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mple we could start reading genome at the first rather than the first base however the previous link demonstrates that there s exactly one whole genome alignment otherwise known as a global alignment or starting index for mtdna the rest of them are simply not credible for the reasons discussed above this makes whole genome comparison super easy and incredibly fast and in fact my software can compare a given genome to all 644 genomes in the dataset in just 0 02 seconds running on an apple m2 pro producing a ton of statistics for the input genome not just the number of matching bases sure it s a great machine but it s not a super computer which means now everyone can do real genetic analysis on consumer devices once popularized these methods will probably make short work of the complete history of mankind and possibly the entire history of life itself since mtdna is not unique to humans further these methods and their results are rock solid empirical evidence for the theory of evolution which as you ll see below is not subject to serious criticism at least with respect to mtdna modern relatives of heidelbergensis as noted above many modern living humans have mtdna that is a 95 or more match to the single heidelbergensis genome in the dataset the genome was found at sima de los huesos and there is apparently some debate about whether it is actually a neanderthal but it is in all cases a very archaic genome from around 500 000 years ago as such though i concede this heidelbergensis genome is a 95 10 match to the third neanderthal genome in my dataset which is from around 100 000 years ago i think it s best to distinguish between the two given the huge amount of time between the two genomes and the fact that they re not exactly the same genome recall that we are comparing whole genomes by simply counting the number of matching bases which we ll call the match count we can therefore set a minimum match count of say i e 90 of the genome and retrieve all genomes that are at least a 90 match to heidelbergensis this produces the chart below where the height of the bar provides the percentage of genomes in the applicable population that are at least a 90 match to the single heidelbergensis genome for example 100 of the iberian romani are at least a 90 match to the heidelbergensis genome producing a height of 1 0 in the chart below the population acronyms can be found at the back of 2 but just to highlight some of the obvious matches kz stands for kazakhstan ib stands for iberian romani it stands for italy and ru stands for russia a chart showing the percentage of each population that is at least a 90 match to heidelbergensis the plain takeaway is that many modern humans carry mtdna that is close to heidelbergensis peaking at a 96 69 match for a kazakh individual as noted above when working with modern genomes you ll often find a basically perfect match that exceeds 99 but when working with archaic genomes that s not always the case and it makes perfect sense since so much time has elapsed that even with the incredibly slow rate of mutation for mtdna a few percentage points of mutation drift is to be expected the phoenician people the phoenicians were a mediterranean people that existed from around 2500 bc to 64 ad though there could be other example genomes the phoenicians are a great case study because they are a partial match to heidelbergensis and a partial match to the pre roman ancient egyptian genome you can already appreciate the intuition that heidelbergensis evolved into the phoenicians and then the phoenicians evolved further into the ancient egyptians now the real story is more complicated and it doesn t look like all of this happened in the mediterranean instead it looks like human life begins in west africa migrates to roughly the mediterranean and eurasia migrates further to somewhere around northern india and then spreads back to europe and africa and further out into east asia you can read 2 for more on this topic this note will instead be focused on the evolution of the individual genomes and less so on claims regarding their historical geographies that is i m going to present you with a set of genomes that begin with heidelbergensis and end in the icelandic people who are almost certainly vikings but i m not going to argue too much about where these mutations happened outside of a few notes for context so that it s not all happening in a void returning to the phoenicians we want to show first that the phoenicians evolved from heidelbergensis all of these steps will involve epistemological reflections so that we can be comfortable that we re asserting reasonable claims that said as you ll see all of these claims are uncertain and plainly subject to falsification but that s science to begin note that there are 6 phoenician genomes in the dataset and that the first phoenician genome in the dataset row 415 is at least a 99 72 match to the other 5 phoenician genomes as such to keep things simple we will treat this first phoenician genome as a representative genome for the entire class of phoenicians further note that the first phoenician genome is a 41 17 match to heidelbergensis if we were comparing two random genomes then the expected match count is 25 of the genome since the distribution is given by the binomial distribution with a probability of success of that is at each base we have two random variables one for each genome and each of those variables can take on a value of a c g or t if it s truly random then there are possible outcomes and only 4 of those outcomes correspond to the bases being the same producing a probability of therefore we can conclude that the match count of 41 17 between heidelbergensis and the phoenician genome is probably not the result of chance the claim that the two genomes are truly related finds further support in the location of the matching bases which are concentrated in the first 3 500 bases which is shown in the chart below the chart below is produced by taking 500 bases at a time starting with the first 500 bases of each genome and counting how many bases within that 500 base segment match between the two genomes the maximum match count is of course 500 bases which would produce a height of 1 0 or 100 this process continues over the entire genomes producing the chart below as you can see the most significant matches are clustered in the first 7 segments representing the first 3 500 bases of the genomes the argument is because there is a significant contiguous segment within the genomes that are highly similar we can confidently rule out chance as the driver of the similarity you can never be totally certain but since it s probably not chance that s driving the similarity the logical conclusion is that heredity and mutation is what caused the similarity between the two genomes now we don t know the direction of time from this analysis alone i e either genome could have evolved into the other but because heidelbergensis is very archaic the logical conclusion is that heidelbergensis mutated eventually forming the phoenician maternal line a chart showing the percentage of matching bases between the heidelbergensis and phoenician genome broken into 500 base segments one important point to note is that even if a genome evolves it does not imply that all instances of that genome evolve for example as noted above 100 of the living iberian romani people are at least a 90 match to heidelbergensis demonstrating that at least some