous studies had shown that they were genetically different from the Italians who initially founded the city but couldnt pinpoint their origin. Now we know the answer, says Reich. The genetic mix found in Romans about 2000 years ago is almost identical to that from Anatolia, suggesting that the people in Imperial Rome were largely descended from Anatolians. Thats not something that the ancient historians mentioned in their voluminous writings. With the DNA, we can see things, like the Anatolian influx in Rome, that that text writers might not have known about or chosen to record due to the biases of the time, says Reich.

At the same time, though, some of the new evidence adds to the mysteries and complexities. The genetic data show overwhelmingly that Greece was one of many destinations for the Yamnaya nomads as they spread across Europe 5,000-4,000 years ago, bringing with them the precursor of todays Greek language. And yet the remains of the so-called Griffin Warrior, a wealthy man buried in an incredibly elaborate grave near the ancient city of Pylos in 1450 BC, show that he had nary a trace of steppe ancestry. One might think that the newer arrivals from the steppe might be more privileged and powerful than those they replaced genetically, says Reich. But here one of the wealthiest people is not associated with the big change, he says. It shows there is complexity in the relationship between ancestry and power.

More broadly, one of the key contributions of the new papers is a technical innovationa statistical framework that makes it possible for all of the published ancient DNA from many parts of the world to be compared and analyzed together. That allows us to think about people from diverse regions who are usually studied separately, Reich explains. The artifacts and settlements unearthed by archeologists often dont point to possible connections among far-flung populations, he says, but the genetics can, making it possible to tell stories that before were unknown. Thanks to the analysis of ancient DNA, we can write a much more detailed history of how human populations changed over time and place, says Reich.

###

Citation

Lazaridis I, Alpaslan-Roodenberg S et. al. The genetic history of the Southern Arc: A bridge between West Asia and Europe, Science. 2022 Aug 26. doi: 10.1126/science.abm4247

Lazaridis I, Alpaslan-Roodenberg et. al., A genetic probe into the ancient and medieval history of Southern Europe and West Asia, Science. 2022 Aug 26. doi: 10.1126/science.abq0755.

Lazaridis I, Alpaslan-Roodenberg S et. al. Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia, Science. 2022 Aug 26. doi: 10.1126/science.abq0762.

Read more here:
Ancient DNA Offers New Insights into the Origins and Spread of Languages and Populations Across the Southern Arc - Howard Hughes Medical Institute

Researchers around the world have been racing to develop new vaccines, antivirals, and other therapies to blunt SARS-CoV-2s attack, even while the virus evolves to become an endemic problem.

While existing vaccines are capable of reducing severe cases of COVID-19, at least with a recent booster, continued mutations and the difficulty of maintaining high booster rates mean that better defenses will need to be developed.

Vaccines are making a huge difference, but vaccines are not universal, and there is still a tremendous need for other approaches, Anders Nr, a professor of metabolic biology at UC Berkeley, said.

While existing vaccines are capable of reducing severe cases of COVID-19, continued mutations and the difficulty of maintaining high booster rates mean that other defenses will need to be developed.

Nr and his Cal colleagues approach uses inhalable, DNA-like molecules to throw a wrench into the coronaviruss replication machine.

A nasal spray that is cheaply available everywhere and that could prevent someone from getting infected or prevent serious disease could be immensely helpful, Nr said.

Gumming up the works: The Berkeley teams nasal spray, published in Nature Communications, uses short snippets of synthetic DNA called antisense oligonucleotides or ASOs for short.

ASOs can be programmed to glom onto specific strings of RNA blocking them from being copied or turned into proteins.

Nr has been studying the use of ASOs for over a decade, trying to figure out how to use them to affect RNA involved in conditions like type 2 diabetes, Duchenne muscular dystrophy, and fatty liver disease.

But when the pandemic hit, they set their sights on a different type of RNA virus RNA.

The SARS-CoV-2 genome is single-stranded RNA, similar to messenger RNA or microRNA, Nr said. We thought perhaps we could use these ASOs to stick onto the viral RNA and prevent it from working.

