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Older Dads have sicker children

February 27, 2014

There is – it seems – an optimal child bearing age for fathers as well as mothers. Older fathers may be richer and more able to support a child but there is an increased risk to the health of their children.

A study by Indiana University, in the US, and Sweden’s Karolinska Institute is the largest and one of the best designed studies on the issue and suggests that mutated sperm with older fathers are the cause.

Seems very plausible.

Brian M. D’Onofrio, Martin E. Rickert, Emma Frans, Ralf Kuja-Halkola, Catarina Almqvist, Arvid Sjölander, Henrik Larsson and Paul Lichtenstein Paternal Age at Childbearing and Offspring Psychiatric and Academic Morbidity, JAMA Psychiatry, doi:10.1001/jamapsychiatry.2013.4525

BBC reports: 

A wide range of disorders and problems in school-age children have been linked to delayed fatherhood in a major study involving millions of people.

Increased rates of autism, attention deficit hyperactivity disorder (ADHD), bipolar disorder, schizophrenia, suicide attempts and substance abuse problems were all reported. …….

…. The researchers looked at 2.6 million people and at the difference between siblings born to the same father as it accounts for differences in upbringing between families.

Comparing children of a 45-year-old dad to those of a 24-year-old father it indicated:

  • autism was more than three times as likely
  • a 13-fold increased risk of ADHD
  • double the risk of a psychotic disorder
  • 25 times more likely to have bipolar disorder
  • 2.5 times more likely to have suicidal behaviour or problems with drugs
  • lower scores at school

There was no starting point after which the risk started to increase, rather any increase in age had an associated increase in risk.

….. One of the researchers, Dr Brian D’Onofrio, said he was shocked by the findings, which suggested a higher risk than previously estimated. He told the BBC: “The implications of the study is that delaying childbearing is also associated with increased risk for psychiatric and academic problems in the offspring. The study adds to a growing body of research, that suggests families, doctors, and society as a whole must consider both the pros and cons of delaying childbearing.”

The social trend for both parents to have children later in life thus seems to have repercussions for the children. Though the risk may be small it could be said that this a social trend which weakens the health and reduces the well-being of succeeding generations. The demographic effect is that the incidence of psychoses will increase. While having children later may allow a maximisation of the economic contributions of the parents to society, it could also lead to increased medical costs for the affected children in the following generations. Genetic screening and abortion could of course mitigate some of the long term consequences for the evolution of humans.

It could be that we are moving towards greater promiscuity during the “best” child-bearing years but without the production of children due to the availability of contraception. Child bearing itself is then postponed to a more economically suitable time of life for the parents, but a less than optimal time for the health of the children so conceived. Apart from genetic screening of foetuses and abortion of some there does not seem to be a “natural” self-correcting mechanism for this social trend.

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The Black Death altered European genes

February 25, 2014

A fascinating study and further support for my view that evolution is not about survival of the fittest but is about the deselection of the weakest.

Reblogged from Science magazine:

The Black Death didn’t just wipe out millions of Europeans during the 14th century. It left a mark on the human genome, favoring those who carried certain immune system genes, according to a new study. Those changes may help explain why Europeans respond differently from other people to some diseases and have different susceptibilities to autoimmune disorders.

Geneticists know that human populations evolve in the face of disease. Certain versions of our genes help us fight infections better than others, and people who carry those genes tend to have more children than those who don’t. So the beneficial genetic versions persist, while other versions tend to disappear as those carrying them die. This weeding-out of all but the best genes is called positive selection. But researchers have trouble pinpointing positively selected genes in humans, as many genes vary from one individual to the next.

Enter Mihai Netea, an immunologist at Radboud University Nijmegen Medical Centre in the Netherlands. He realized that in his home country, Romania, the existence of two very distinct ethnic groups provided an opportunity to see the hand of natural selection in the human genome. A thousand years ago, the Rroma people—commonly known as gypsies—migrated into Europe from north India. But they intermarried little with European Romanians and thus have very distinct genetic backgrounds. Yet, by living in the same place, both of these groups experienced the same conditions, including the Black Plague, which did not reach northern India. So the researchers sought genes favored by natural selection by seeking similarities in the Rroma and European Romanians that are not found in North Indians.

Celebrating differences. The migration of gypsies from India 1000 years ago (see map) set the stage for a telling study about how diseases can influence the genome.

