DNA FACT & FICTION
DNA
Fact & Fiction
Long before we even knew about organic evolution (or about genetics, for that matter), we were already envisioning our genealogical ties to our ancestors as well as relatives in terms of blood, thereby making them seem more natural. As a result, we also tend to regard the essentially genealogical communities that are based on them (families, ethnic groups) as natural, organically delineated communities.
The very primitive animal layers are supposed to be inherited through the sympathetic system, and the relatively later animal layers belonging to the vertebrate series are represented by the cerebrospinal system. ~Carl Jung, 1925 Seminar, Page 140
Coalescence
The four main processes thought to affect population genetics -- mutation, genetic drift, gene flow, and selection -- are all unguided. The first three are random in their effect on evolution, meaning that they can be positive, negative or neutral in their effects on fitness; only natural selection acts in a directional manner to increase fitness.
The theory is that in small populations (smaller than a trillion, say) drift can overwhelm the power of selection. In such a case, organisms do not have sufficient numbers for beneficial mutations to arise and be fixed with any frequency. Most mutations are lost to drift before becoming established, even when they are beneficial. The significance of natural selection is thus greatly reduced in shaping evolutionary history.
The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption -- that the vast majority of mutations are neutral and have no effect on an organism's survival. (For a review go here.) Under this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn't matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don't matter.
Here's the way a recent article put it:
... the genealogical relationship (gene tree) of neutral alleles can be simply depicted by a coalescence process in which lineages randomly coalesce with each other backward in time. The coalescence model is simple in the sense that it assumes little or no effect of evolutionary forces such as selection, recombination, and gene flow, instead giving a prominent role to random genetic drift.
Thus, according to this theory, if it can be assumed that most mutations or allelic states have no effect on fitness, a genealogy can be created randomly without any input from the genotype. Therefore the spread of variation can be modeled as a diffusion process or Markov chain run backwards, the mean time to coalescence can be estimated, and the effective population size can be estimated from that, based on mutation rate and generation time.
http://www.evolutionnews.org/2012/08/on_retrospectiv062881.html
The genetic patterns indicate that there was selection in the genome against the introgressed variants, so Neanderthals and modern humans exhibited hybrid breakdown. In light of no such genomic evidence for admixture of Eurasian ancestry into KhoeSan (I’ve asked, people have looked), that suggests we know that for hominins hybrid incompabilities seem to arise on the scale of between 200,000 and 600,000 years. It also seems that due meta-population dynamics lineage extinctions were very common in hominins. The genetic relatedness of Neanderthals across human swaths of territory indicate that they were subject to this dynamic, where there were massive lineage pruning events over the 600,000 years that this group was a distinct population. With modern humans, we now know that first settlers do not always leave a genetic impact later on because of extinction events. With these facts under our belt it is less surprising if there were “false dawns” of the “triumph of humanity.” What these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion, where the hominin-made-man swept all before them. Probably the best illustration of this thesis can be found in Richard Klein’s 2002 book, The Dawn of Human Culture. In it he proposes that 50,000 years ago there was a single mutation which resulted in a pleiotropic cascade, and allowed for the emergence of full elaborated language and ergo the package of features which we associate with behavioral modernity. This model was presaged in the earlier decade with popularizations of “mitochondrial Eve” which implied that all humans were descended from a very small tribe resident in East Africa on the order of ~100,000 years ago. (the date varied as a function of the vicissitudes of mutational rate estimates)
Here’s what we know now that changes this. First, there are populations within Africa, in particular the the San of the far south, who diverged much earlier than 50,000 years ago. The most recent genomic estimates are suggesting divergence dates as early as ~200,000 years before the present. Second, the effective population size of humans outside of Africa is incredibly small, suggesting expansion from a very small founding population, but one should be cautious about generalizing to groups within Africa. That is, the blitzkrieg sweep model of modern human expansion does not hold to within Africa, and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently. And, these lineages may have admixed with modern humans just as they have outside of Africa.
Finally, the emergence of H. sapiens sapiens supremacy seems to have been a process, not a singular event which emerged de novo like a supernovae in the hominin firmament. The Omo remains in Ethiopia were anatomically modern humans. The people who gave rise to Omo lived ~200,000 years ago. The encephalization of the human lineage increased gradually up until around ~200,000 years ago, and Neanderthals were famously the most encephalized of all. Therefore, some form of modern humans were present within Africa for 150,000 years while other lineages were dominant elsewhere. Remains from places like China suggest though that offshoots of African humanity did push into the rest of the world…but they may not have left much of a genetic trace. This may have been part of movements due to climate change during the Pleistocene, or one of the natural migrations which a consequence of Malthusian pressures and inter-deme competition which afflicted humans. But they clearly did not conquer all before them. Why? We don’t know. And we don’t know why the situation was different 50,000 years ago. As a null hypothesis one might entertain the possibility that it was random. That periodically turnovers occur, and it just so happened that an African lineage lucked out in a massive extinction event. But that’s hard to credit when you consider that these modern humans crossed into Sahul and Siberia after sweeping aside other groups, and then eventually crossed over into the New World. There was something different about us. Additionally, the modern humans eventually absorbed or extirpated other lineages within Africa too.
A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.
http://www.unz.com/gnxp/the-blood-of-the-first-men-runs-thin-in-our-kind/
A piece of fossilized jaw discovered at Ledi-Geraru, Ethiopia, pushes back the date when the first members of the human genus evolved by 400,000 years. The research, in Science, shows that the jaw is about 2.8 million years old. It’s one of the few hominin fossils that date to between 2.5 million and 3 million years ago, when a small-brained australopith was evolving into the larger-brained Homo genus.
http://discovermagazine.com/2016/janfeb/28-the-first-of-our-kind
Suppose that you wanted a written record of your every ancestor…with the Ancestral Pyramid, a doubling of ancestors each generation back, by the 12th generation back you have 2048, and 60,000 direct ancestors going back to the Crusades. By Generation 40, you have more than one trillion ancestors.
Ancient DNA
http://www.dailymail.co.uk/sciencetech/article-3432060/An-unknown-chapter-human-history-took-place-Europe-15-000-years-ago-DNA-shows-hunter-gatherers-replaced-mystery-group-people-Ice-Age.html
http://www.scientificamerican.com/article/a-surprise-source-of-life-s-code/
Genetic Genealogy
You don't have DNA from all or even most of your ancestors. About 360 years, or just short of 15 generations. At 15 generations, an individual living today would carry only three thousands of 1% (00.003052%) of the DNA of an ancestor who was “pure” anything 15 generations ago. So even if one ancestor was indeed Mediterranean 15 generations ago, unless they continuously intermarried within a pure Mediterranean population, the amount would drop by 50% with each
generation to the miniscule amount that would be found in today’s current generation. With today’s technology, this is simply untraceable in autosomal DNA. An autosomal DNA test only goes back 8 generations. For genealogy within the most recent fifteen generations, STR markers help define paternal lineages.
We have about 43 genetic ancestors out of 1024 genealogical ancestors after 10 generations. The probability of having DNA from all of your genealogical ancestors at a particular generation becomes vanishingly small very rapidly; there is a 99.6% chance that you will have DNA from all of your 16 great-great grandparents, only a 54% of sharing DNA with all 32 of your G-G-G grandparents, and a 0.01% chance for your 64 G-G-G-G grandparents. You only have to go back 5 generations for genealogical relatives to start dropping off your DNA tree.
We also care about how many genetic ancestors we have after a certain number of generations: The number of genetic ancestors starts off growing exponentially, but eventually flattens out to around 125 (at 10 generations, 120 of your 1024 genealogical ancestors are genetic ancestors).
The percentage of DNA you would carry from a single ancestor who lived 20,000 years ago, assuming you only descended from that ancestor 1 time, is infinitesimally small. There are more zeroes following that decimal point than I have patience to type. Let’s call that ancestor Xenia and let’s say she is a female.However, you did inherit DNA from many of your ancestors who lived 20,000 years ago, thousands of them, because all of them, through their descendants, make up the DNA you carry today.