The nasal spray uses DNA-like molecules to gum up SARS-CoV-2s replication.

The hairpin bend: Working with the Innovative Genomics Institute and Berkeley researcher Sarah Stanleys lab, the team sicced hundreds of different ASOs all designed to attack different parts of the genome on SARS-CoV-2.

One target in particular proved effective: a non-coding portion of the virus RNA that forms a hairpin and seems to play a key role in replication. With an ASO stuck to its hairpin, the virus was unable to replicate.

The ASOs stopped the coronavirus from replicating in human cells in the lab, and in animal experiments, it both prevented infection, when given early, and treated COVID-19 after infection.

We showed that if you bind an ASO to this hairpin, it dissolves the hairpin, and the RNA forms a straight line instead of a bubble structure, Nr said. We think that this prevents the virus from effectively translating and replicating, and we found that it was incredibly effective at preventing viral replication in human cells.

When sprayed in the noses of mice and hamsters, the ASO protected against and treated COVID-19, but just as importantly, it did not spark an immune response of its own suggesting it likely wont cause toxic side effects in people.

The hairpin is found in all known variants of SARS-CoV-2, and the teams ASOs were shown to be effective against variants of concern, including Delta and Omicron.

A nasal spray that is cheaply available everywhere and that could prevent someone from getting infected or prevent serious disease could be immensely helpful.

Next steps: ASOs are stable and relatively cheap to produce at scale, the researchers said, making them a potential boon for fighting the virus around the world.

Theyre also a promising way to attack other RNA viruses, like influenza, RSV, and other respiratory viruses, since they can be designed to stick to any RNA genome. The team has already found an ASO which sticks to a target in SARS-1, and they have begun preliminary work on influenza.

More research will be required before human clinical trials can begin, though.

Its very clear that this virus is not going away, Nr said. We need a lot of different avenues to tackle it, and therapeutics like ours that are agnostic to the variants could play a major role.

Wed love to hear from you! If you have a comment about this article or if you have a tip for a future Freethink story, please email us at [emailprotected]

Go here to read the rest:
Synthetic DNA nasal spray could stop COVID, flu, and other viruses - Freethink

John Gurda| Milwaukee Journal Sentinel

As summer ends and we put away the beach toys, our focus shifts to more sedentary pursuits, things we can do on rainy days and in the cold calm of the approaching winter. For millions of Americans, that means genealogy. Since the 1960s, probing our roots has been one the nations most popular hobbies, and interest in the field has only grown since then, the result of a sea change in technology.

For centuries, family history was largely the province of African griots and European royalty, whose privilege depended on pedigree. The past has been radically democratized in recent years. Genealogists once had to scroll through miles of microfilm to unearth census tables, naturalization records, birth certificates, obituaries, military recordsand other rich archival ore. Now those sources are as close to the surface as the nearest computer.

But digitized vital records arent the whole story. Perhaps the most astounding development in the entire history of family history is the recent use of DNA to establish ancestry a tool that has been in popular use for little more than a decade. It turns out that each of us bears in our own cells, in the fiber of our physical being, every step in the evolution of our families and in fact of our entire species. The biological pageant of humanity is recorded in every strand of our hair and every particle of our skin. We may move freely and widely throughout the world, but we carry with us the traceable imprint of uncounted earlier generations.

More: DNA testing can share all your family secrets. Are you ready for that?

More: Could DNA tests bring home missing kids? Lack of diversity in databases hinders searches

The portal to the past is comparison. All of todays ancestry services rely on voluminous databases of DNA drawn from individuals around the world whose families have lived in one place for centuries, before the mobility revolution of the 1800s. Until fairly recently, most humans rarely ventured beyond the confines of their own valley or forest or plain, which severely limited their choices of a mate. Intermarriage was inevitable, and the result over thousands of years was a gene pool unique to each region. The descendants of those earlier generations who have remained in place carry a book of DNA that sets their locale apart from every other volume in the worlds ethnic library.

