Posts Tagged ‘DNA’

Skin colour is written in your DNA

May 14, 2018

There have been taboos in science about studying race and genetics and race and intelligence and genetics and behaviour, among many other “forbidden subjects”. It has been particularly incorrect to study race and intelligence, even though it might seem obvious that race (as a clustering of visible physical attributes) is genetic and that intelligence is partially hereditary and must also have a large genetic component. It has not been  politically correct to study the link between genetics and behaviour especially if the genetics can then be linked to race. Studies concerning the impact of crime and DNA have been deemed taboo.

image IUPUI

But some of these taboos are breaking down. A new tool can accurately use DNA markers to predict skin colour, eye colour and hair colour.

Lakshmi Chaitanya, Krystal Breslin, Sofia Zuñiga, Laura Wirken, Ewelina Pośpiech, Magdalena Kukla-Bartoszek, Titia Sijen, Peter de Knijff, Fan Liu, Wojciech Branicki, Manfred Kayser, Susan Walsh. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Science International: Genetics, 2018; 35: 123 DOI: 10.1016/j.fsigen.2018.04.004

Science Daily writes:

An international team, led by scientists from the School of Science at IUPUI and Erasmus MC University Medical Center Rotterdam in the Netherlands, has developed a novel tool to accurately predict eye, hair and skin color from human biological material — even a small DNA sample — left, for example, at a crime scene or obtained from archeological remains. This all-in-one pigmentation profile tool provides a physical description of the person in a way that has not previously been possible by generating all three pigment traits together using a freely available webtool.

The tool is designed to be used when standard forensic DNA profiling is not helpful because no reference DNA exists against which to compare the evidence sample.

The HIrisPlex-S DNA test system is capable of simultaneously predicting eye, hair and skin color phenotypes from DNA. Users, such as law enforcement officials or anthropologists, can enter relevant data using a laboratory DNA analysis tool, and the webtool will predict the pigment profile of the DNA donor.

“We have previously provided law enforcement and anthropologists with DNA tools for eye color and for combined eye and hair color, but skin color has been more difficult,” said forensic geneticist Susan Walsh from IUPUI, who co-directed the study. “Importantly, we are directly predicting actual skin color divided into five subtypes — very pale, pale, intermediate, dark and dark to black — using DNA markers from the genes that determine an individual’s skin coloration. This is not the same as identifying genetic ancestry. You might say it’s more similar to specifying a paint color in a hardware store rather than denoting race or ethnicity.

“If anyone asks an eyewitness what they saw, the majority of time they mention hair color and skin color. What we are doing is using genetics to take an objective look at what they saw,” Walsh said.

The innovative high-probability and high-accuracy complete pigmentation profile webtool is available online without charge.

The study, “HIrisPlex-S System for Eye, Hair and Skin Colour Prediction from DNA: Introduction and Forensic Developmental Validation,” is published in the peer-reviewed journal Forensic Science International: Genetics.

“With our new HIrisPlex-S system, for the first time, forensic geneticists and genetic anthropologists are able to simultaneously generate eye, hair and skin color information from a DNA sample, including DNA of the low quality and quantity often found in forensic casework and anthropological studies,” said Manfred Kayser of Erasmus MC, co-leader of the study.

 

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You are not just your genes, you are how they are expressed

December 8, 2013

As genetics advance it is becoming clear that an individual’s genes are only a part of the story. The same genes may be expressed in many different ways. And how a gene or a group of genes are expressed depends upon environmental and other triggers which are yet to be fully understood. Your genes may be your blueprint but you are what the manufacturer then produces depending upon the materials and resources available to him. In fact “blueprint” may not be the best analogy since a “blueprint” today may well even define the method of manufacture to be followed and the materials to be used. A set of genes being a “pattern” to follow may be a better representation. How the pattern is read and put into effect then determines the final product.

David Dobbs has an interesting article about how the simplistic view of the all-determining gene is changing.