Celebrating differences. The migration of gypsies from India 1000 years ago (see map) set the stage for a telling study about how diseases can influence the genome.

Netea; evolutionary biologist Jaume Bertranpetit of Pompeu Fabra University in Barcelona, Spain; and their colleagues looked for differences at more than 196,000 places in the genomes of 100 Romanians of European descent and 100 Rroma. For comparison, the researchers also cataloged these differences in 500 individuals who lived in northwestern India, where the Rroma came from. Then they analyzed which genes had changed the most to see which were most favored by selection.

Genetically, the Rroma are still quite similar to the northwestern Indians, even though they have lived side by side with the Romanians for a millennium, the team found. But there were 20 genes in the Rroma and the Romanians that had changes that were not seen in the Indians’ versions of those genes, Netea and his colleagues report online today in the Proceedings of the National Academy of Sciences. These genes “were positively selected for in the Romanians and in the gypsies but not in the Indians,” Netea explains. “It’s a very strong signal.”

Those genes included one for skin pigmentation, one involved in inflammation, and one associated with susceptibility to autoimmune diseases such as rheumatoid arthritis. But the ones Netea and Bertranpetit were most excited about were a cluster of three immune system genes found on chromosome 4. These genes code for toll-like receptors, proteins which latch on to harmful bacteria in the body and launch a defensive response. “We knew they must be important for host defense,” Netea says.

What events in history might have favored these versions of the genes in gypsies and Romanians, but not in Indians? Netea and his colleagues tested the ability of the toll-like receptors to react to Yersinia pestis, the bacterium that caused the Black Death. They found that the strength of the immune response varied depending on the exact sequence of the toll-like receptor genes.

Netea and Bertranpetit propose that the Rroma and European Romanians came to have the same versions of these immune system genes because of the evolutionary pressure exerted byY. pestis. Other Europeans, whose ancestors also faced and survived the Black Death, carried similar changes in the toll-like receptor genes. But people from China and Africa—two other places the Black Death did not reach—did not have these changes. (There have been multiple plagues throughout history around the world, but none have been so deadly as the Black Death, which killed an estimated one in every four Europeans, and so exerted very strong selection.) The similarities in the other genes were likely caused by other conditions experienced by Rroma and Europeans, but not Indians.

“The use of two populations living in the same geographic area is very clever,” says human population geneticist Oscar Lao of Erasmus MC in Rotterdam, the Netherlands, who was not involved in the study. “This experimental evidence is very important,” he adds. It shows that the Black Death bacterium does indeed interact with the proteins coded for by the genes favored by natural selection. “That should be the goal for all those type of analyses.”

“It’s a nice hypothesis that they are putting forward,” agrees Lluis Quintana-Murci, a human population geneticist at the Pasteur Institute in Paris who was not involved in the study. The genetic changes may have modern-day effects. “The presence of these particular versions of these genes may give the evolutionary basis for why certain populations are more at risk” for certain types of diseases, says Douglas Golenbock, an immunologist at the University of Massachusetts Medical School in Worcester. “The side effect seems to be that the Europeans have a more proinflammatory immune system than those who have never experienced Black Death.”

However, Lao and Quintana-Murci wonder if the convergence in these genes might be explained another way. It’s possible that these favorable versions were introduced into the Rroma by interbreeding between the Rroma and the Romanians, they suggest. Additional sequencing of the converged genetic regions should answer this question, Quintana-Murci says. It’s also important to check how these toll-like receptors respond to other deadly bacteria to see if other diseases might have been the cause of the changes. That will likely happen, Quintana-Murci adds. “This will inspire other labs to see if other bacterial infections could also explain the [selection].”

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Posted in Disease, Evolution, Genetics | 1 Comment »

Evolution is not – and never has been – the “survival of the fittest”

February 15, 2014

I was listening to a Professor expounding on evolution on the radio and found his glib assertions about the “survival of the fittest” both irritating and lightweight. (A person who talks down to his audience or who is incapable of explaining his theses to a lay audience should never – I think – be allowed to become a “Professor”).

Evolution does not lead to the excellence of survival traits.

While the individuals of any species best fitted to survival will likely survive, they are not the only individuals to survive. All those not weak enough to perish will also survive. And if these individuals – who only just clear the survival stakes – are adept (or lucky) in the reproduction competition then it is their genes which are carried forward. And the resultant genes carried forward we call “evolution”.