I was intrigued with genetic genealogy from the beginning, even though my own ethnic story seemed straightforward. I come from peasant stock on both sides of my family. My Norwegian ancestors tilled the stony soil north of Oslo, and my Polish forebears worked more tractable land near the Baltic Sea. Both of my grandfathers, John Johnson and John Gurda, were born in Europe (my first name was a given), and their wives were second-generation Americans of matching stock.

But physical corroboration of that story was irresistible. In 2015 I spit into a tube and sent it off with $89.95 to AncestryDNA, the company with the largest DNA reference database. The results, I must say, surprised me. The first broad strokes confirmed my family narrative: 50%Scandinavian and 42%Eastern European. But I also came up as 6%Irish. How did that happen? Who was this person wanderer or settler, lover or slave who introduced a touch of the Celt to my bloodline? A sailor washed up in Gdansk? A Dublin girl carried home by a Viking?

The revelation didnt make me feel any different. My hair wasnt curlier or thicker. My accent was the same innocuous Midwestern dialect Ive always had, without a trace of brogue. And I didnt feel either more or less interested in potatoes and cabbage. But I longed to learn more. First of all, was that Irish ancestor on my mothers side or my fathers? Equipped with only an English majors understanding of DNA and a diploma from a Catholic high school that didnt offer biology, I prevailed upon my dads sistermy last aunt or uncle by genes on either side to take the spit test. She was analyzed as 86%Eastern European, with a minor element of Scandinavian and barely a trace of Irish.

My Celtic forebear was evidently not on the Polish side, but the results, I learned, couldnt possibly be as precise as Id imagined. Each of us gets exactly half of our DNA from each parent, but the composition of each half is absolutely random, a genetic shuffle that can produce lopsided ancestry results. But there were apparently Irish genes somewhere in there.

Then, just as I was recalibrating my self-image and wondering if we should have named our sons Seamus and Declan, Ancestry sent me (at no additional charge) an update based on new information from its ever-evolving DNA database. My revised ethnic mix was 41%Swedish and Danish, 32%Norwegian, and only 18%Eastern European not even close to what my family had always assumed. Goodbye, Ireland, and, for that matter, goodbye, Poland.

Such a radical shift in results over just a few years turned on my skeptical gene. If the same DNA could have that many interpretations, perhaps the whole concept was flawed. A 2022 update slightly eased my doubts, estimating my ancestry as 43%Norwegian and 31%Eastern European, with smaller proportions of Swedish, Danishand Baltic. But its clear that describing my results as imprecise would be an understatement.

On admittedly scant evidence, I suspect that part of the problem is an inherent limitation of the process. The standard autosomal test doesnt date-stamp your DNA; different periods in the evolution of an ancestral line can be conflated and confused. Our actual migration stories disappear into the mists of time, going back into the preliterate, even prehistoric past that starts, for every one of us, in Africa.

Not everyones test results are as muddled as mine. My wife, Sonja, who has always prided herself on being a purebred Norwegian, turns out to be a purebred Norwegian. The first results from AncestryDNA pegged her as 3% Micronesian, to her amazement and amusement, but the companys updates confirmed that all of her ancestors are from Norway. The most recent estimates even correctly identified her familys counties of origin in the southwestern part of the country.

Although most of us are hoping to find our roots when we take the test, AncestryDNA has started offering, for an extra fee, information about inherited traits that have nothing to do with ancestral geographies. The company carefully avoids worrisome markers like those for cancer, depression, addiction, heart diseaseand other maladies, testing instead for more innocuous qualities. I ponied up my 20 bucks and found that Im genetically predisposed to be lousy at remembering dreams (false), a good sprinter (once upon a time), a devotee of caffeine (false), blue-eyed (true), cleft-chinned (sort of), freckled (false), wavy-haired (in days gone by), and unibrowed (false). Oh, and my urine has a distinctive smell after I eat asparagus. Hardly earth-shaking, and just as imprecise as my estimated ethnic origins.