So infinitesimally small or not, you do carry some of the DNA of some of those ancestors. It’s just broken into extremely small pieces today and their individual contributions to you may be extremely small. You don’t carry any DNA from some of them, actually, probably most of them, due to the recombination event, dividing their DNA in half, happening 800 times, give or take.
Now, given that your ancestors’ DNA is divided in every generation by approximately half, and we know there are about 3 billion base pairs on all of your chromosomes combined, this means that by generation 32 or 33, on average, you carry 1 segment from this ancestor. By generation 45, you carry, on average, .00017 segments of this ancestor’s DNA. And for those math aficionados among us, this is the mathematical notation for how much of our ancestor’s DNA we carry after 800 generations: 4.4991E-232.
But, we also know that this dividing in half, on the average, doesn’t always work exactly that way in reality, because some of those ancestors from 20,000 years ago did in fact pass their DNA to you, despite the infinitesimal odds against that happening. Some of their DNA was passed intact generation after generation, to you, and you carry it today. The DNA contributed by any one ancestor from 800 generations ago is probably limited to one or two locations, or bases, but still, it’s there, and it’s the combined DNA of those ancient ancestors that make us who we are today.
The autosomal DNA of any specific ancestor from long ago is probably too small and fragmented to recognize as “theirs” and attribute to them. Of course, the beauty of Y DNA and mitochondrial is that it is passed in tact for all of those generations. But for autosomal DNA and genealogy, we need hundreds of thousands of DNA pieces in a row from a particular ancestor to be recognizable as “theirs.” http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/
Direct Line paths of inheritance for both the Y-line, blue, and the mitochondrial DNA, red, are shown below. Contributions from the white genealogical lines may be small to nil, and dwindle quickly. Only men have the Y chromosome which is passed from father to son, usally along with the surname. Males carry their mother’s mitochondrial DNA (mtDNA) but they don’t pass it on. Mitochondrial DNA testing gives a haplogroup which defines deep ancestry, such as European, African, Asian or Native American, and percentages of ethnicity. Humans have 22 pairs of autosomes and one pair of sex chromosomes (the X and Y chromosomes).
Fifty percent of our autosomal DNA (atDNA) comes from our mother and 50% comes from our father. Since our parents each received 50% of their atDNA from each of their parents, we inherited about 25% of our atDNA from each of our grandparents. This percentage is cut in half with each generation as we go further up our family tree. We inherit about 12.5% of our atDNA from each great grandparent and about 6.25% from each of our 2nd great grandparents.
Autosomal DNA (not the 23rd chromosomal gender pair) tends to be transferred in groupings, which ultimately give us positive and negative family traits. Autosomal DNA is inherited from the autosomal chromosomes -- any of the numbered chromosomes, as opposed to the sex chromosomes. Only Autosomal DNA tests the rest of the DNA provided by both parents on the 23 chromosomes, not just two direct lines, as with Y-line and mitochondrial DNA. Autosomal inheritance paths include all of the various ancestral lines, including the lines that contribute the Y-line and mitochondrial line.
http://dna-explained.com/2012/10/01/4-kinds-of-dna-for-genetic-genealogy/
Contained in the nucleus of each cell are twenty-three pairs of chromosomes. Twenty-two of these matched pairs of chromosomes are called "autosomes," while the 23rd pair determines your sex (male or female). Autosomal DNA is inherited from both parents, and includes random contributions from their parents, grandparents, and so on. Therefore, your autosomes essentially contain a complete genetic record, with all branches of your ancestry at some point contributing a piece of your autosomal DNA.
For each of your twenty-two pairs of autosomal chromosomes, you received one from your mother and one from your father. Before they passed these chromosomes down to you, the contents were randomly jumbled in a process called "recombination" (this is why you and your siblings are all a little different from each other). Your parents, in turn, received their chromosomes from their parents (your grandparents).
Your autosomal DNA, therefore, contains random bits of DNA from your great-grandparents, great-great grandparents, and so on.
Close relatives will share large fragments of DNA from a common ancestor. Connections arising from more distant relatives will result in smaller fragments of shared DNA. The smaller the fragment of shared autosomal DNA, generally the further back the connection in your family tree.
Even these tiny segments of shared DNA can potentially hold a clue, however! The way in which your individual DNA has recombined through the generations also means that you may no longer carry DNA from a particular ancestor. Distant relatives often share no genetic material at all, although it is also possible to match an individual through a very distant ancestor.
An autosomal DNA test surveys a person’s entire genome at over 700,000 locations. It covers both the maternal and paternal sides of the family tree, so it covers all lineages. The Y-DNA test only reflects the direct father-to-son path in your family tree, and the mtDNA test only reflects the direct mother-to-child path in your family tree.
FOUNDER EFFECT
The founder effect is one way that nature can randomly create new species from existing populations. In this lesson, learn about the founder effect and how it can be seen in all humans across the globe.
In human genetics, Mitochondrial Eve is the matrilineal most recent common ancestor (MRCA), in a direct, unbroken, maternal line, of all currently living humans, who is estimated to have lived approximately 100,000–200,000 years ago.
The Logic Behind the Founder Effect
Think about the following scenario: A random group of ten men and ten women are suddenly stranded on a tropical island. Nineteen of the castaways have green eyes and one has blue eyes. The castaways decide that they have no chance of rescue, but they have plenty of supplies to start a new civilization. No outsiders ever find the island, but the civilization flourishes and many generations are born.
Now, consider this question: What color of eyes will most people on the island have? Considering that all but one of the original castaways had green eyes, you would be correct if you guessed that most of the descendants would likely have green eyes. You may not know the exact term for this phenomenon, but you have just demonstrated the logic behind what is known as the founder effect.
How the Founder Effect Works
A sequence of DNA that codes for a trait, such as eye color, is called a gene. Alleles are alternative forms of specific genes that are responsible for variations in a trait, such as green versus blue versus brown eyes. By examining the number of people that have each of these different eye colors, you can determine the frequency of the alleles in the population.
Occasionally, throughout history, small populations of a species have moved to an area that is sufficiently distant or physically isolated from the original population. This isolation prevents breeding between the two populations. By random chance alone, the allelic frequencies of one or more genes in the new population can be quite different than those of the original population.
This shift in allelic frequency due to the creation of a new, isolated population is called the founder effect. Using the example of eye color from above, if a small group of people with only green eyes is isolated on an island, the allelic frequency of green eyes in the new (founder) population will be much higher than that of the original (source) population.
The founder effect can occur during a migration if a small population moves sufficiently far from the home territory to prevent any interbreeding. The founder effect is also evident on islands. Small populations isolated on islands, arriving either via flight or floating on debris, can have different allelic frequencies simply by chance. If the founder population has alleles that impact their survival, either positively or negatively, evolution can lead to greater divergence between the two populations. Eventually, the founder population can become a new species, related to the original but unable to interbreed.
Examples of the Founder Effect
There are several classic examples of the founder effect. We'll start with the Pennsylvania Amish. In the 1700s, a small group (i.e., a founder population) of Europeans settled in Eastern Pennsylvania. Among this small group was an individual who carried an allele for Ellis-van Creveld syndrome. Ellis-van Creveld syndrome is a very rare form of dwarfism, causing short stature, extra fingers (known as polydactyly), abnormal teeth and nails, and heart defects. The allele for Ellis-van Creveld syndrome is found at a frequency of 7% in the Pennsylvania Amish in comparison to only 0.1% in the general population. The low allelic frequency of 0.1% was also the allelic frequency of the original European population from which the Amish migrated.
The higher allelic frequency in the Amish community is most likely due to the founder effect. While the Amish live in close proximity to large, diverse human populations that would be capable of breeding, the culture of the Amish restricts marriage outside of the group. This results in genetic isolation and group interbreeding that allows the frequency of the allele for Ellis-van Creveld syndrome to not only persist but increase over time.
Another example is the blood types of Native Americans. The original colonizers of the Americas most likely arrived by crossing the Bering Strait land bridge around 20,000 years ago and gradually moved south through North America and into South America. This founder population probably had many allelic variations from the original population.