… The grasshopper, he noted, sports long legs and wings, walks low and slow, and dines discreetly in solitude. The locust scurries hurriedly and hoggishly on short, crooked legs and joins hungrily with others to form swarms that darken the sky and descend to chew the farmer’s fields bare.

Related, yes, just as grasshoppers and crickets are. But even someone as insect-ignorant as I could see that the hopper and the locust were wildly different animals — different species, doubtless, possibly different genera. So I was quite amazed when Rogers told us that grasshopper and locust are in fact the same species, even the same animal, and that, as Jekyll is Hyde, one can morph into the other at alarmingly short notice. 

Not all grasshopper species, he explained (there are some 11,000), possess this morphing power; some always remain grasshoppers. But every locust was, and technically still is, a grasshopper — not a different species or subspecies, but a sort of hopper gone mad. If faced with clues that food might be scarce, such as hunger or crowding, certain grasshopper species can transform within days or even hours from their solitudinous hopper states to become part of a maniacally social locust scourge. They can also return quickly to their original form.

In the most infamous species, Schistocerca gregaria, the desert locust of Africa, the Middle East and Asia, these phase changes (as this morphing process is called) occur when crowding spurs a temporary spike in serotonin levels, which causes changes in gene expression so widespread and powerful they alter not just the hopper’s behaviour but its appearance and form. Legs and wings shrink. Subtle camo colouring turns conspicuously garish. The brain grows to manage the animal’s newly complicated social world, which includes the fact that, if a locust moves too slowly amid its million cousins, the cousins directly behind might eat it.

How does this happen? Does something happen to their genes? Yes, but — and here was the point of Rogers’s talk — their genes don’t actually change. That is, they don’t mutate or in any way alter the genetic sequence or DNA. Nothing gets rewritten. Instead, this bug’s DNA — the genetic book with millions of letters that form the instructions for building and operating a grasshopper — gets reread so that the very same book becomes the instructions for operating a locust. Even as one animal becomes the other, as Jekyll becomes Hyde, its genome stays unchanged. Same genome, same individual, but, I think we can all agree, quite a different beast. ….

…. Gene expression is what makes a gene meaningful, and it’s vital for distinguishing one species from another. We humans, for instance, share more than half our genomes with flatworms; about 60 per cent with fruit flies and chickens; 80 per cent with cows; and 99 per cent with chimps. Those genetic distinctions aren’t enough to create all our differences from those animals — what biologists call our particular phenotype, which is essentially the recognisable thing a genotype builds. This means that we are human, rather than wormlike, flylike, chickenlike, feline, bovine, or excessively simian, less because we carry different genes from those other species than because our cells read differently our remarkably similar genomes as we develop from zygote to adult. The writing varies — but hardly as much as the reading.

This raises a question: if merely reading a genome differently can change organisms so wildly, why bother rewriting the genome to evolve? How vital, really, are actual changes in the genetic code? Do we even need DNA changes to adapt to new environments? Is the importance of the gene as the driver of evolution being overplayed?

I think the idea that anything drives evolution is the wrong end of the stick. Evolution is a result of response to change. The resultant evolution is by deselection of those individuals who cannot survive the change – it is not a pro-active selection of desirable traits for some change yet to come.

So it seems to me that it is perfectly logical that a set of genes only describe and define an envelope of possibilities. It is gene expression which then – reacting to environmental or other triggers – determines the particular model from within the envelope that will materialise. But the set of genes are still critical in that they set the constraints – they define the envelope of possibilities. And no matter how creatively they are expressed, the constraints and the envelope still apply. I suspect that we have only just begun to understand the incredibly wide variation that gene expression permits with any given set of genes and how such expression can be triggered.

This variability is sufficiently wide that one twin can be a saint and the other can be a sinner but this variability is not so great that we can suddenly morph into chimpanzees.