Even if its nowhere close to definitive, DNA testing is an interesting exercise. My own results demonstrate that the road back can have as many twists and turns as the road ahead. I will never make his acquaintance, but I cherish the thought of some peasant ancestor long gone to dust, a Peder or a Janek, known in his village as a near-sighted fellow with a decent memory and a penchant for solitude or perhaps as the serious one who would rather read than plow but still liked his tankard of beer. That familiar personage is one of countless characters who reside in my familys indeterminate past, and he lives on today, however mutely, in every strand of my DNA.

John Gurda writes a column on local history for the Ideas Lab on the first Sunday of every month. Email:mail@johngurda.com

Our subscribers make this reporting possible. Please consider supporting local journalism by subscribing to the Journal Sentinel at jsonline.com/deal.

See the article here:
It may be in the genes, but DNA testing offers a bumpy ride to the past - Milwaukee Journal Sentinel

ABSTRACT breaks down mind-bending scientific research, future tech, new discoveries, and major breakthroughs.

Death is a universal fact of life, unless you're a jellyfish. As explained in a new study, the jellyfish Turritopsis dohrnii "is the only species able to rejuvenate repeatedly after sexual reproduction, becoming biologically immortal," and its DNA might hold the answer to the secret of eternal life.

T. dohrnii pulls off an amazing biological feat to cheat death. Every member of the species is an identical clone, and starts life as a polyp that becomes a mature organism called a medusa. This isn't particularly unique, but what's amazing about T. dohrnii is that if the medusas get injured, sick, or old, they don't throw in the towel. Instead, they become a "cyst" that turns back into a polyp and restarts the whole process, churning out more clones. While it might be a bit different from the idea of living forever in a vampire story, it is, strictly speaking, biological immortality. You can also call it, as scientists do, "life cycle reversal." It would be like if a person got old and turned back into a fetus, or a chicken into an egg.

In a study published on Monday in the journal PNAS by researchers at the University of Oveidas in Spain, the authors describe how they compared the DNA of T. dohrnii to another closely-related jellyfish species that is not immortal to determine what makes it special.

Specifically, they compared "genes involved in aging and DNA repair, together with the transcriptome [mRNA] analysis of life cycle reversal (LCR) of T. dohrnii," which has now "provided new insights into the molecular mechanisms underlying Turritopsis plasticity, which may contribute to the immortal phenotype of T. dohrnii," they wrote in the study.

Indeed, the researchers found several differences that they pinned as likely having an effect contributing to the jellyfish's immortality. Overall, these changes "suggest that T. dohrnii may have more efficient replicative mechanisms and repair systems" than other species, the authors write.

For example, they found more copies of POLD1 and POLA2 geneswhich encode different proteinsin T. dohrnii than in its mortal relatives, which "suggest enhanced replicative capabilities in this species," the study notes. The species also had more copies of genes governing DNA repair, and those that govern telomerase, which are enzymes that replenish the telomeres on DNA that shorten with age. This "may contribute to a reduced telomere attrition and as a consequence to an enhanced cellular plasticity," the authors write, and "may indicate that telomerase activity could be enhanced or more finely regulated in this species."

While this knowledge isn't going to let humans become "biologically immortal" like T. dohrniiand even if it could, would we want it?it is an astounding jump forward in our understanding of age and how some species defeat it entirely.

Read the rest here:
Scientists Analyzed DNA of Immortal Jellyfish to Find Secret to Eternal Life - VICE

COVID and monkeypox seem to have come out of nowhere and exploded across continents. But the phenomenon of natural selection acting on genetic variants of viruses or organisms that have an advantage in a certain place and time is ages old. The rabbits of Australia provide a powerful example of natural selection run amok, favoring a particularly robust mix of domestic and wild traits against an environmental backdrop of plenty of food and a paucity of predators.

The animals that have overrun the continent eat almost any plant, their appetites reverberating along food webs, costing an estimated $200 million a year. Over decades, interventions to control their numbers from rabbit-proof fences to intentional infections with nasty viruses to shooting have all failed. In Australia, the rabbit has survived drought, fire, flood, diseases, predators, poisons and other stratagems devised by man and remains this countrys most serious vertebrate pest, wrote Brian Coman in Tooth and Nail: The Story of the Rabbit in Australia.

