Tuesday, March 25, 2014

A Family Tree of all Mankind - part 6

Charts and Graphs.
      So back to my project. What the heck does the family tree for all of humanity even look like? We can answer this taking it in small pieces. Let's start with a chart of human population over time:

    

      Human population is trying to grow exponentially while also being constrained by a ceiling of finite resources. Let's flip that on it's side by rotating clockwise to imagine what a descending tree from a single ancestor (like Adam) looks like:

      But my ascending tree is building up in the other direction starting from my trunk in the present. My ascending tree resides within the larger descending boundary of world population. They are both growing exponentially in opposite directions toward each other, until they meet:


   

      And you get something like a diamond shape on the inside. That's what my ancestor tree should look like in theory. It expands outward until it hits the limits of world population at which point it can't grow anymore because that's impossible! This is all dramatically over-simplified of course because the whole world isn't one giant pool of population. There were geographically isolated groups of people whose separate gene pools were like different little petri dishes all cultivating their own stuff, with little bits occasionally being transferred across and between like strands. Occasionally we had major migrations and invasions, and mainly royal families intermarrying across larger geographic distances. Globally, we had major petri dishes like the Americas, Indonesia, China, and Africa etc. Then within those we had smaller, more locally integrated petri dishes like France, Spain, Britain, Germany, and Scandinavia etc. So I envision my local ancestor tree within the global descendant tree as this sort of football-shaped overlapping lattice structure that I'm going to try to draw in paint, but it really doesn't do the image in my mind much justice:

 
   

      Lol. Do I get an A for effort for this masterpiece of art? C+ maybe? Most other articles I've read refer to this phenomenon as a "diamond" shape, or a 4-pointed-star rather than a football I think. And they may have a point (ha ha pun), but I do prefer to think of it as a football because a football is more 3D. This is only a very rough 2D depiction of a higher dimensional landscape of our ancestors. I think it would be very excellent if someone created an interactive 3D model or space to display the whole world's family tree (ascending and descending both) in which time is along the z axis and geographical location is along the x and y. So imagine that you had a Cartesian map of the Earth on the floor making up the x and y dimensions. The present day (time = z = 0) is the floor level, and going up in the +z direction goes back in time. Within a computer model, such a simulation could handle all ancestors and cousins as points that could be connected by lines of relationship. Following the lines, either up or down, one would see the tree branching out, and fusing back together. This would be really cool to zoom in and out of, and click on individuals to bring up info, and trace certain pathways, and get a more visual understanding of what deeper trees really look like instead of just many separate slices of it, 2D at a time. I don't have the time or ability to create this, but if someone else reading this does have the programming skills, I think would be really educational and insightful to build a platform for this network. It would be an interesting alternative to the way genealogy is being displayed now on the internet with hyperlinked webpages for the nodes. These provide an "inside-view" of the footballs but never the whole bigger-picture at any given time.
      Everyone now living or who has ever lived and is known could conceivably be plotted/imported in, as well as primates, mammals, dinosaurs and the whole gamut of the rest of life's evolution too. And I'm certain that by getting a better visualization of certain aspects of a network of individuals in a population like this, some insights can be gleaned that are applicable to understanding the relationships and interfaces between different species, in particular - primates.
      For example, we know that during evolution mutations occur, and some of those are favorable and eventually come to dominate in the population, while the competing traits/genes that were inferior go extinct. It's tempting to simply understand this by imagining all the later population being descended from the one individual who made the original mutation, but not descended from the rest of the population that didn't mutate. But this is not correct. Remember I showed on an earlier page how everyone is descended from ~80% of a whole population, and no one is descended from the remaining ~20% whose progeny went extinct. (80 and 20 are just variables of course, that would differ between species and situations) The evolution of the genes in the pool is separate and subtly different from the evolution of the individuals, which are massive conglomerations of the genes. The interface between different species are therefore not singular "points" of connection (or a single pair of 1 male + 1 female), but are regions of width and length in the xy plane of my imagined model. Like when humans passed through the Toba Catastrophe genetic bottleneck 70k years ago, this is what that would look like:



      You could imagine tracing only your mother's mother's mother's line etc... until you can get no further. Then you could extend that by what you know about your mitochondrial DNA, which only females pass on. I read a wonderful book by Bryan Sykes called The Seven Daughers of Eve that lays out a depiction of what genetic analysis has to say about humanity's matrilinear ancestries. A case is made that depending on which humans on Earth you sample, there are seven major genetic Eves from which humans might descend. Those 7 Eves lived at very different times and places, and are themselves further descended from all humanity's singular most-recent Mitochondrial-Eve (M-Eve's mother would also be an M-Eve, but at some point there must be a most recent one). On the other hand you can trace your father's father's father's line etc... and extrapolate that together with your Y-Chromosomal DNA to do the same thing patrilinially to your Y-chromosomal Adam. These 2 extremes within your tree form a special boundary or outline of what your personal ancestor tree looks like, but there is also everywhere else in-between the outlines. If you go up one generation (to your parents) and do the same for them, and plot out their matrilineal and patrilineal lines, they will follow different pathways back through the intermediate Adams/Eves on their way back to the first universal ones. This hypothetical ancestor is called LUCA for Last Universal Common Ancestor. It's important but subtle to also understand that the LUCA-Adam did not necessarily need to live contemporaneously with the LUCA-Eve.
      I've read that scientists now believe Neanderthals and our Cro-Magnon ancestors that displaced them did interbreed to an extent, and some small percentage of our DNA today comes from them. I also recall reading somewhere the hypothesis that they couldn't interbreed because of different chromosome numbers, which would cause their offspring to be sterile (like how the Mule is a cross between horse and donkey), but I suppose that hypothesis was falsified. Anyway, the point is that if this is true we are all descended from the whole population of Neanderthals (or ~80% thereof), not just a few specific ones. And if it was possible for other species of the ancient primates to interbreed, then scientists' quest to find the missing link of our human evolutionary pathway through the primates may not be asking the exact right question. There may in fact be multiple correct pathways.