While we have very little information on the allelic variation of the original population, today it is very rare to find a Native American with Type B blood. This suggests that in the founder population the occurrence or frequency of the Type B blood allele was very low. During much of the history of North America, until the arrival of the Europeans, the Native Americans, for the most part, would have been geographically isolated. This isolation, over thousands of years, resulted in the low frequency of Type B blood in Native Americans observed today.
Europeans with blue eyes are pretty closely related. Scientists can tell this by looking at their DNA.One piece of evidence is that most blue eyed Europeans share the exact same DNA difference that causes their blue eyes. Given that there are lots of ways to get blue eyes, this suggests that the people who share this DNA difference all came from the same original ancestor (or founder). By studying the DNA in a bit more detail, scientists have concluded that this original blue-eyed ancestor probably lived around 6,000-10,000 years ago.
It is important to note here that not everyone with the same trait is necessarily so closely related. For example, red haired Europeans get their red hair from a variety of DNA differences. Not all redheads can trace their history back to an original red haired ancestor.
Now the fact that blue eyes appeared out of nowhere isn’t that weird…our DNA is much less stable than a lot of people think. Changes in DNA (or mutations) can and do happen all the time so it isn’t surprising that occasionally one will happen in just the right place to cause blue eyes. This probably happened a number of times throughout human history.
No the weird part is that the blue eye mutation from that original ancestor took hold and spread through Europe. Usually this means that the mutation had to have an advantage. If it didn’t, then like most neutral mutations, it would stay at some low level or disappear entirely. But it is obviously still around and going strong.
http://www.livescience.com/42838-european-hunter-gatherer-genome-sequenced.html?li_source=LI&li_medium=more-from-livescience
http://www.livescience.com/37092-southern-europeans-have-african-genes.html?li_source=LI&li_medium=more-from-livescience
EPIGENETICS
At the heart of this new field is a simple but contentious idea -- that genes have a 'memory'. That the lives of your grandparents -- the air they breathed, the food they ate, even the things they saw -- can directly affect you, decades later, despite your never experiencing these things yourself. And that what you do in your lifetime could in turn affect your grandchildren.
The conventional view is that DNA carries all our heritable information and that nothing an individual does in their lifetime will be biologically passed to their children. To many scientists, epigenetics amounts to a heresy, calling into question the accepted view of the DNA sequence -- a cornerstone on which modern biology sits.
Epigenetics adds a whole new layer to genes beyond the DNA. It proposes a control system of 'switches' that turn genes on or off -- and suggests that things people experience, like nutrition and stress, can control these switches and cause heritable effects in humans.
For example, a famine at critical times in the lives of the grandparents can affect the life expectancy of the grandchildren. This is the first evidence that an environmental effect can be inherited in humans.
Seven thousand five hundred fifty-six (7556) haplotypes of 46 subclades in 17 major haplogroups were considered in terms of their base (ancestral) haplotypes and timespans to their common ancestors, for the purposes of designing of time-balanced haplogroup tree. It was found that African haplogroup A (originated 132,000 ± 12,000 years before present) is very remote time-wise from all other haplogroups, which have a separate common ancestor, named β-haplogroup, and originated 64,000 ± 6000 ybp. It includes a family of Europeoid (Caucasoid) haplogroups from F through T that originated 58,000 ± 5000 ybp. A downstream common ancestor for haplogroup A and β-haplogroup, coined the α-haplogroup emerged 160,000 ± 12,000 ybp. A territorial origin of haplogroups α- and β-remains unknown; however, the most likely origin for each of them is a vast triangle stretched from Central Europe in the west through the Russian Plain to the east and to Levant to the south. Haplogroup B is descended from β-haplogroup (and not from haplogroup A, from which it is very distant, and separated by as much as 123,000 years of “lat- eral” mutational evolution) likely migrated to Africa after 46,000 ybp. The finding that the Europeoid haplogroups did not descend from “African” haplogroups A or B is supported by the fact that bearers of the Europeoid haplogroups, as well as all non-African haplogroups do not carry either SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 (haplogroup A and its subclades SNPs) or M60, M181, P90 (haplogroup B), as it was shown recently in “Walk through Y” FTDNA Project (the reference is incorporated therein) on several hundred people from various haplogroups.
Klyosov, A. & Rozhanskii, I. (2012). Re-Examining the "Out of Africa" Theory and the Origin of Europeoids (Caucasoids) in Light of DNA Genealogy. Advances in Anthropology, 2, 80-86. doi: 10.4236/aa.2012.22009.
http://www.scirp.org/journal/PaperInformation.aspx?paperID=19566
Among his fellow Russian, (and other),
researchers Klyosov is considered a whack job. Here is an excerpt from a
biodiversity forum:"Vadim Verenich
2012-03-26, 16:04
To put it briefly, Klyosov's "arguments" in a nutshell:
This garbage, non-science was "published" by a discredited Russian ultra-nationalist (with a reputation for being a ding-bat), claiming that all humans outside Africa did not originate in Africa but actually originated in a "vast triangle" between, wait for it, _Russia_, The Levant and Central Europe. Except that it was *not* actually published; certainly not in a genuine, accredited, peer-reviewed scientific journal. It was merely "put on the internet" through a medium that will post any garbage dependent only on the author's willingness to pay. Thus, the garbage in that paper was doubtless rejected by many journals until the authors decided to pay SciRP.org, a thoroughly scurrilous and disreputable heap of shit, whatever fee they were demanding. SciRP.org is *so* disreputable that the entire editorial board of _Advances in Anthropology_ resigned in protest, _en masse_, in 2014.
You only have to read the paper in that e-rag to see that the conclusions are spurious and misleading, even without any previous, in-depth knowledge of Y haplotypes. One obvious error (or fraud) is that they talk about the African haplogroup as if it is virtually monomorphic, when anyone with even the vaguest knowledge of the subject knows that the San bushmen population in Southern Africa has the greatest degree of Y haplotype variation on the entire planet.
This paper is very far from genuine science and constitutes actual scientific fraud.
Deep within your DNA, a tiny parasite lurks, waiting to pounce from its perch and land in the middle of an unsuspecting healthy gene. If it succeeds, it can make you sick.
Like a jungle cat, this parasite sports a long tail. But until now, little was known about what role that tail plays in this dangerous jumping.
Today, scientists report that without a tail, this parasitic gene can't jump efficiently. The findings could help lead to new strategies for inhibiting the movement of the parasite, called a LINE-1 retrotransposon.
The research, published in Molecular Cell by a team from the University of Michigan Medical School and the Howard Hughes Medical Institute, answers a key question about how "jumping genes" move to new DNA locations.
The parasite in question isn't a foreign beast, but rather a piece of DNA that carries its own instructions for making a piece of "rogue" genetic material and two proteins that can help it jump. "Jumping" allows this rogue copy to land anywhere in the DNA of a cell, causing a change called a mutation.
Jumping LINE-1s - and other genetic parasites like it - are responsible for about one in every 250 disease producing mutations in humans. They've been blamed for causing a number of diseases, including hemophilia, Duchenne muscular dystrophy, and cancer. Copies of this parasite litter our DNA, though most of them can no longer jump and cause damage.
For these reasons, scientists want to understand as much as possible about how this process works. Perhaps someday, this new understanding could help fight the effects of these jumps - or prevent the parasites from leaping in the first place.
"Now, we have a mechanism to explain how sequences that comprise one-third of our genome have moved," says John Moran, Ph.D., senior author of the new paper and a longtime U-M and HHMI researcher studying jumping genes. "By understanding how LINE-1 jumps, we can understand how it contributes to disease."
A cat without a tail, a tail without a cat
The gene that's responsible for LINE-1 jumping does its damage by first creating an RNA copy of itself. That RNA copy tells the cell to make two proteins that help make it possible for the LINE-1 RNA itself to jump into a new spot.
Each copy of LINE-1 RNA has a long tail at its end that's made up of multiple copies of a substance called adenosine. Known as a "poly(A) tail", it's long been suspected of playing a role in LINE-1 jumping. But it was impossible to figure this role out because removing the tail also eliminates another key function it serves, in getting the RNA to the location where proteins are made.
Like the Cheshire Cat of Alice in Wonderland, if the tail vanished, the rest of the "cat" would too.