Now researchers from the University of Cambridge and CIBIO Institute in Portugal have wed genetics to history to illuminate the precise source of Australias problem. Their report is in the Proceedings of the National Academy of Sciences.

The colonisation of Australia by the European rabbit is one of the most iconic and devastating biological invasions in recorded history. Here, we show that despite numerous introductions over a 70-year period, this invasion was triggered by a single release of a few animals that spread thousands of kilometres across the continent, the researchers write.

Feral rabbits once-domestic animals relocated, where novel behaviors emerge remain a problem in Australia, where they number more than 150 million. Its an interesting mammal, in terms of the relationships to us. The rabbit has, in various times and places, been a treasured pet, a commercial farm animal, a valued subject of the hunt, a major ecological force and an economic pest, wrote Coman, to which Id add a valuable model organism in the lab.

Thirteen Rascally Rabbits

The rabbit invasion of Australia began with a mixing of genomes sex among 13 animals shipped from England in 1859. But those werent the first rabbits just the first to take over.

Historical records trace the pioneer rabbits to 1788, when the First Fleet of 11 ships six convict transports, three ships of goods, and two Royal Navy vessels brought the founding European and African settlers from Portsmouth, England, to Botany Bay, New South Wales. Among the 1400 humans were five silver grey domestic bunnies. These pets were taken to Sydney, supposedly never released into the wild.

At least 90 times after that, domestic rabbits came to Australia, but the populations stayed small. Then in 1859 wild rabbits nosed into a shipment of domestics and all hell broke loose.

The animals spread 100 kilometers a year for the next half-century, munching their way through native plants and starving the indigenous herbivores and then carnivores that had evolved there over millions of years. The new genetic analysis reveals that it was specific genes that spawned the fastest colonization rate for an introduced mammal ever recorded.

What happened in and after 1859 to propel these particular wild rabbits into reproductive overdrive? DNA provides the answer. But first, more backstory.

Local lore as well as the historical record trace the origin of Australias rabbit plague to Thomas Austin, master of the Barwon Park estate Winchelsea, southwest of Melbourne.

On October 6, 1859, Thomass brother William, who lived at the family estate in Baltonsborough, Somerset, England, sent the 13 rabbits to Australia. It was a mixed bunch. Wild rabbits were by no means common round Baltonsborough. It was only with great difficulty that he managed to get six; these were half-grown specimens taken from their nests and tamed. To make up the number he bought seven grey rabbits that the villagers had kept in hutches, either as pets or to eat, recalled Williams granddaughter Joan Palmer. Eighty days later, on Christmas, two dozen rabbits arrived in Australia theyd clearly bred on the journey.

The domestic and wild rabbit genomes mixing on this particular trip from England brewed a gene combination that enabled the animals to explode in numbers once let loose into the vast new land full of food from the new pastoral practices. One such trait from the domestic camp was the colored coat that provided protection across the land, and the burgeoning rabbit population came to be called the grey blanket.

Within three years, the animals had expanded to thousands. In 1865, Austin killed 20,000 rabbits at his estate, alarmed by the extraordinary fecundity of the English rabbit. A year later, hunters bagged 14,000 more there.

Austins rabbits spread, finding plentiful food and no predators. From 1880 to 1894, they took over New South Wales, Queensland, and Western Australia. An article from the National Museum Australia provides context: It took rabbits 700 years to spread throughout Britain, but 50 years to colonize two-thirds of Australia, which is about 25 times larger.

By the late 1940s the animals numbered 600 million, despite many people eating them during the depression and war years. Robust harvests following abundant rainfall fed the rabbits, while men who could build more fences were in short supply.

DNA Analysis Reveals 5 Founding Females Echoing History

The researchers sequenced the exomes (the protein-encoding parts of the genome) of 187 rabbits. Most were wild, from Australia, Tasmania, and New Zealand, but a few were from France and Britain. The analysis included nearly 2 million gene variants.