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DNA sequenced from a 400,000 year old hominin from Spain

December 4, 2013

After developing techniques for extracting and analysing DNA from ancient (c. 40,000 years ago) Neanderthal and Denisovan specimens the Max Planck team have now taken a giant leap backwards in time in extracting and analysing an almost complete mitochondrial genome sequence of a 400,000-year-hominin. The specimen is from  Sima de los Huesos, a unique cave site in Northern Spain. The results show that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neandertals in Asia. DNA this old has until recently been retrieved only from the permafrost.

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The Sima de los Huesos hominins lived approximately 400,000 years ago during the Middle Pleistocene. © Kennis & Kennis, Madrid Scientific Films

The result itself is of great interest but it is the development of the techniques for extracting and analysing – without any contamination – and with sufficient confidence, the entire MtDNA sequence in such old specimens that is quite revolutionary. Archaeological evidence – and particularly of of such age – is subject to a great deal of subjective interpretation. But dating techniques and now DNA extraction techniques are removing much of this subjectivity and they are now providing the anchor points around which the evolutionary narrative must be built. And this narrative is now of a much more complex story of hominin expansions and admixture than has generally been thought. Ancient and presumed extinct hominin species are now showing themselves within us.

“Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neandertals and Denisovans. It is tremendously exciting” says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology.

Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Svante Pääbo. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 2013; DOI: 10.1038/nature12788

Read the whole post in 6,000 Generations

 

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180 million Neanderthals are among us

April 16, 2013

From John Hawks Weblog

Just got back proofs of a book chapter I have coming out soon with Zach Throckmorton. My favorite paragraph:

Nearly seven billion people inhabit our planet. At least six billion carry the genes of Neandertal ancestors. Inheritance from Neandertals makes up approximately 3% of the genomes of randomly chosen people outside sub-Saharan Africa today (Green et al., 2010; Reich et al., 2010). A back-of-the-envelope calculation shows if we took all of the Neandertal genes from today’s human population, we would have enough raw material to make up 180 million Neandertals.

I love that because it makes the Neandertals into the evolutionary success story they really were. They succeeded by becoming part of us.

The idea that all the various hominids who developed bipedalism have all disappeared except Anatomically Modern Humans does not appeal. I prefer to think that many of them – and not just the Neanderthals and Denisovans – live on; in us.

File:Homo-Stammbaum, Version Stringer.jpg

Possible archaic human admixture with modern Homo sapiens (Wikipedia)

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Junkies versus Non-junkies: Junk genes are not junk — or maybe they are

February 24, 2013

Myopic “scientists” bitching about each other is always interesting. Scientific theories have their own evolutionary life as some wither and die and some – gradually – become accepted and “proven”.  But it is the behaviour of the protagonists of rival theories which is entirely human. Rivalry, back-biting and childish insults in the world of evolutionary biology between junk-gene supporters and junk-gene debunkers are now getting entertaining.

Animation of the structure of a section of DNA...

from wikipedia

In September last year the ENCODE Project made a major splash when they published some 30 papers in front-line journals showing that most of the human genome dismissed earlier as as “junk genes”  did in fact show biological activity and probably had some as yet unknown function. They reported that they had transcribed some 76% of “junk” DNA and that more than 50% of all genes could be accessible to proteins which can control genetic behaviour and they concluded that over 80% of human DNA serves some purpose.

The term “non-coding” DNA, then popularised as”junk” genes, was coined in 1972. This idea  gradually gained favour and by 2003 the human genome was supposed to consist of some  26,000 protein-coding genes within a large amount of non-coding DNA where the non-coding or “junk” DNA represented some 98% of the whole genome. The results of the ENCODE project turned this idea on its head. The junk gene supporters were not amused. It has taken them a little while to circle the wagons and formulate a response to the flood of papers published in September. And the response resorts to unusually harsh language for scientific discourse. It would seem that the “junk” gene protagonists have been prodded in their vitals and feel their life-work and their livelihoods being threatened!

Junkies versus Non-junkies! The battle-lines have been drawn. They have now published an open-access diatribe: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE

The Guardian: “Everything that Encode claims is wrong. Their statistics are horrible, for a start,” the lead author of the paper, Professor Dan Graur, of Houston University, Texas, told the Observer. “This is not the work of scientists. This is the work of a group of badly trained technicians.”