So, a postdoctoral fellow, Aurélien Doucet, Ph.D., now a research associate at the Institute for Research on Cancer and Aging in Nice, or CNRS, in France, collaborated with Jeremy Wilusz, Ph.D., now an assistant professor at the University of Pennsylvania Perelman School of Medicine, to figure out a way to delete the LINE-1 poly(A) tail to determine if it affected LINE-1 jumping.
They succeeded in making a LINE-1 RNA, without a poly(A) tail, that got where it needed to in the cell to make proteins.
The substitute tail allowed the scientists to see what happened when LINE-1 RNA could get to the protein-making spot, but without its usual appendage.
Here's where it gets interesting. Without the poly(A) tail, almost no jumping happened - because the tailless LINE-1 RNA couldn't interact well with a protein called ORF2p.
ORF2p is actually one of the two proteins that the LINE-1 RNA tells the cell to make. Once ORF2p binds to the RNA's tail, it sets in motion the steps needed for a jump to occur.
Moran compares it to a Lego set - where one kind of tail could get unplugged and another slotted in to serve some, but not all, of the same functions.
In other words, the LINE-1 parasite is especially crafty.
A parasite of a parasite?
LINE-1 also has a competitor parasite, called Alu. And when LINE-1 RNA lacked the tail and couldn't jump, Alu RNA did much better at jumping.
Alu RNA also sports a poly(A) sequence at its end, which has already been shown to be vital to its ability to jump. But the Alu RNA doesn't contain the instructions for making a protein. This suggests, says Moran, that the two parasites compete to have access to ORF2p proteins. That is, Alu is a parasite of a parasite.
Moran and his team continue to build on their new finding that poly(A) sequences are crucial for retrotransposition. They're studying how Alu interacts with ORF2p, and how the use of a replacement for the poly(A) tail may be helpful in other research. They're also interested in how the cell, or host, fights off jumping genes and protects DNA from damage.
"Our DNA is a sea of junk copies of LINE-1 that can't jump, and a small minority of LINE-1s that can," says Moran, who is the Gilbert S. Omenn Collegiate Professor of Human Genetics in the U-M Department of Human Genetics. "We need to understand at the RNA level how these LINE-1 RNAs are chosen for jumping, and how we can stop them."
http://phys.org/news/2015-11-parasite-tail-team-gene-mystery.html?utm_content=buffer39119&utm_medium=social&utm_source=facebook.com&utm_campaign=buffer
Ancient DNA shows Stone Age humans
evolved quickly as they took up farming
By Joel Achenbach November 23
People in western Eurasia underwent evolutionary changes as they adopted farming as a way of life.
Prehistoric people who adopted farming as a way of life underwent evolutionary changes to adapt to their new lifestyle, a dramatic example of natural selection operating on the human species in the relatively recent past.
That's one of the conclusions of a new study of the genomes of 230 individuals who lived thousands of years ago and whose bones have been recovered from Western Eurasia — a broad area that includes what is now Turkey, the Russian Steppe and Europe.
The research, published Monday in the journal Nature, identified 12 specific genetic mutations that corresponded to the rise of agriculture and the migration of people into new regions. They include the ability to digest milk and metabolize fats. The mutations also favored greater height at maturity, lighter skin and lighter eye color in northern populations. There are also genetic markers that appear to be connected to resistance against such diseases as leprosy and tuberculosis.
Ancient DNA shows Stone Age humans evolved quickly as they took up farming
By Joel Achenbach
Prehistoric people who adopted farming as a way of life underwent evolutionary changes to adapt to their new lifestyle, a dramatic example of natural selection operating on the human species in the relatively recent past.
That's one of the conclusions of a new study of the genomes of 230 individuals who lived thousands of years ago and whose bones have been recovered from Western Eurasia — a broad area that includes what is now Turkey, the Russian Steppe and Europe.
The research, published Monday in the journal Nature, identified 12 specific genetic mutations that corresponded to the rise of agriculture and the migration of people into new regions. They include the ability to digest milk and metabolize fats. The mutations also favored greater height at maturity, lighter skin and lighter eye color in northern populations. There are also genetic markers that appear to be connected to resistance against such diseases as leprosy and tuberculosis.
swer to the question of how agriculture arrived in Europe. There have been two competing scenarios. One is that agricultural people — farmers — arrived as migrants, replacing indigenous populations. The other is the practices of farming were transmitted culturally, a contagion of innovation known to anthropologists as "cultural diffusion."
The new research strongly supports the first scenario, showing that the people who began farming in Europe, starting about 8,500 years ago, were closely connected to a population of farmers in Anatolia, a region that largely overlaps with modern-day Turkey.
“It is a migration. It’s a movement of people. The farmers in Europe from Germany and Spain are genetically almost identical to the farmers from Turkey," said Iain Mathieson, a geneticist at Harvard Medical School and the lead author of the new report.
[Research shows Stone Age farmers and hunters didn't mingle]
Modern human beings spent many tens of thousands of years as hunters and gatherers. But at the end of the last Ice Age, as temperatures stabilized, people in Mesopotamia and the Levant — the Fertile Crescent — began planting crops and domesticating animals as livestock. The farmers and their new way of life spread to other parts of Eurasia. Farming allowed greater population density, but it was a difficult way of life that at first led to poor nutrition and zoonotic diseases associated with living in close quarters with domesticated animals.
[The switch to farming made our skeletons more fragile (because we got lazier)]
“It's a change in the food people are eating. It’s a change in social organization. People are living in much bigger communities. People are living in much closer proximity to animals," Mathieson said.
That was a technological revolution that had genetic repercussions. Natural selection functions as a filter, favoring people with certain genetic mutations that allow them to more easily reach maturity and have children who are themselves advantaged. Thus, around 4,000 years ago, according to the new study, Europeans begun showing a genetic change associated with lactase persistence — the ability to digest milk into adulthood.
That such evolutionary changes have been taking place in the relatively recent past is not a surprise. Indeed, scientists have modeled many of these genetic adaptions simply by looking at people alive today and comparing their genomes. But this new work is more of a direct look at the prehistoric evolutionary processes as they were happening.
“It's taking ancient DNA to actually go back in the past," said Rasmus Nielsen, an evolutionary biologist at the University of California at Berkeley. He was not part of the team that published the new findings. "The paper is able to verify many of the predictions that have been done in the past 20 years from looking at modern populations. In some sense we have this scientific time machine," he said.
One possible implication of this research is that the popular "Paleo Diet," which embraces foods available to Stone Age people and avoids the dairy products and grains that came along only in the last 10,000 years, ignores the recent evolutionary changes in the human species. But Mathieson did not take a stance on this latest food fad.
"I don't think we can really speak to this," he said. "We show that people were able to adapt genetically to an agricultural diet, but it's rather an open question how well they adapted."
Fact & Fiction
Long before we even knew about organic evolution (or about genetics, for that matter), we were already envisioning our genealogical ties to our ancestors as well as relatives in terms of blood, thereby making them seem more natural. As a result, we also tend to regard the essentially genealogical communities that are based on them (families, ethnic groups) as natural, organically delineated communities.
The very primitive animal layers are supposed to be inherited through the sympathetic system, and the relatively later animal layers belonging to the vertebrate series are represented by the cerebrospinal system. ~Carl Jung, 1925 Seminar, Page 140
Coalescence
The four main processes thought to affect population genetics -- mutation, genetic drift, gene flow, and selection -- are all unguided. The first three are random in their effect on evolution, meaning that they can be positive, negative or neutral in their effects on fitness; only natural selection acts in a directional manner to increase fitness.
The theory is that in small populations (smaller than a trillion, say) drift can overwhelm the power of selection. In such a case, organisms do not have sufficient numbers for beneficial mutations to arise and be fixed with any frequency. Most mutations are lost to drift before becoming established, even when they are beneficial. The significance of natural selection is thus greatly reduced in shaping evolutionary history.
The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption -- that the vast majority of mutations are neutral and have no effect on an organism's survival. (For a review go here.) Under this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn't matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don't matter.