The animals had been caught between 1865 and 2018. Theyd become pests in New Zealand and Tasmania in the decades following their introduction too. The common denominator among the Australian, New Zealand, and Tasmanian rabbits, the investigators conclude, was the arrival of a new genotype that was better adapted to the natural environment, which is arid and semi-arid.

We managed to trace the ancestry of Australias invasive population right back to the South-West of England, where Austins family collected the rabbits in 1859. Our findings show that despite the numerous introductions across Australia, it was a single batch of English rabbits that triggered this devastating biological invasion, the effects of which are still being felt today, said lead author Joel Alves.

The genetic diversity of the rabbits fell as the animals migrated away from Barwon Park and natural selection favored the gene variants that accelerated growth and fitness. In the lexicon of Darwin, fitness means reproductive success.

If an environmental change beginning in 1859 was the only force that had spurred the rabbit population explosion, such as agriculture, then several small rabbit populations would have expanded across the continent. But the petering out of pre-1859 rabbits and the new DNA evidence argue against that explanation, pointing to a single event that led to a hardy, adaptive genome.

What traits could have propelled the rabbits success? Animals introduced earlier had the hallmarks of pets: floppy ears, complex coat coloring, and tameness. But Austins rabbits also brought in a combination of traits that conferred a changed body shape that enabled the animals to withstand a much greater temperature range which enabled them to take over and eat nearly any plant. The historical record indicates that Austins rabbit shipment was the only one to include wild animals.

Even more compelling evidence comes from analysis of mitochondrial DNA, which is passed from mothers to all offspring. Remember mitochondrial Eve from 1987? She was the theoretical most recent woman from whom all living humans descend, deduced from comparing mitochondrial DNA from 147 people from 5 diverse populations. Similar analysis of rabbit mitochondrial DNA indicated 5 female rabbits having seeded the millions of invasive descendants and that matches, precisely, the historical record of Austins original 13 rabbits, which included 5 wild females.

In all my years of science writing, I cant think of a more elegant example of converging genetic and historical evidence.

What happened after Austins rabbits reached Australia was a phenomenon called allele surfing. An allele is an older term for gene variant. When the alleles conferring grey color and a svelte body came to Australia, the geographic expansion triggered a sudden amplification of the alleles conferring these traits because the characteristics were, and continue to be, so adaptive. In other words, alleles that were rare in the ancestral British population exploded under the environmental conditions in Australia.

Summed up Alves:

More than 150 years have passed since Thomas Austin asked his brother to send him some wild rabbits from their family property in England. Unbeknown to him, this request caused a cascade of events that changed forever the landscape of an entire continent and resulted in the greatest pastoral pest of the 20th century.

These findings matter because biological invasions are a major threat to global biodiversity and if you want to prevent them you need to understand what makes them succeed. Environmental change may have made Australia vulnerable to invasion, but it was the genetic makeup of a small batch of wild rabbits that ignited one of the most iconic biological invasions of all time. This serves as a reminder that the actions of just one person, or a few people, can have a devastating environmental impact.

Read more:
DNA Analysis Solves the Mystery of the Rabbit Invasion of Australia - DNA Science - PLOS

Neanderthals have served as a reflection of our own humanity since they were first discovered in 1856. What we think we know about them has been shaped and moulded to fit our cultural trends, social norms and scientific standards. They have changed from diseased specimens to primitive sub-human lumbering cousins to advanced humans.

We now know Homo neanderthalensis were very similar to ourselves and we even met them and frequently interbred. But why did they go extinct, while we survived, flourished and ended up taking over the planet?

Neanderthals evolved over 400,000 years ago, most likely from an earlier ancestor Homo heidelbergensis. They were extremely successful and spread across an area from the Mediterranean to Siberia. They were highly intelligent, with brains on average bigger than Homo sapienss.

They hunted for big game, collected plants, fungi, and seafood, controlled fire to cook, made composite tools, made clothes from animal skins, made beads from shells, and were able to carve symbols on to cave walls. They took care of their young, old and weak, created shelters for protection, lived through harsh winters and warm summers, and they buried their dead.