Evolution is only the result of survival x reproduction. As the environment around the individual changes (climate, competition…), the traits that will permit survival will also change. If a species has a wide variety of traits available among its individuals then it is more likely that some individuals will survive in the changing conditions. If this variability of the available traits is insufficient to cope with the magnitude of the change that species will become extinct as all its individuals perish.

Those individuals who succeed best in the “fitness for survival” stakes are not necessarily those who reproduce most. And in the reproduction stakes it is the number of offspring that counts. As genetic studies are now showing the leading lion in a pride is not always the sole male producing offspring. Sneaky young lions from outside the pride and some of the lionesses who have roving eyes often succeed in cuckolding the dominant male. Even birds who were presumed to mate for life apparently have little flings on the side from time to time. Birds of Paradise who have the showiest and most colourful displays are not necessarily the strongest or the fastest but they are the most expert at getting their way with their ladies. The traits needed for individual survival are not necessarily those most suited to successful reproduction (number of offspring).

Survival is not of the “fittest” but of all those not weak enough to perish.

Evolution is thus controlled first by individuals who are just good enough to survive but –  more importantly – who excel at reproduction. 

Human society now sees to it – or tries to – that a lack of “fitness” of any kind is not a bar to either survival or reproduction. In consequence the evolution of humans will then be controlled by individuals in stories like these who – by any stretch of the imagination – are far from being the “fittest”:

  1. Father of 22 children by 11 women …
  2. Man who fathered THIRTY kids ….

  3.  ….. fathered up to 600 children through sperm bank ….. 

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Neanderthal genes are everywhere

January 30, 2014

Neanderthal genes are everywhere

We seek them here, we seek them there,

We met them often – but when? And where?

They are in our skins and in our hair,

Neanderthal genes are everywhere

From, Sriram Sankararaman et al, The genomic landscape of Neanderthal ancestry in present-day humans. Nature, 2014; DOI:10.1038/nature12961

Harvard Press Release: Remnants of Neanderthal DNA in modern humans are associated with genes affecting type 2 diabetes, Crohn’s disease, lupus, biliary cirrhosis and smoking behavior. They also concentrate in genes that influence skin and hair characteristics. At the same time, Neanderthal DNA is conspicuously low in regions of the X chromosome and testes-specific genes.

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Dark-skinned, blue-eyed hunter gatherer

January 27, 2014

Light skin genes in Europe less than 7,000 years old

Genetic analysis of ancient skeletons is bringing pictures of our ancestors to light in vivid colours. What is particularly astounding to me is the mobility of our ancestors – and their genes – already in the pleistocene.

Less than 350 generations for the light skin gene to have spread all over Europe seems to be a very short time. But that is what is concluded from the genetic analysis of two hunter-gatherer skeletons discovered in a cave in the mountains of north-west Spain in 2006.

hunter gatherer from brana

 

Read the rest of this post

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Asimov’s 1964 predictions for 2014

January 6, 2014

Isaac Asimov‘s expectations back in 1964 for how the world would change in 50 years do not need much commentary. In general the IT revolution has gone much further than he thought possible but styles of living and the gadgetry around us have not changed as much as he thought they would. His population estimates were not far wrong but the necessity for population control he envisaged is not necessary. Fertility rates are dropping much faster than he imagined possible. Unemployment is surely one of the greatest challenges of the day but not – as Asimov implied – due to a surfeit of leisure. All in all, pretty close!

From the New York Times of 16th August 1964:

Isaac.Asimov01.jpg

Asimov in 1965 (wikipedia)

Visit to the World’s Fair of 2014

By ISAAC ASIMOV

The New York World’s Fair of 1964 is dedicated to “Peace Through Understanding.” Its glimpses of the world of tomorrow rule out thermonuclear warfare. And why not? If a thermonuclear war takes place, the future will not be worth discussing. So let the missiles slumber eternally on their pads and let us observe what may come in the nonatomized world of the future.

What is to come, through the fair’s eyes at least, is wonderful. The direction in which man is traveling is viewed with buoyant hope, nowhere more so than at the General Electric pavilion. There the audience whirls through four scenes, each populated by cheerful, lifelike dummies that move and talk with a facility that, inside of a minute and a half, convinces you they are alive.