Here's the way a recent article put it:
... the genealogical relationship (gene tree) of neutral alleles can be simply depicted by a coalescence process in which lineages randomly coalesce with each other backward in time. The coalescence model is simple in the sense that it assumes little or no effect of evolutionary forces such as selection, recombination, and gene flow, instead giving a prominent role to random genetic drift.
Thus, according to this theory, if it can be assumed that most mutations or allelic states have no effect on fitness, a genealogy can be created randomly without any input from the genotype. Therefore the spread of variation can be modeled as a diffusion process or Markov chain run backwards, the mean time to coalescence can be estimated, and the effective population size can be estimated from that, based on mutation rate and generation time.
http://www.evolutionnews.org/2012/08/on_retrospectiv062881.html
The genetic patterns indicate that there was selection in the genome against the introgressed variants, so Neanderthals and modern humans exhibited hybrid breakdown. In light of no such genomic evidence for admixture of Eurasian ancestry into KhoeSan (I’ve asked, people have looked), that suggests we know that for hominins hybrid incompabilities seem to arise on the scale of between 200,000 and 600,000 years. It also seems that due meta-population dynamics lineage extinctions were very common in hominins. The genetic relatedness of Neanderthals across human swaths of territory indicate that they were subject to this dynamic, where there were massive lineage pruning events over the 600,000 years that this group was a distinct population. With modern humans, we now know that first settlers do not always leave a genetic impact later on because of extinction events. With these facts under our belt it is less surprising if there were “false dawns” of the “triumph of humanity.” What these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion, where the hominin-made-man swept all before them. Probably the best illustration of this thesis can be found in Richard Klein’s 2002 book, The Dawn of Human Culture. In it he proposes that 50,000 years ago there was a single mutation which resulted in a pleiotropic cascade, and allowed for the emergence of full elaborated language and ergo the package of features which we associate with behavioral modernity. This model was presaged in the earlier decade with popularizations of “mitochondrial Eve” which implied that all humans were descended from a very small tribe resident in East Africa on the order of ~100,000 years ago. (the date varied as a function of the vicissitudes of mutational rate estimates)
Here’s what we know now that changes this. First, there are populations within Africa, in particular the the San of the far south, who diverged much earlier than 50,000 years ago. The most recent genomic estimates are suggesting divergence dates as early as ~200,000 years before the present. Second, the effective population size of humans outside of Africa is incredibly small, suggesting expansion from a very small founding population, but one should be cautious about generalizing to groups within Africa. That is, the blitzkrieg sweep model of modern human expansion does not hold to within Africa, and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently. And, these lineages may have admixed with modern humans just as they have outside of Africa.
Finally, the emergence of H. sapiens sapiens supremacy seems to have been a process, not a singular event which emerged de novo like a supernovae in the hominin firmament. The Omo remains in Ethiopia were anatomically modern humans. The people who gave rise to Omo lived ~200,000 years ago. The encephalization of the human lineage increased gradually up until around ~200,000 years ago, and Neanderthals were famously the most encephalized of all. Therefore, some form of modern humans were present within Africa for 150,000 years while other lineages were dominant elsewhere. Remains from places like China suggest though that offshoots of African humanity did push into the rest of the world…but they may not have left much of a genetic trace. This may have been part of movements due to climate change during the Pleistocene, or one of the natural migrations which a consequence of Malthusian pressures and inter-deme competition which afflicted humans. But they clearly did not conquer all before them. Why? We don’t know. And we don’t know why the situation was different 50,000 years ago. As a null hypothesis one might entertain the possibility that it was random. That periodically turnovers occur, and it just so happened that an African lineage lucked out in a massive extinction event. But that’s hard to credit when you consider that these modern humans crossed into Sahul and Siberia after sweeping aside other groups, and then eventually crossed over into the New World. There was something different about us. Additionally, the modern humans eventually absorbed or extirpated other lineages within Africa too.
A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.
http://www.unz.com/gnxp/the-blood-of-the-first-men-runs-thin-in-our-kind/
A piece of fossilized jaw discovered at Ledi-Geraru, Ethiopia, pushes back the date when the first members of the human genus evolved by 400,000 years. The research, in Science, shows that the jaw is about 2.8 million years old. It’s one of the few hominin fossils that date to between 2.5 million and 3 million years ago, when a small-brained australopith was evolving into the larger-brained Homo genus.
http://discovermagazine.com/2016/janfeb/28-the-first-of-our-kind
Suppose that you wanted a written record of your every ancestor…with the Ancestral Pyramid, a doubling of ancestors each generation back, by the 12th generation back you have 2048, and 60,000 direct ancestors going back to the Crusades. By Generation 40, you have more than one trillion ancestors.
Ancient DNA
http://www.dailymail.co.uk/sciencetech/article-3432060/An-unknown-chapter-human-history-took-place-Europe-15-000-years-ago-DNA-shows-hunter-gatherers-replaced-mystery-group-people-Ice-Age.html
http://www.scientificamerican.com/article/a-surprise-source-of-life-s-code/
Genetic Genealogy
You don't have DNA from all or even most of your ancestors. About 360 years, or just short of 15 generations. At 15 generations, an individual living today would carry only three thousands of 1% (00.003052%) of the DNA of an ancestor who was “pure” anything 15 generations ago. So even if one ancestor was indeed Mediterranean 15 generations ago, unless they continuously intermarried within a pure Mediterranean population, the amount would drop by 50% with each
generation to the miniscule amount that would be found in today’s current generation. With today’s technology, this is simply untraceable in autosomal DNA. An autosomal DNA test only goes back 8 generations. For genealogy within the most recent fifteen generations, STR markers help define paternal lineages.
We have about 43 genetic ancestors out of 1024 genealogical ancestors after 10 generations. The probability of having DNA from all of your genealogical ancestors at a particular generation becomes vanishingly small very rapidly; there is a 99.6% chance that you will have DNA from all of your 16 great-great grandparents, only a 54% of sharing DNA with all 32 of your G-G-G grandparents, and a 0.01% chance for your 64 G-G-G-G grandparents. You only have to go back 5 generations for genealogical relatives to start dropping off your DNA tree.
We also care about how many genetic ancestors we have after a certain number of generations: The number of genetic ancestors starts off growing exponentially, but eventually flattens out to around 125 (at 10 generations, 120 of your 1024 genealogical ancestors are genetic ancestors).
The percentage of DNA you would carry from a single ancestor who lived 20,000 years ago, assuming you only descended from that ancestor 1 time, is infinitesimally small. There are more zeroes following that decimal point than I have patience to type. Let’s call that ancestor Xenia and let’s say she is a female.However, you did inherit DNA from many of your ancestors who lived 20,000 years ago, thousands of them, because all of them, through their descendants, make up the DNA you carry today.
So infinitesimally small or not, you do carry some of the DNA of some of those ancestors. It’s just broken into extremely small pieces today and their individual contributions to you may be extremely small. You don’t carry any DNA from some of them, actually, probably most of them, due to the recombination event, dividing their DNA in half, happening 800 times, give or take.
Now, given that your ancestors’ DNA is divided in every generation by approximately half, and we know there are about 3 billion base pairs on all of your chromosomes combined, this means that by generation 32 or 33, on average, you carry 1 segment from this ancestor. By generation 45, you carry, on average, .00017 segments of this ancestor’s DNA. And for those math aficionados among us, this is the mathematical notation for how much of our ancestor’s DNA we carry after 800 generations: 4.4991E-232.
But, we also know that this dividing in half, on the average, doesn’t always work exactly that way in reality, because some of those ancestors from 20,000 years ago did in fact pass their DNA to you, despite the infinitesimal odds against that happening. Some of their DNA was passed intact generation after generation, to you, and you carry it today. The DNA contributed by any one ancestor from 800 generations ago is probably limited to one or two locations, or bases, but still, it’s there, and it’s the combined DNA of those ancient ancestors that make us who we are today.