Neanderthals did meet our ancestors on several occasions over the course of tens of thousands of years and the two species shared the European continent for at least 14,000 years. They even mated with each other.

The most significant difference between Neanderthals and ourselves is that they went extinct about 40,000 years ago. The precise cause of their demise still eludes us, but we think it was probably the result of a combination of factors.

First the climate of the last ice age was very variable, shifting from cold to warm and back again, which put pressure on animal and plant food sources and meant Neanderthals constantly had to adapt to environmental change. Second there were never that many Neanderthals, with the overall population never exceeding the tens of thousands.

They lived in groups of five to 15 individuals, compared with Homo Sapiens that had groups of up to 150 individuals. These small isolated Neanderthal populations may have been increasingly genetically unsustainable.

Third there was competition with other predators, particularly the groups of modern humans that emerged from Africa about 60,000 years ago. We speculate that many Neanderthals may have been assimilated into the larger bands of Homo sapiens.

Neanderthals left numerous traces for us to examine tens of thousands of years later, much of which can be seen at the special exhibition we have helped curate at the Natural History Museum of Denmark. Over the past 150 years we have collected fossil bones, stone and wooden tools, found trinkets and jewellery they left behind, uncovered burials, and now mapped their genome from ancient DNA. It seems that 99.7% of Neanderthal and modern human DNA is identical and they are our closest extinct relatives.

Perhaps the most surprising fact was evidence of interbreeding that has left traces of DNA in living humans today. Many Europeans and Asians have between 1% and 4% Neanderthal DNA while African people south of the Sahara have almost zero. Ironically, with a current world population of about 8 billion people, this means that there has never been more Neanderthal DNA on Earth.

The Neanderthal genome also helps us understand more of what they looked like, as there is evidence that some Neanderthals evolved pale skin and red hair long before Homo sapiens. The many genes that are shared between Neanderthals and modern humans are linked to anything from the ability to taste bitter foods to the capacity to speak.

We have also increased our knowledge of human health. For instance, some Neanderthal DNA that might have been beneficial to humans tens of thousands of years ago now seems to cause issues when combined with a modern western lifestyle.

There are links to alcoholism, obesity, allergies, blood clotting, and depression. Recently, scientists suggested an ancient gene variant from Neanderthals might increase the risk of serious complications from contracting COVID-19.

Like the dinosaurs, the Neanderthals didnt know what was coming. The difference is that the dinosaurs disappeared suddenly following a giant meteorite hit from outer space. To the Neanderthals extinction happened gradually. They eventually lost their world, a comfortable home they had successfully occupied for hundreds of thousands of years that slowly turned against them, until existence itself was unsustainable.

In that sense, Neanderthals now serve a different purpose. We see our reflection in them. They didnt know what was happening to them and they had no choice but to continue down the road that eventually led to extinction. We on the other hand are painfully aware of our situation and the impact we have on this planet.

Human activity is changing the climate and is leading straight into a sixth mass extinction. We can reflect on the mess we have landed ourselves in and we can do something about it.

If we dont want to end up like the Neanderthals, we better get our act together and collectively work for a more sustainable future. Neanderthal extinction reminds us that we should never take our existence for granted.

Link:
Neanderthals died out 40,000 years ago, but there has never been more of their DNA on Earth - The Conversation Indonesia

The largest RNA study ever conducted in hereditary cancer analyzed more than 43,000 patients who received Ambrys +RNAinsight testing and found that 1 in 950 had an elusive clinically actionable result that would have been missed by DNA-only testing.

Combined DNA and RNA testing identified cancer risk in an additional 1 out of 79 patients compared to DNA-only testing.

ALISO VIEJO, Calif., August 29, 2022--(BUSINESS WIRE)--Ambry Genetics, a leader in clinical diagnostic testing and a subsidiary of REALM IDx, Inc., announced today the findings of a study that showed paired RNA and DNA genetic testing, conducted at the same time, detected elusive pathogenic variants in 1 of every 950 patients that were missed by DNA testing alone. The findings, published in npj Genomic Medicine, highlight the importance of combining RNA and DNA analysis in hereditary cancer testing to give clinicians and their patients the most accurate and comprehensive genetic data needed to inform patient care and achieve the best outcomes.