The scenes, set in or about 1900, 1920, 1940 and 1960, show the advances of electrical appliances and the changes they are bringing to living. I enjoyed it hugely and only regretted that they had not carried the scenes into the future. What will life be like, say, in 2014 A.D., 50 years from now? What will the World’s Fair of 2014 be like?

I don’t know, but I can guess.

One thought that occurs to me is that men will continue to withdraw from nature in order to create an environment that will suit them better. By 2014, electroluminescent panels will be in common use. Ceilings and walls will glow softly, and in a variety of colors that will change at the touch of a push button.

Windows need be no more than an archaic touch, and even when present will be polarized to block out the harsh sunlight. The degree of opacity of the glass may even be made to alter automatically in accordance with the intensity of the light falling upon it.

There is an underground house at the fair which is a sign of the future. if its windows are not polarized, they can nevertheless alter the “scenery” by changes in lighting. Suburban houses underground, with easily controlled temperature, free from the vicissitudes of weather, with air cleaned and light controlled, should be fairly common. At the New York World’s Fair of 2014, General Motors’ “Futurama” may well display vistas of underground cities complete with light- forced vegetable gardens. The surface, G.M. will argue, will be given over to large-scale agriculture, grazing and parklands, with less space wasted on actual human occupancy.

Gadgetry will continue to relieve mankind of tedious jobs. Kitchen units will be devised that will prepare “automeals,” heating water and converting it to coffee; toasting bread; frying, poaching or scrambling eggs, grilling bacon, and so on. Breakfasts will be “ordered” the night before to be ready by a specified hour the next morning. Complete lunches and dinners, with the food semiprepared, will be stored in the freezer until ready for processing. I suspect, though, that even in 2014 it will still be advisable to have a small corner in the kitchen unit where the more individual meals can be prepared by hand, especially when company is coming.

Robots will neither be common nor very good in 2014, but they will be in existence. The I.B.M. exhibit at the present fair has no robots but it is dedicated to computers, which are shown in all their amazing complexity, notably in the task of translating Russian into English. If machines are that smart today, what may not be in the works 50 years hence? It will be such computers, much miniaturized, that will serve as the “brains” of robots. In fact, the I.B.M. building at the 2014 World’s Fair may have, as one of its prime exhibits, a robot housemaid*large, clumsy, slow- moving but capable of general picking-up, arranging, cleaning and manipulation of various appliances. It will undoubtedly amuse the fairgoers to scatter debris over the floor in order to see the robot lumberingly remove it and classify it into “throw away” and “set aside.” (Robots for gardening work will also have made their appearance.)

General Electric at the 2014 World’s Fair will be showing 3-D movies of its “Robot of the Future,” neat and streamlined, its cleaning appliances built in and performing all tasks briskly. (There will be a three-hour wait in line to see the film, for some things never change.)

The appliances of 2014 will have no electric cords, of course, for they will be powered by long- lived batteries running on radioisotopes. The isotopes will not be expensive for they will be by- products of the fission-power plants which, by 2014, will be supplying well over half the power needs of humanity. But once the isotype batteries are used up they will be disposed of only through authorized agents of the manufacturer. ….

…. In 2014, there is every likelihood that the world population will be 6,500,000,000 and the population of the United States will be 350,000,000. Boston-to-Washington, the most crowded area of its size on the earth, will have become a single city with a population of over 40,000,000.

….

Even so, mankind will suffer badly from the disease of boredom, a disease spreading more widely each year and growing in intensity. This will have serious mental, emotional and sociological consequences, and I dare say that psychiatry will be far and away the most important medical specialty in 2014. The lucky few who can be involved in creative work of any sort will be the true elite of mankind, for they alone will do more than serve a machine.

Indeed, the most somber speculation I can make about A.D. 2014 is that in a society of enforced leisure, the most glorious single word in the vocabulary will have become work!

Read the whole article.

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Human evolution as a braided stream rather than a branching tree

January 4, 2014
An interspecies love child? from Nature (Christoph P.E. Zollikofer)

An interspecies love child? from Nature (Christoph P.E. Zollikofer)

The genetic history of modern humans is creating a vast jigsaw puzzle. Genetic evidence is mounting that most people today carry some Neanderthal genes, that some carry what have been labelled “Denisovan” genes, that Denosivans and Neanderthals not only had a common ancestor but that there also was admixture between some Denisovans and some Neanderthals and that there was at least one other as yet unnamed archaic honim which interbred with the Denisovans. It now becomes clear that viewing all these various archaic humans as different species could be wrong. They could all well be the same species.