The autosomal DNA of any specific ancestor from long ago is probably too small and fragmented to recognize as “theirs” and attribute to them. Of course, the beauty of Y DNA and mitochondrial is that it is passed in tact for all of those generations. But for autosomal DNA and genealogy, we need hundreds of thousands of DNA pieces in a row from a particular ancestor to be recognizable as “theirs.” http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/
Direct Line paths of inheritance for both the Y-line, blue, and the mitochondrial DNA, red, are shown below. Contributions from the white genealogical lines may be small to nil, and dwindle quickly. Only men have the Y chromosome which is passed from father to son, usally along with the surname. Males carry their mother’s mitochondrial DNA (mtDNA) but they don’t pass it on. Mitochondrial DNA testing gives a haplogroup which defines deep ancestry, such as European, African, Asian or Native American, and percentages of ethnicity. Humans have 22 pairs of autosomes and one pair of sex chromosomes (the X and Y chromosomes).
Fifty percent of our autosomal DNA (atDNA) comes from our mother and 50% comes from our father. Since our parents each received 50% of their atDNA from each of their parents, we inherited about 25% of our atDNA from each of our grandparents. This percentage is cut in half with each generation as we go further up our family tree. We inherit about 12.5% of our atDNA from each great grandparent and about 6.25% from each of our 2nd great grandparents.
Autosomal DNA (not the 23rd chromosomal gender pair) tends to be transferred in groupings, which ultimately give us positive and negative family traits. Autosomal DNA is inherited from the autosomal chromosomes -- any of the numbered chromosomes, as opposed to the sex chromosomes. Only Autosomal DNA tests the rest of the DNA provided by both parents on the 23 chromosomes, not just two direct lines, as with Y-line and mitochondrial DNA. Autosomal inheritance paths include all of the various ancestral lines, including the lines that contribute the Y-line and mitochondrial line.
http://dna-explained.com/2012/10/01/4-kinds-of-dna-for-genetic-genealogy/
Contained in the nucleus of each cell are twenty-three pairs of chromosomes. Twenty-two of these matched pairs of chromosomes are called "autosomes," while the 23rd pair determines your sex (male or female). Autosomal DNA is inherited from both parents, and includes random contributions from their parents, grandparents, and so on. Therefore, your autosomes essentially contain a complete genetic record, with all branches of your ancestry at some point contributing a piece of your autosomal DNA.
For each of your twenty-two pairs of autosomal chromosomes, you received one from your mother and one from your father. Before they passed these chromosomes down to you, the contents were randomly jumbled in a process called "recombination" (this is why you and your siblings are all a little different from each other). Your parents, in turn, received their chromosomes from their parents (your grandparents).
Your autosomal DNA, therefore, contains random bits of DNA from your great-grandparents, great-great grandparents, and so on.
Close relatives will share large fragments of DNA from a common ancestor. Connections arising from more distant relatives will result in smaller fragments of shared DNA. The smaller the fragment of shared autosomal DNA, generally the further back the connection in your family tree.
Even these tiny segments of shared DNA can potentially hold a clue, however! The way in which your individual DNA has recombined through the generations also means that you may no longer carry DNA from a particular ancestor. Distant relatives often share no genetic material at all, although it is also possible to match an individual through a very distant ancestor.
An autosomal DNA test surveys a person’s entire genome at over 700,000 locations. It covers both the maternal and paternal sides of the family tree, so it covers all lineages. The Y-DNA test only reflects the direct father-to-son path in your family tree, and the mtDNA test only reflects the direct mother-to-child path in your family tree.
FOUNDER EFFECT
The founder effect is one way that nature can randomly create new species from existing populations. In this lesson, learn about the founder effect and how it can be seen in all humans across the globe.
In human genetics, Mitochondrial Eve is the matrilineal most recent common ancestor (MRCA), in a direct, unbroken, maternal line, of all currently living humans, who is estimated to have lived approximately 100,000–200,000 years ago.
The Logic Behind the Founder Effect
Think about the following scenario: A random group of ten men and ten women are suddenly stranded on a tropical island. Nineteen of the castaways have green eyes and one has blue eyes. The castaways decide that they have no chance of rescue, but they have plenty of supplies to start a new civilization. No outsiders ever find the island, but the civilization flourishes and many generations are born.
Now, consider this question: What color of eyes will most people on the island have? Considering that all but one of the original castaways had green eyes, you would be correct if you guessed that most of the descendants would likely have green eyes. You may not know the exact term for this phenomenon, but you have just demonstrated the logic behind what is known as the founder effect.
How the Founder Effect Works
A sequence of DNA that codes for a trait, such as eye color, is called a gene. Alleles are alternative forms of specific genes that are responsible for variations in a trait, such as green versus blue versus brown eyes. By examining the number of people that have each of these different eye colors, you can determine the frequency of the alleles in the population.
Occasionally, throughout history, small populations of a species have moved to an area that is sufficiently distant or physically isolated from the original population. This isolation prevents breeding between the two populations. By random chance alone, the allelic frequencies of one or more genes in the new population can be quite different than those of the original population.
This shift in allelic frequency due to the creation of a new, isolated population is called the founder effect. Using the example of eye color from above, if a small group of people with only green eyes is isolated on an island, the allelic frequency of green eyes in the new (founder) population will be much higher than that of the original (source) population.
The founder effect can occur during a migration if a small population moves sufficiently far from the home territory to prevent any interbreeding. The founder effect is also evident on islands. Small populations isolated on islands, arriving either via flight or floating on debris, can have different allelic frequencies simply by chance. If the founder population has alleles that impact their survival, either positively or negatively, evolution can lead to greater divergence between the two populations. Eventually, the founder population can become a new species, related to the original but unable to interbreed.
Examples of the Founder Effect
There are several classic examples of the founder effect. We'll start with the Pennsylvania Amish. In the 1700s, a small group (i.e., a founder population) of Europeans settled in Eastern Pennsylvania. Among this small group was an individual who carried an allele for Ellis-van Creveld syndrome. Ellis-van Creveld syndrome is a very rare form of dwarfism, causing short stature, extra fingers (known as polydactyly), abnormal teeth and nails, and heart defects. The allele for Ellis-van Creveld syndrome is found at a frequency of 7% in the Pennsylvania Amish in comparison to only 0.1% in the general population. The low allelic frequency of 0.1% was also the allelic frequency of the original European population from which the Amish migrated.
The higher allelic frequency in the Amish community is most likely due to the founder effect. While the Amish live in close proximity to large, diverse human populations that would be capable of breeding, the culture of the Amish restricts marriage outside of the group. This results in genetic isolation and group interbreeding that allows the frequency of the allele for Ellis-van Creveld syndrome to not only persist but increase over time.
Another example is the blood types of Native Americans. The original colonizers of the Americas most likely arrived by crossing the Bering Strait land bridge around 20,000 years ago and gradually moved south through North America and into South America. This founder population probably had many allelic variations from the original population.
While we have very little information on the allelic variation of the original population, today it is very rare to find a Native American with Type B blood. This suggests that in the founder population the occurrence or frequency of the Type B blood allele was very low. During much of the history of North America, until the arrival of the Europeans, the Native Americans, for the most part, would have been geographically isolated. This isolation, over thousands of years, resulted in the low frequency of Type B blood in Native Americans observed today.
Europeans with blue eyes are pretty closely related. Scientists can tell this by looking at their DNA.One piece of evidence is that most blue eyed Europeans share the exact same DNA difference that causes their blue eyes. Given that there are lots of ways to get blue eyes, this suggests that the people who share this DNA difference all came from the same original ancestor (or founder). By studying the DNA in a bit more detail, scientists have concluded that this original blue-eyed ancestor probably lived around 6,000-10,000 years ago.
It is important to note here that not everyone with the same trait is necessarily so closely related. For example, red haired Europeans get their red hair from a variety of DNA differences. Not all redheads can trace their history back to an original red haired ancestor.
Now the fact that blue eyes appeared out of nowhere isn’t that weird…our DNA is much less stable than a lot of people think. Changes in DNA (or mutations) can and do happen all the time so it isn’t surprising that occasionally one will happen in just the right place to cause blue eyes. This probably happened a number of times throughout human history.
No the weird part is that the blue eye mutation from that original ancestor took hold and spread through Europe. Usually this means that the mutation had to have an advantage. If it didn’t, then like most neutral mutations, it would stay at some low level or disappear entirely. But it is obviously still around and going strong.