      Back to my tree project - the next chart shows a sideways view of the football structure from my above artistic-masterpiece. I'm able to take some actual data from my tree and show how it compares to the "diamond point" or star or football theory. This next chart shows the "width" of my tree project's data. Keep in mind, in practice the width is determined by how many ancestors at a given generational slice are known and therefore entered into the software, and in theory the width would be much greater if we had complete information. But we'll take what we can get, and hope that in practice and in theory correlate to some degree. Which I think they do.



      On the X axis is the number of generations going back from the present time. On the Y axis I have number of people (For example, if you went back 3 generations your width at that point would be 8 people, assuming no pedigree collapse.) This chart is at its widest 28 generations ago. Using 28.5 years per generation, that is 800 years ago at around 1200 AD. What's significant about this chart are the two curves 1.) along the uphill slope on the left, and 2.) along the downhill slope on the right. The curve on the left is an exponential - It's growing at a rate of 2^n, or at least it would be if all the ancestor slots were filled in. But of course they aren't, as I explained earlier, so the growth is slower than 2^n. The downhill curve on the right shows exactly what you would expect to see in a deep-time family tree, and that is the pedigree collapse, which again, is where the same sets of ancestors start appearing in multiple places in the pedigree. In my tree at around 800 years ago, the rate of pedigree collapse starts to overtake the rate of exponentiation to new unique ancestors.

      Let's examine the timing of the peak at 800 years ago. Imagine that inbreeding doesn't happen, and that all our ancestors were unique. That comes out to 2^28 = 268 million people. What was the population of the World at that time? Well it was something like 350 million. But let's forget about the world as a whole and let's just talk about Europe, because 99% of all the people listed in my tree from 1200 are in Europe. Actually my tree at this point probably gives a pretty fair representation across Europe as a whole, including France, Spain, Germany, Britain etc. The population of Europe in 1200 AD was close to 100 million. Clearly 268 million unique ancestors at this time is impossible, not to mention that my listed names are mainly the rich and aristocratic who made up only a minority of the actual population. Objectively, most of our ancestors were the peasants and the poor. So clearly, pedigree collapse has been happening to a great extent well BEFORE the peak at 28 generations, but to repeat what I said earlier, it is the RATE of pedigree collapse that overtakes the RATE of exponentiation that this peak at 800 years ago represents. Another interesting observation: There is an unusual, significant spike right before the main spike that occurs at about 26 generations back. It seems to me that the obvious explanation for this anomaly is the bubonic plague. After all, it is occurring at just the right time when the plague decimated Europe. (The word decimated actually doesn't do the plague justice, since the etymology of that word comes from when the Roman legions' commanders would kill 1 out of every 10 soldiers - hence the prefix "deci". So if decimation kills only 1 in 10, it doesn't quite do the plague justice. But I digress.) I suppose the plague killed off the wealthy less-so than the poor, but regardless of the actual casualty rates between the rich and poor, and given our chart's bias toward the rich, the concern people had with record keeping would have also probably declined at this time. Who is going to concern themselves about genealogy and record keeping when everyone's dying? When 30% to as high as 70% of a population gets wiped out, you might expect genealogical data we have 700 years later to be attenuated, and that does seem to be the case.

      Another observation: The chart also shows a local peak at around generation 15. Let's do the math (15 * 28.5 = 430) which puts us back at 1575 AD. The immigration of people to the Americas is a notoriously difficult bridge for genealogists to gap. Most family lines dead end without a trace around this time, so we are not surprised to see this peak here either, being immediately followed by an attenuation in the chart. It's pretty common to be able to trace back a few generations from the individuals that actually did the immigration, but still 1575 AD seems a little on the early side to be seeing a peak for the American immigration. It turns out, the small peak at generation 15 comes mostly from the French Canadians which seem to have keep excellent family tree records back until about 1600 AD. What about that small but discernible bulge of expansion out at 70 generations ago? That is the Roman empire. 70 generations would put us right back at around the year 0. As before, that bulge is indeed correlated to increased record keeping, and availability of genealogical data. The Roman Empire has been described as a beacon of light in the otherwise barbaric past, and so it's no coincidence that the bulge occurs right where you might expect to see more data and person entries in the tree.

      I said earlier that my Family Tree Maker 2005 software only allows me to handle a maximum 99 generations at a time, so that's why the chart ends at 99. Because of the nature of how I produced this chart using FTM 2005, and because the way it handles duplicate ancestors (pedigree collapse), this chart is only a good approximation to the way things actually occur in the tree. And of course my family tree itself is only an approximation to the way our ancestors actually were in reality. So I'm just pointing out that this approximation of an approximation to reality is less than perfect, and there's an inherent margin of error. Furthermore the software wasn't at all designed for this level of insanity. It's more of a consumer product for retirees that want to upload photos and produce pretty charts within say the last 200 years.

For good measure, here's the same chart as above but shown cumulatively:





      Note that this chart approaches the number 24,523 asymptotically because that's the total number of ancestors in the tree. If I could plot the x axis all the way out to the end, the last data point would occur at (186,Y-2):

The fabled Adam and Eve.

Continued on page 7.
page 1,2,3,4,5,6,7,8,9 page

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