Chris Finlayson reviews the  paleoanthropology advances during 2013:

The conclusion of the Dmanisi study was that the variation in skull shape and morphology observed in this small sample, derived from a single population of Homo erectus, matched the entire variation observed among African fossils ascribed to three species – H. erectus, H. habilis and H. rudolfensis.

The five highly variable Dmanisi fossils belonged to a single population of H. erectus, so how could we argue any longer that similar variation among spatially and temporally widely distributed fossils in Africa reflected differences between species? They all had to be the same species. 

I have been advocating that the morphological differences observed within fossils typically ascribed to Homo sapiens (the so-called modern humans) and the Neanderthals fall within the variation observable in a single species.

It was not surprising to find that Neanderthals and modern humans interbred, a clear expectation of the biological species concept. …. If the fossils of 1.8 or so million years ago and those of the more recent Neanderthal-modern human era were all part of a single, morphologically diverse, species with a wide geographical range, what is there to suggest that it would have been any different in the intervening periods?

Probably not so different if we take the latest finds from the Altai Mountains in Siberia into account. Denisova Cave has produced yet another surprise, revealing that, not only was there gene flow between Neanderthals, Denisovans and modern humans, but that a fourth player was also involved in the gene-exchange game.

The identity of the fourth player remains unknown but it was an ancient lineage that had been separate for probably over a million years. H. erectus seems a likely candidate. Whatever the name we choose to give this mystery lineage, what these results show is that gene flow was possible not just among contemporaries but also between ancient and more modern lineages.

Just to show how little we really know of the human story, another genetic surprise has confounded palaeoanthropologists. Scientists succeeded in extracting the most ancient mitochondrial DNA so far, from the Sima de los Huesos site in Atapuerca, Spain.

The morphology of these well-known Middle Pleistocene (approximately 400,000 years old) fossils have long been thought to represent a lineage leading to the Neanderthals.

When the results came in they were actually closer to the 40,000 year-old Denisovans from Siberia. We can speculate on the result but others have offered enough alternatives for me to not to have to add to them. The conclusion that I derive takes me back to Dmanisi: We have built a picture of our evolution based on the morphology of fossils and it was wrong.

Some time ago we replaced a linear view of our evolution by one represented by a branching tree. It is now time to replace it with that of an interwoven plexus of genetic lineages that branch out and fuse once again with the passage of time

A braided stream rather than the branches of a tree is the better analogy where  – as John Hawkes describes it:

The “braided stream” analogy captures different information about human origins than the usual branching tree. The branches of a tree do not reconnect with each other above the point where they initially separate. A tree will never admit to exchanging sap between its branches, and there are no little xylem hyphae between branches to carry sap anyway. Our evolution was truly a network in which multiple populations existed and contributed to our process of adaptation.

But the braided stream is not quite satisfactory for the picture that is emerging:

promiscuity in the pleistocene

John Hawkes again:

I admit that the braided stream is not a perfect analogy. Diverging rivulets within a valley almost always come together again, forming a complicated network as they form sandbars and islets. None of them flow into a cul-de-sac. Some human populations of the past did become extinct, they did not inexorably flow back into the mainstream of our evolutionary history. Some of them may have flowed back into the mainstream only through very small channels of genetic exchange. When we go far enough back, some populations really did branch off into their own direction. It’s just not clear yet which populations those were. Maybe an evolutionary swamp would be a better analogy, full of algae-covered bayous.

I like the braided stream, and it’s clear that its time has come. Ancient DNA has begun to show the process of genetic exchange was not a minor player in our evolution. All human populations today evidence some mixture of ancient populations that existed well before the “origin of modern humans”. Genetic exchanges between different populations were dominant in the formation of some human adaptations. Some ancient populations can be understood only as the mixed descendants of other, yet more ancient ones. It’s mixing all the way back.

braided-stream-leone

A braided river from http://cloudman23.wordpress.com/ Image – Yann Arthus-Bertrand

The story will most likely become much more complex – as further pieces of the jigsaw are revealed – before the whole picture can be seen But it is already becoming apparent that the origin of modern humans includes genetic exchange with many “species” supposed to have predated AMH and this exchange was not insignificant.