Scientists are being called technicians — no less!

The junkies write:

From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it. All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genomic functionality is actively protected by selection, it will accumulate deleterious mutations and will cease to be functional. The absurd alternative, which unfortunately was adopted by ENCODE, is to assume that no deleterious mutations can ever occur in the regions they have deemed to be functional. Such an assumption is akin to claiming that a television set left on and unattended will still be in working condition after a million years because no natural events, such as rust, erosion, static electricity, and earthquakes can affect it. The convoluted rationale for the decision to discard evolutionary conservation and constraint as the arbiters of functionality put forward by a lead ENCODE author (Stamatoyannopoulos 2012) is groundless and self-serving.

Would the Junkies  – I wonder – allow 98% of their DNA – or that of their children – to be excised if it could be?

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Migration from India brought genes, tools and dingoes to Australia 4,200 years ago

January 15, 2013

It is generally assumed that the expansion of AMH from Africa (or Africarabia) reached S-E Asia around 70,000 years ago and Australia some 40,000 – 50,000 years ago. The Australian population then remained virtually isolated until quite recently. But a new genome-wide study suggests that there was migration from India to Australia some 4,200 years ago during the Holocene and that they brought stone-tools and the ancestor of the dingo with them. The study suggests that after the first migrants originally arrived in Sahul, the Australian, New Guinea and Mamanwa populations split from each other some 36,000 years ago. But by – an as yet unknown route – migrants from India arrived in Australia between 4,000 and 5,000 years ago.

Though this coincides with the height of the Indus Valley civilization in 2600 BC, I think it is more likely that any ocean-based, island-hopping migration at this time would have started – at least geographically – from S-E India rather than from the Indus Valley civilization in N-W India. But coastal navigation around the Indian coastline of that time would have been well within the capabilities of the Indus valley inhabitants. This is also the period when proto-Dravidian was the language across most of India (including in the Indus valley civilization) and it would be interesting if there are any traces in language which match this genetic data.

Genome-wide data substantiate Holocene gene flow from India to Australia, by Irina Pugach, Frederick Delfin, Ellen Gunnarsdóttir, Manfred Kayser, and Mark Stoneking, Proceedings of the National Academy of Sciences, 

http://www.pnas.org/content/early/2013/01/09/1211927110

Abstract:The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

BBC reports:

“For a long time, it has been commonly assumed that following the initial colonization, Australia was largely isolated as there wasn’t much evidence of further contact with the outside world,” explained Prof Mark Stoneking, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

“It is one of the first dispersals of modern humans – and it did seem a bit of a conundrum that people who got there this early would have been so isolated.”

To study the early origins of Australia’s population, the team compared genetic material from Aboriginal Australians with DNA from people in New Guinea, South East Asia and India.

By looking at specific locations, called genetic markers, within the DNA sequences, the researchers were able to track the genes to see who was most closely related to whom.

They found an ancient genetic association between New Guineans and Australians, which dates to about 35,000 to 45,000 years ago. At that time, Australia and New Guinea were a single land mass, called Sahul, and this tallies with the period when the first humans arrived.

But the researchers also found a substantial amount of gene flow between India and Australia.

Prof Stoneking said: “We have a pretty clear signal from looking at a large number of genetic markers from all across the genome that there was contact between India and Australia somewhere around 4,000 to 5,000 years ago.”

He said the genetic data could not establish the route the Indians would have taken to reach the continent, but it was evidence that Australia was not as cut off as had been assumed.

“Our results show that there were indeed people that made a genetic contribution to Australians from India,” Prof Stoneking explained.

The researchers also looked at fossils and other archaeological discoveries that date to this period.

They said changes in tool technology and new animals could possibly be attributed to the new migrants.

Prof Stoneking said: “We don’t have direct evidence of any connection, but it strongly suggestive that microliths, dingo and the movement of people were all connected.”