The Gypsies (a misnomer, derived from an early legend about Egyptian origins) defy the conventional definition of a population: they have no nation-state, speak different languages, belong to many religions and comprise a mosaic of socially and culturally divergent groups separated by strict rules of endogamy. Referred to as “the invisible minority”, the Gypsies have for centuries been ignored by Western medicine, and their genetic heritage has only recently attracted attention. Common origins from a small group of ancestors characterise the 8–10 million European Gypsies as an unusual trans-national founder population, whose exodus from India played the role of a profound demographic bottleneck. Social and economic pressures within Europe led to gradual fragmentation, generating multiple genetically differentiated subisolates. The string of population bottlenecks and founder effects have shaped a unique genetic profile, whose potential for genetic research can be met only by study designs that acknowledge cultural tradition and self-identity. BioEssays 27:1084–1094, 2005. © 2005 Wiley Periodicals, Inc.
Founder populations are characterized by a single ancestor and by a large number of individuals and families who all are related to the ancestor and thereby carry the same disease-causing mutation.- A study by an international team suggests the central and eastern European Jewish population, known as Ashkenazi Jews, from whom most American Jews are descended, started from a founding population of about 350 people between 600 and 800 years ago. Further, that group of Jews who experienced this "bottleneck" was of approximately evenly mixed Middle Eastern and European descent. http://www.livescience.com/47755-european-jews-are-30th-cousins.html
http://www.livescience.com/42838-european-hunter-gatherer-genome-sequenced.html?li_source=LI&li_medium=more-from-livescience
http://www.livescience.com/37092-southern-europeans-have-african-genes.html?li_source=LI&li_medium=more-from-livescience
EPIGENETICS
At the heart of this new field is a simple but contentious idea -- that genes have a 'memory'. That the lives of your grandparents -- the air they breathed, the food they ate, even the things they saw -- can directly affect you, decades later, despite your never experiencing these things yourself. And that what you do in your lifetime could in turn affect your grandchildren.
The conventional view is that DNA carries all our heritable information and that nothing an individual does in their lifetime will be biologically passed to their children. To many scientists, epigenetics amounts to a heresy, calling into question the accepted view of the DNA sequence -- a cornerstone on which modern biology sits.
Epigenetics adds a whole new layer to genes beyond the DNA. It proposes a control system of 'switches' that turn genes on or off -- and suggests that things people experience, like nutrition and stress, can control these switches and cause heritable effects in humans.
For example, a famine at critical times in the lives of the grandparents can affect the life expectancy of the grandchildren. This is the first evidence that an environmental effect can be inherited in humans.
Seven thousand five hundred fifty-six (7556) haplotypes of 46 subclades in 17 major haplogroups were considered in terms of their base (ancestral) haplotypes and timespans to their common ancestors, for the purposes of designing of time-balanced haplogroup tree. It was found that African haplogroup A (originated 132,000 ± 12,000 years before present) is very remote time-wise from all other haplogroups, which have a separate common ancestor, named β-haplogroup, and originated 64,000 ± 6000 ybp. It includes a family of Europeoid (Caucasoid) haplogroups from F through T that originated 58,000 ± 5000 ybp. A downstream common ancestor for haplogroup A and β-haplogroup, coined the α-haplogroup emerged 160,000 ± 12,000 ybp. A territorial origin of haplogroups α- and β-remains unknown; however, the most likely origin for each of them is a vast triangle stretched from Central Europe in the west through the Russian Plain to the east and to Levant to the south. Haplogroup B is descended from β-haplogroup (and not from haplogroup A, from which it is very distant, and separated by as much as 123,000 years of “lat- eral” mutational evolution) likely migrated to Africa after 46,000 ybp. The finding that the Europeoid haplogroups did not descend from “African” haplogroups A or B is supported by the fact that bearers of the Europeoid haplogroups, as well as all non-African haplogroups do not carry either SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 (haplogroup A and its subclades SNPs) or M60, M181, P90 (haplogroup B), as it was shown recently in “Walk through Y” FTDNA Project (the reference is incorporated therein) on several hundred people from various haplogroups.
Klyosov, A. & Rozhanskii, I. (2012). Re-Examining the "Out of Africa" Theory and the Origin of Europeoids (Caucasoids) in Light of DNA Genealogy. Advances in Anthropology, 2, 80-86. doi: 10.4236/aa.2012.22009.
http://www.scirp.org/journal/PaperInformation.aspx?paperID=19566
Among his fellow Russian, (and other),
researchers Klyosov is considered a whack job. Here is an excerpt from a
biodiversity forum:"Vadim Verenich
2012-03-26, 16:04
To put it briefly, Klyosov's "arguments" in a nutshell:
This garbage, non-science was "published" by a discredited Russian ultra-nationalist (with a reputation for being a ding-bat), claiming that all humans outside Africa did not originate in Africa but actually originated in a "vast triangle" between, wait for it, _Russia_, The Levant and Central Europe. Except that it was *not* actually published; certainly not in a genuine, accredited, peer-reviewed scientific journal. It was merely "put on the internet" through a medium that will post any garbage dependent only on the author's willingness to pay. Thus, the garbage in that paper was doubtless rejected by many journals until the authors decided to pay SciRP.org, a thoroughly scurrilous and disreputable heap of shit, whatever fee they were demanding. SciRP.org is *so* disreputable that the entire editorial board of _Advances in Anthropology_ resigned in protest, _en masse_, in 2014.
You only have to read the paper in that e-rag to see that the conclusions are spurious and misleading, even without any previous, in-depth knowledge of Y haplotypes. One obvious error (or fraud) is that they talk about the African haplogroup as if it is virtually monomorphic, when anyone with even the vaguest knowledge of the subject knows that the San bushmen population in Southern Africa has the greatest degree of Y haplotype variation on the entire planet.
This paper is very far from genuine science and constitutes actual scientific fraud.
Deep within your DNA, a tiny parasite lurks, waiting to pounce from its perch and land in the middle of an unsuspecting healthy gene. If it succeeds, it can make you sick.
Like a jungle cat, this parasite sports a long tail. But until now, little was known about what role that tail plays in this dangerous jumping.
Today, scientists report that without a tail, this parasitic gene can't jump efficiently. The findings could help lead to new strategies for inhibiting the movement of the parasite, called a LINE-1 retrotransposon.
The research, published in Molecular Cell by a team from the University of Michigan Medical School and the Howard Hughes Medical Institute, answers a key question about how "jumping genes" move to new DNA locations.
The parasite in question isn't a foreign beast, but rather a piece of DNA that carries its own instructions for making a piece of "rogue" genetic material and two proteins that can help it jump. "Jumping" allows this rogue copy to land anywhere in the DNA of a cell, causing a change called a mutation.
Jumping LINE-1s - and other genetic parasites like it - are responsible for about one in every 250 disease producing mutations in humans. They've been blamed for causing a number of diseases, including hemophilia, Duchenne muscular dystrophy, and cancer. Copies of this parasite litter our DNA, though most of them can no longer jump and cause damage.
For these reasons, scientists want to understand as much as possible about how this process works. Perhaps someday, this new understanding could help fight the effects of these jumps - or prevent the parasites from leaping in the first place.
"Now, we have a mechanism to explain how sequences that comprise one-third of our genome have moved," says John Moran, Ph.D., senior author of the new paper and a longtime U-M and HHMI researcher studying jumping genes. "By understanding how LINE-1 jumps, we can understand how it contributes to disease."
A cat without a tail, a tail without a cat
The gene that's responsible for LINE-1 jumping does its damage by first creating an RNA copy of itself. That RNA copy tells the cell to make two proteins that help make it possible for the LINE-1 RNA itself to jump into a new spot.
Each copy of LINE-1 RNA has a long tail at its end that's made up of multiple copies of a substance called adenosine. Known as a "poly(A) tail", it's long been suspected of playing a role in LINE-1 jumping. But it was impossible to figure this role out because removing the tail also eliminates another key function it serves, in getting the RNA to the location where proteins are made.
Like the Cheshire Cat of Alice in Wonderland, if the tail vanished, the rest of the "cat" would too.