Perhaps the concept of “Anatomically Modern Humans” has to be expanded and pushed back in time. Rather than an origin some 200,000 years ago the start of “modern humans” could need to be pushed back to about 500,000 years ago and has to somehow bring Neanderthals and Denisovans (and some others) back into the fold.

And maybe our ancestors of 20,000 generations ago were just as shocked at a Denisovan-Neanderthal marriage as some in India are today at an “inter-caste” marriage!

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Promiscuity in the pleistocene

January 2, 2014

Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology and his colleagues from various institutions are making stunning advances in the analysis of ancient DNA. The complete genome of a Neanderthal has now been reconstructed with a remarkable level of detail.

The complete genome sequence of a Neanderthal from the Altai Mountains, Kay Prüfer et al, Nature 505, 43–49 (02 January 2014),  doi:10.1038/nature12886

Editors Summary: Recent excavations in the Denisova Cave in the Altai Mountains of southern Siberia have yielded a wealth of hominin fossils from a site that has been occupied for perhaps 250,000 years or more. Now a high-quality genome sequence has been determined from a circa 50,000-year-old toe bone — a proximal toe phalanx — excavated from the east gallery of Denisova Cave in 2010. The sequence is that of a Neanderthal woman whose parents were closely related — perhaps half-siblings or uncle and niece. Such inbreeding was also common among her recent ancestors. Comparisons with other archaic and present-day human genomes reveal several gene-flow events among Neanderthals, the closely related Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. The high-quality Neanderthal genome also helps to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

promiscuity in the pleistocene

But what is also becoming clear is that there were more “species” of homo erectus who existed in parallel than has generally been assumed and also that sexual encounters and interbreeding between these cousin-species has been a regular occurrence over some 250,000 years. And so there have been times when Anatomically Modern Humans (AMH), Neanderthals, Denisovans and the “unknown” hominim have co-existed.

The AMH-Neanderthals split is thought to have occurred about 400,000 years ago. The split with the unknown hominims then must have been around 500,000 years ago. The Denisovans split off from the Neanderthals perhaps about 300,000 years ago. The Out-of-Africa split among AMH was around 100,000 years ago.

A Neanderthal in our time. (copyright Nenderthal Museum / H Neumann)

A Neanderthal in our time. (copyright Nenderthal Museum / H Neumann)

These ancient splits were all probably in and around Africa even if the Out-of-Africa event for AMH is now more likely to have been  many such events and an expansion out of Africarabia. But it also means that a wave of “unknown hominims” split off from the mainline after a mainline group had left Africa and then spread out to unknown areas. Neanderthals probably split from their parent line of descent also outside of Africa but there must first have come a migration from Africa. The Neanderthal-Denisovan split must also have taken place outside of Africa. Clearly there have been many migrations Out of Africa over the last 400,000 years.

Carl Zimmer writes, “Evolution is a mixture of flow–the cascade of genes from parents to offspring, and the criss-cross movement between populations and species”.

But this generates a myriad of new questions. How large were the troops or tribes or clans of these ancient hunter-gatherers that they could sustain such large migrations? For how long and in what proximity did these different species of man co-exist. These troops – it is thought – probably did not number more than about 50. Some critical population would have been required for sufficient interactions to have taken place between the species. At any one time the total human population – of all species – may have approached 10 million (for if this was – say – just 1 million the opportunities to interbreed would not have been many). They all had fire, but did they all have some form of speech?

But most fascinating of all is how the interbreeding took place. Was it just a product of normal rape and pillage? Did violent clashes lead to the victors impregnating the vanquished, or were there other scenarios for individuals to mate? At some point there must have been children who were 50% Neanderthal and 50% AMH. And some who were 50% Neanderthal and 50% Denisovan. How did they survive? What kind of society existed in these ancient times that would permit such offspring not only to survive but also to mate and produce offspring in their turn? But however it happened, our ancestors in the pleistocene were a promiscuous lot.

Could it be that it was only among AMH  – after they had been vanquished and raped and pillaged by Neanderthal raids – that such mixed children were allowed not only to survive but also to thrive?

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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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Posted in Anthropology, Archeology, Evolution, History, Humans | Comments Off on DNA sequenced from a 400,000 year old hominin from Spain

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