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Sasquatch (“Bigfoot”) DNA study has the makings of a hoax intended to be found out

November 27, 2012

A press release was issued on Saturday 24th November. A team of scientists can verify that their 5-year long DNA study, currently under peer-review, confirms the existence of a novel hominin hybrid species, commonly called “Bigfoot” or “Sasquatch,” living in North America.

It feels like a PR campaign to me rather than any scientific study. It has all the makings of a hoax for publicity purposes where the inevitable debunking of the hoax is expected – but where criminal fraud cannot be proved.

The critical weakness lies in the purported samples from Bigfoot which have apparently been undergoing genetic study. The “scientists” are decoupled from the authenticity or the contamination/manipulation of the samples and are protected from charges of fraud. Of course nothing has been peer-reviewed or published yet. No data has been made available either. Where the samples came from and how they were “prepared” also remains to be seen. And the “study”  has a rather obvious commercial interest (The scientist leading the study, Dr. Melba Ketchum is the founder of DNA Diagnostics). I have a strong suspicion that the objective of the hoax is simply publicity and the main objectives of the hoax will be to keep the story going for as long as “genetically”  possible. The results and data leaked must therefore also be stage-managed to be difficult to debunk or disprove so that the assertions can live as long as possible.

(more…)

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Acquired, hereditary epignetic codes could evolve faster than genetic mutations

October 3, 2011

Lamarckism  – after the French biologist Jean-Baptiste Lamarck (1744–1829) – is the idea that an organism can pass on characteristics that it has acquired during its lifetime to its offspring (soft inheritance). Publication of Charles Darwin’s theory of natural selection, and Mendelian genetics led to the general abandonment of the Lamarckian theory of evolution in biology. Despite this abandonment, interest in Lamarckism has recently increased, as several studies in the field of epigenetics have highlighted the possible inheritance of behavioral traits acquired by the previous generation.

Hard inheritance is the passing down of the constant nucleotide sequence of DNA which only changes by rare random mutation. The very slowness of this rate of mutation – and since mutations are usually not beneficial – has been a problem in explaining the variation and diversity observed in particular species. The variations observed in modern humans and which have presumably been generated within just the last 50,000 to 100, 000 years are difficult to explain by natural selection alone especially since there have only been some 5,000 generations available for this diversity to have been established.

A mechanism has long been sought for soft inheritance where environmental influences can be brought into play. Epigenetic mechanisms leave DNA sequence unaltered but can affect DNA by preventing the expression of genes.

A new paper in Science provides some further evidence that the epigenome may well be the hereditary “carrier” of environmental effects but may also cause much more rapid change than genetic mutations.

Science Daily: A “hidden” code linked to the DNA of plants allows them to develop and pass down new biological traits far more rapidly than previously thought, according to the findings of a groundbreaking study by researchers at the Salk Institute for Biological Studies. The study, published September 16 in the journal Science, provides the first evidence that an organism’s “epigenetic” code — an extra layer of biochemical instructions in DNA — can evolve more quickly than the genetic code and can strongly influence biological traits. ……..

…. Now that they have shown the extent to which spontaneous epigenetic mutations occur, the Salk researchers plan to unravel the biochemical mechanisms that allow these changes to arise and get passed from one generation to the next.

They also hope to explore how different environmental conditions, such as differences in temperature, might drive epigenetic change in the plants, or, conversely, whether epigenetic traits provide the plants with more flexibility in coping with environmental change.

“We think these epigenetic events might silence genes when they aren’t needed, then turned them back on when external conditions warrant,” Ecker said. “We won’t know how important these epimutations are until we measure the effect on plant traits, and we’re just now to the point where we can do these experiments. It’s very exciting.”

Read Article

R. J. Schmitz, M. D. Schultz, M. G. Lewsey, R. C. O’Malley, M. A. Urich, O. Libiger, N. J. Schork, J. R. Ecker.Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants. Science, 2011; DOI:10.1126/science.1212959

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