So, a postdoctoral fellow, Aurélien Doucet, Ph.D., now a research associate at the Institute for Research on Cancer and Aging in Nice, or CNRS, in France, collaborated with Jeremy Wilusz, Ph.D., now an assistant professor at the University of Pennsylvania Perelman School of Medicine, to figure out a way to delete the LINE-1 poly(A) tail to determine if it affected LINE-1 jumping.
They succeeded in making a LINE-1 RNA, without a poly(A) tail, that got where it needed to in the cell to make proteins.
The substitute tail allowed the scientists to see what happened when LINE-1 RNA could get to the protein-making spot, but without its usual appendage.
Here's where it gets interesting. Without the poly(A) tail, almost no jumping happened - because the tailless LINE-1 RNA couldn't interact well with a protein called ORF2p.
ORF2p is actually one of the two proteins that the LINE-1 RNA tells the cell to make. Once ORF2p binds to the RNA's tail, it sets in motion the steps needed for a jump to occur.
Moran compares it to a Lego set - where one kind of tail could get unplugged and another slotted in to serve some, but not all, of the same functions.
In other words, the LINE-1 parasite is especially crafty.
A parasite of a parasite?
LINE-1 also has a competitor parasite, called Alu. And when LINE-1 RNA lacked the tail and couldn't jump, Alu RNA did much better at jumping.
Alu RNA also sports a poly(A) sequence at its end, which has already been shown to be vital to its ability to jump. But the Alu RNA doesn't contain the instructions for making a protein. This suggests, says Moran, that the two parasites compete to have access to ORF2p proteins. That is, Alu is a parasite of a parasite.
Moran and his team continue to build on their new finding that poly(A) sequences are crucial for retrotransposition. They're studying how Alu interacts with ORF2p, and how the use of a replacement for the poly(A) tail may be helpful in other research. They're also interested in how the cell, or host, fights off jumping genes and protects DNA from damage.
"Our DNA is a sea of junk copies of LINE-1 that can't jump, and a small minority of LINE-1s that can," says Moran, who is the Gilbert S. Omenn Collegiate Professor of Human Genetics in the U-M Department of Human Genetics. "We need to understand at the RNA level how these LINE-1 RNAs are chosen for jumping, and how we can stop them."
http://phys.org/news/2015-11-parasite-tail-team-gene-mystery.html?utm_content=buffer39119&utm_medium=social&utm_source=facebook.com&utm_campaign=buffer
Ancient DNA shows Stone Age humans
evolved quickly as they took up farming
By Joel Achenbach November 23
People in western Eurasia underwent evolutionary changes as they adopted farming as a way of life.
Prehistoric people who adopted farming as a way of life underwent evolutionary changes to adapt to their new lifestyle, a dramatic example of natural selection operating on the human species in the relatively recent past.
That's one of the conclusions of a new study of the genomes of 230 individuals who lived thousands of years ago and whose bones have been recovered from Western Eurasia — a broad area that includes what is now Turkey, the Russian Steppe and Europe.
The research, published Monday in the journal Nature, identified 12 specific genetic mutations that corresponded to the rise of agriculture and the migration of people into new regions. They include the ability to digest milk and metabolize fats. The mutations also favored greater height at maturity, lighter skin and lighter eye color in northern populations. There are also genetic markers that appear to be connected to resistance against such diseases as leprosy and tuberculosis.
Ancient DNA shows Stone Age humans evolved quickly as they took up farming
By Joel Achenbach
Prehistoric people who adopted farming as a way of life underwent evolutionary changes to adapt to their new lifestyle, a dramatic example of natural selection operating on the human species in the relatively recent past.
That's one of the conclusions of a new study of the genomes of 230 individuals who lived thousands of years ago and whose bones have been recovered from Western Eurasia — a broad area that includes what is now Turkey, the Russian Steppe and Europe.
The research, published Monday in the journal Nature, identified 12 specific genetic mutations that corresponded to the rise of agriculture and the migration of people into new regions. They include the ability to digest milk and metabolize fats. The mutations also favored greater height at maturity, lighter skin and lighter eye color in northern populations. There are also genetic markers that appear to be connected to resistance against such diseases as leprosy and tuberculosis.
swer to the question of how agriculture arrived in Europe. There have been two competing scenarios. One is that agricultural people — farmers — arrived as migrants, replacing indigenous populations. The other is the practices of farming were transmitted culturally, a contagion of innovation known to anthropologists as "cultural diffusion."
The new research strongly supports the first scenario, showing that the people who began farming in Europe, starting about 8,500 years ago, were closely connected to a population of farmers in Anatolia, a region that largely overlaps with modern-day Turkey.
“It is a migration. It’s a movement of people. The farmers in Europe from Germany and Spain are genetically almost identical to the farmers from Turkey," said Iain Mathieson, a geneticist at Harvard Medical School and the lead author of the new report.
[Research shows Stone Age farmers and hunters didn't mingle]
Modern human beings spent many tens of thousands of years as hunters and gatherers. But at the end of the last Ice Age, as temperatures stabilized, people in Mesopotamia and the Levant — the Fertile Crescent — began planting crops and domesticating animals as livestock. The farmers and their new way of life spread to other parts of Eurasia. Farming allowed greater population density, but it was a difficult way of life that at first led to poor nutrition and zoonotic diseases associated with living in close quarters with domesticated animals.
[The switch to farming made our skeletons more fragile (because we got lazier)]
“It's a change in the food people are eating. It’s a change in social organization. People are living in much bigger communities. People are living in much closer proximity to animals," Mathieson said.
That was a technological revolution that had genetic repercussions. Natural selection functions as a filter, favoring people with certain genetic mutations that allow them to more easily reach maturity and have children who are themselves advantaged. Thus, around 4,000 years ago, according to the new study, Europeans begun showing a genetic change associated with lactase persistence — the ability to digest milk into adulthood.
That such evolutionary changes have been taking place in the relatively recent past is not a surprise. Indeed, scientists have modeled many of these genetic adaptions simply by looking at people alive today and comparing their genomes. But this new work is more of a direct look at the prehistoric evolutionary processes as they were happening.
“It's taking ancient DNA to actually go back in the past," said Rasmus Nielsen, an evolutionary biologist at the University of California at Berkeley. He was not part of the team that published the new findings. "The paper is able to verify many of the predictions that have been done in the past 20 years from looking at modern populations. In some sense we have this scientific time machine," he said.
One possible implication of this research is that the popular "Paleo Diet," which embraces foods available to Stone Age people and avoids the dairy products and grains that came along only in the last 10,000 years, ignores the recent evolutionary changes in the human species. But Mathieson did not take a stance on this latest food fad.
"I don't think we can really speak to this," he said. "We show that people were able to adapt genetically to an agricultural diet, but it's rather an open question how well they adapted."
(c)2013-2016; All Rights Reserved, Iona Miller, Sangreality Trust
[email protected]
Fair Use Notice
This site contains copyrighted material the use of which has not always been specifically authorized by the copyright owner. We are making such material available in our efforts to advance understanding of environmental, political, human rights, economic, democracy, scientific, and social justice issues, etc. We believe this constitutes a 'fair use' of any such copyrighted material as provided for in section 107 of the US Copyright Law. In accordance with Title 17 U.S.C. Section 107, the material on this site is distributed without profit to those who have expressed a prior interest in receiving the included information for research and educational purposes. If you wish to use copyrighted material from this site for purposes of your own that go beyond 'fair use', you must obtain permission from the copyright owner.
[email protected]
Fair Use Notice
This site contains copyrighted material the use of which has not always been specifically authorized by the copyright owner. We are making such material available in our efforts to advance understanding of environmental, political, human rights, economic, democracy, scientific, and social justice issues, etc. We believe this constitutes a 'fair use' of any such copyrighted material as provided for in section 107 of the US Copyright Law. In accordance with Title 17 U.S.C. Section 107, the material on this site is distributed without profit to those who have expressed a prior interest in receiving the included information for research and educational purposes. If you wish to use copyrighted material from this site for purposes of your own that go beyond 'fair use', you must obtain permission from the copyright owner.