According to the National Library of Medicine, as of August 2017, there were approximately 75,000 genetic tests on the market, representing 10,000 unique test types. Unfortunately, many of these DNA-only tests exclude large portions of DNA such as introns, a sequence of DNA that is spliced out before an RNA molecule is translated into a protein. In addition to omitting large portions of introns, DNA-only testing lacks the functional context to determine whether a variant increases cancer risk, which can lead to inconclusive results. These limitations may prevent patients and their families from getting accurate results to inform their preventative or therapeutic care.

Concurrent RNA and DNA testing helps identify more patients at risk by determining if an uncertain result from DNA testing is normal or disease-causing, and expands the range of genetic testing to identify mutations that DNA-only testing misses.

"With our +RNAinsight test we were the first company to offer upfront paired DNA and RNA sequencing to give clinicians and their patients the most accurate and comprehensive information about their cancer risk," said Tom Schoenherr, CEO, Ambry Genetics. "This study confirms that conducting RNA and DNA testing together is critical to help identify high-risk individuals who would have been missed by DNA-only testing."

Story continues

Previously, published evidence of the value of RNA sequencing has been limited by studies with small sample sizes and enriched cohorts. This study by Ambry is the largest to examine the impact of paired DNA and RNA analysis in hereditary cancer testing. In the study, tests from 43,524 patients who underwent paired DNA-RNA genetic testing using Ambrys +RNAinsight from March 2019 through April 2020 were examined to determine if the paired sequencing detected more pathogenic variants than DNA testing alone. The analysis identified patients who had disease-causing alterations that DNA testing alone would have misinterpreted. Examining the RNA data resolved variant findings in 549 patients (1 in 79 patients) by providing the required functional data for more accurate interpretation of splicing variants. In addition, the analysis showed that 1 of every 950 patients had a pathogenic deep intronic variant that would not have appeared in DNA testing alone.

The results from the study may underestimate the total clinical impact because some of the patients families who are now eligible for genetic testing were not tested. In addition, the ripple effect created by these updated results extends to past and future patients. These downstream benefits were not quantified in the current study.

"This is the largest study of its kind to show the importance of RNA testing in predicting cancer risk," said Carrie Horton, senior clinical research specialist for oncology and first author of the study. "Its clear that RNA analysis has the potential to become a standard practice for genetic testing to improve hereditary cancer care."

A webinar, open to the media, genetic counselors, clinicians and other interested parties, will be conducted on Thursday, September 15 at 10 a.m. PT to review the study findings. Registration information is here.

Ambrys +RNAinsight was the first test to provide comprehensive gene coverage for RNA analysis to help classify and detect DNA variants associated with a variety of cancers including breast, ovarian, prostate, colon, pancreatic and uterine. +RNAinsight enables more accurate identification of patients with increased genetic risks for cancer, finds actionable results that may otherwise be missed and decreases the frequency of inconclusive results.

About Ambry Genetics

Ambry Genetics, a subsidiary of REALM IDx, Inc., translates scientific research into clinically actionable test results based upon a deep understanding of the human genome and the biology behind genetic disease. It is a leader in genetic testing that aims to improve health by understanding the relationship between genetics and disease. Its unparalleled track record of discoveries over 20 years, and growing database that continues to expand in collaboration with academic, corporate and pharmaceutical partners, means Ambry Genetics is first to market with innovative products and comprehensive analysis that enable clinicians to confidently inform patient health decisions.

View source version on businesswire.com: https://www.businesswire.com/news/home/20220829005605/en/

Contacts

Media Contact

Brad LottermanCommunications DirectorREALM IDx949-401-0465blotterman@realmidx.com

Go here to read the rest:
Ambry Genetics Publishes 43,000 Patient Study Showing Combined RNA and DNA Analysis Identifies Patients Who Are High-Risk for Cancer but Would Have...