heidelbergensis genomes did not evolve into the phoenician line and instead remained roughly the same over time as such we can say confidently that mtdna is very slow to mutate as a general matter but the rates of mutation are heterogenous just to close this section with some context for modern humans that carry the phoenician line 80 of living sardinians and 33 33 of living vedda aboriginals are at least a 90 match to the phoenicians obviously it s a bit shocking that you d have phoenician mtdna in asia but if you read 2 you ll quickly learn that these are global maternal lines that often contain multiple disparate people two common sense explanations 1 the phoenicians really made it to asia or 2 there s a common ancestor for both the phoenician and vedda people presumably somewhere in asia hypothesis 2 finds support in the fact that 10 52 of mongolians are also at least a 90 match to the phoenicians this is a complicated topic and it s just for context the real point of this note is that you can plainly see that heidelbergensis evolved which is already interesting and compelling evidence for the theory of evolution and specifically it evolved into the phoenician maternal line the ancient egyptians introduction the ancient egyptians were a mediterranean civilization that lasted from around 3150 bc to 30 bc until it was ruled by rome from around 30 bc to 642 ad there are two ancient egyptian genomes in the dataset one from approximately 2000 bc before roman rule and another genome from approximately 129 to 385 ad during roman rule this is a huge amount of time and so it s not surprising that the demographics changed but the ancient egyptians present a shocking demographic shift from earlier rulers that were plainly of asian origin to rulers that looked and were known to be european for example see the panel of images below with nefertiti 1353 to 1336 bc on the left then king menkaure and his queen 2550 bc to 2503 bc and finally cleopatra 51 to 30 bc on the right who is known to be macedonian queen nefertiti image courtesy of wikipedia king menkaure and queen image courtesy of museum of fine arts boston queen cleopatra image courtesy of wikipedia the hypothesis that the earlier egyptians were of asian origin is further supported by the chart below which shows the distribution of genomes that are at least a 99 match to the pre roman egyptian genome the full set of population acronyms are in 2 but for now note that np stands for nepal jp stands for japan fn stands for finland no stands for norway eg stands for modern day egypt dn stands for denmark ga stands for georgia th stands for thailand fp stands for philippines and kr stands for korea as you can plainly see the pre roman egyptian genome is very common in northern europe and east asia with very little representation in africa outside of modern day egypt though there is some nuance to this see 2 for more the point is the pre roman egyptian genome probably comes from asia and spread to northern europe north africa and east asia and as far as i know this is not exactly accepted history but it s clearly the case a chart showing the percentage of each population that is at least a 99 match to the pre roman egyptian genome ancestry from heidelbergensis and phoenicia as noted above the pre roman egyptian genome row 320 is a partial match to the phoenician genome with a match count of 88 of the genome this is obviously very high so we can be confident that this is not the result of chance and is instead the result of heredity and mutation further because we have assumed that heidelbergensis is the ancestor of the phoenician genome since it is archaic it cannot be the case that the ancient egyptian genome is also the ancestor of the phoenician genome specifically because mtdna is inherited directly from the mother to its offspring there can be only one ancestral maternal line for a given genome though there can be intermediate ancestors for example genome a mutates into genome b which in turn mutates into genome c however because the ancient egyptian genome has a match count of 29 73 to heidelbergensis the ancient egyptian genome cannot credibly be an intermediate ancestor of the phoenicians between heidelbergensis and the ancient egyptians therefore it must be the case given our assumption that heidelbergensis is the ancestor of the phoenicians that the pre roman ancient egyptian genome is the descendant of the phoenicians historically this is counterintuitive because the ancient egyptians are more ancient than the phoenicians but as noted above these maternal lines are broader groups i m simply labelling them by using the most famous civilizations that have the genomes in question further as noted above a lot of this evolution probably happened in asia not the mediterranean so one sensible hypothesis is that heidelbergensis travelled east mutated to the phoenician line somewhere in asia and then that phoenician line mutated further into the pre roman ancient egyptian line again probably somewhere in asia this is consistent with the fact that 76 67 of kazakh genomes 44 44 of indian genomes and 66 67 of russian genomes are at least a 95 match to heidelbergensis making it plain that heidelbergensis travelled to eurasia and asia in contrast as noted above the pre roman ancient egyptian line is found generally in northern europe east asia and north africa consistent with a further migration from eurasia and asia into those regions the roman era egyptian genome as noted above the ancient egyptians were ruled by rome from around 30 bc to 642 ad though it is reasonable to assume that there were resultant demographic changes we re only looking at two genomes from ancient egypt and so the point is not that these two genomes are evidence of that demographic change the evidence of the demographic changes are above in the form of archeological evidence of completely different people ruling their civilization the point of this section is instead that there is a second genome that was found in egypt that is dated to around 129 to 385 ad squarely during rome s rule over egypt that is related to the other ancient egyptian genome discussed above specifically the roman era egyptian genome row 321 is a 42 20 match to the pre roman egyptian genome row 320 now that is significantly above chance i e 25 but we can also perform the same analysis we did above looking to 500 base segments for confirmation that the match count is not the result of chance which is shown below again the most similar regions are concentrated in the first seven 500 base segments plainly suggesting heredity rather than chance because we have assumed the phoenician genome is the ancestor of the pre roman egyptian genome it cannot be the case that the roman era egyptian genome is the ancestor of the pre roman egyptian genome we can further rule out the possibility of an intermediate relationship by noting that the match count between the roman era egyptian genome and the phoenician genome is 30 50 therefore we have established a credible claim that heidelbergensis evolved into the phoenician maternal line which in turn evolved into the pre roman egyptian maternal line and then further into the roman era egyptian maternal line iceland and the vikings the dataset contains a single icelandic genome though it was collected from a person in canada so it s fair to express some skepticism as people can deliberately deceive researchers though i m not sure why you wou...
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