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Thanks to interbreeding, just 7% of our DNA is unique to modern humans: study
- qyph 5y agoIs this for some subset of our DNA? Quick skim of the article didn't tell me. But there is a popular factoid that human dna is 98.8% similar to chimpanzee dna on average. Is that factoid false?
- sokoloff 5y agoI’d heard that as well and thought that 7% unique seemed extraordinarily high compared to the factoids I’d integrated over time.
- Swenrekcah 5y agoFrom the paper [0] they say in the abstract that the differences are 1.5% - 7%. So the lower end of that lines up with the 98.x% similarity. Then in the paper there is this paragraph: > Our ARG strategy allows us to bin the human genome into regions containing archaic admixture in at least some humans, regions of ILS, and regions free of both archaic admixture and ILS in all humans (hereafter archaic “deserts”). We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where one or more humans has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome (Fig. 4A). Maybe someone here understands what these words mean and can clarify? [0]: https://advances.sciencemag.org/content/7/29/eabc0776 https://advances.sciencemag.org/content/7/29/eabc0776
- dekhn 5y agoI asked the author (I was a postdoc at the lab he was a grad student in about 20 years ago). My question: """Are these differences evaluated/inferred using data from all regions of the genome (intergenic, viral repeats, etc) or just genes? I recall that the early reports that compared primates to humans just used genes (or maybe just the easily aligned regions, but out of order) which seemed like a big omission.""" His answer: """We used the Simons Genome Diversity panel (full phased genomes for ~300 people), along with Neanderthal and Denisovan genomes to make an ancestral recombination graph (ARG). The ARG is a sequence of trees describing relationships between everyone all along the genome. It's really just a sequence of trees at each variable site. Then, you can look at these trees and find segments where the archaics fall outside the variation of the humans. These are regions where no human shares ancestry with archaic either by recent admixture or by incomplete-lineage sorting. Turns out that's about 7% of the genome. What's in that 7%? It's a lot of genes and specifically a lot of genes involved in neural development and neural function! The method itself is blind to what is genic or nongenic. But this method is about the genealogy of genes across the genome, i.e., from whom they were inherited and not necessarily how different the versions were. In other words, it's about the topology of the trees across the genome, not their branch lengths.""" Beyond that things start to get really complicated, you need to understand concepts like haptotype blocks, how new genes arise, etc.
- deleted 5y ago[deleted]
- clucas 5y agoI just spent some time looking for the source, but I seem to have lost it, so take this all with a grain of salt, but based on some article I read: My understanding of the "shared DNA" factoids is that they are based on a very rudimentary analysis of DNA sequences. The human-chimp 98.8% thing is "true" in that 98.8% of sequences that appear in the human genome also appear in the chimp genome. But this ignores other axes of differences: Humans may have multiple copies of certain sequences, while chimps only have one. Or certain sequences may appear in completely different parts of the genome in one or the other. And all of these differences are relevant. TL;DR: 98.8% is true, but not really relevant for determining how "different" we are from chimps.
- tshanmu 5y agoNitpick: factoids are unverified and mostly inaccurate and false. Facts are true. Edit: corrected factoid definition to be a bit more accurate.
- dekhn 5y agothe chimpanzee factoid was distorted in a way that made the number look much larger than it really was. It only compared highly conserved regions in common between both organisms.
- andi999 5y agoSo what would be the 'real' number?
- dekhn 5y agodunno how you would measure it, for example if humans have an extra chromosome with a bunch of novel genes, how does that count? Or if the genes are identical but scrambled in order? It's sort of not even a really useful metric unless defined carefully.
- mmmrtl 5y agoThe popular factoid is correct, but the confusion here is that these are different measurements. Humans and chimps' genomes are similar in that if you align all the bases [A,C,T,G] that can be unambiguously aligned between the two genomes, 98.8% of the bases are identical. For modern humans to Neanderthals, that number is 99.7%, and between two random modern humans, it would be ~99.9% on average. This paper is asking a subtly different question - how much of the modern human genome is strictly human, not by simply lining up bases and running a diff, but looking at the inheritance of chunks of DNA ("haplotype blocks", size determined by processes of recombination, etc.) to try to understand how much and which regions of the modern human genome came from interbreeding with Neanderthals or Denisovans. There was variation in the pre-human population before the human/Neanderthal split, which means that if you compare just a single human to a single neanderthal, you'll find unique variants to each. However, most of those variants will have existed in both the human and neanderthal populations, so they should count neither as uniquely human nor neanderthal (knows as Incomplete Lineage Sorting, or ILS). The chunks in modern humans that derive from Neanderthals or Denisovans are different in different people and broadly across population groups (e.g. highest percent introgressed in Melanesians, lowest in Africans). But across all the modern humans in the study, there are regions where Neanderthal/Denisovan inheritance or shared variation (ILS) was never seen - that's 7% of the genome ("deserts"). And just 1.5% of the genome was in chunks where moderns human commonly have a unique mutation compared to Denisovans/Neanderthals.
- eloff 5y agoThis comment is better quality content than the article. I just wish I understood more of it.
- dekhn 5y agohuman genetics/genomics papers assume you understand an enormous amount of details of human genetics, the knowledge of which has been hard-won over a century. I worked in this field for decades, know a ton, and still have to read every sentence in this paper carefully, multiple ttimes, and check various sources to remind myself of technical concepts. There's a reason I switched to working on computing full time- a lot of these state of the art arguments can only be contributed to by people who are, well, state of the art, thick-skinned, and well-funded.
- decremental 5y agoI wonder if we knew the Neanderthals were a different species. It seems weird that we would have chosen to breed with them if they were obviously not the same species as us.
- whalesalad 5y agolaws all over the land that say it is illegal to have sex with animals demonstrate the fact that we, as humans, will breed with literally anything
- momirlan 5y agoThat's bestiality, not breeding as it doesn't produce offspring. It's like saying "i breed with my hand"
- jjk166 5y agoWell we have no way of knowing if the couplings that produced human-neanderthal hybrids were done with the intention of producing offspring. If you stick your dick in what you think is a bull but is actually the queen of Crete in a bull costume, your bestiality may very well result in a child.
- londons_explore 5y agoRumours always swirl about the disgusting things people from $X_NEARBY_CITY do to animals even today...
- ASalazarMX 5y agoIf Neanderthals were attractive and the offspring was viable, that's all they needed to know. I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc.
- dotcommand 5y ago> I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc. This is simply false. We know for a fact that humans have an in-group bias. Studies have shown that even infants and toddlers are biased toward their own in-group. https://phys.org/news/2017-04-infants-racial-bias-members.html https://phys.org/news/2017-04-infants-racial-bias-members.ht... https://time.com/67092/baby-racists-survival-strategy/ https://time.com/67092/baby-racists-survival-strategy/ If what you claim is true, we would never have had miscegnation laws. Most people in the world wouldn't encourage marrying their own kind. Just think about it. If people naturally favored the out-group ( people who look different ), racial/ethnic groups and diversity wouldn't exist. Blue eyes and blonde hair wouldn't exist because they are recessive traits. We wouldn't have any diversity because ethnic/racial groups require in-group bias to exist. The fact that we have black people, white people, indian people, chinese people, etc shows that in-group bias is the norm. People naturally find their own kind and traits to be attractive. We know it's innate since it exists in babies. To find out-group features to be desirable requires external pressure - media, education, etc. Edit: Since so many here are downvoting science because of their political agenda... "We Choose Friends Who Are Genetically Similar to Us" https://www.smithsonianmag.com/smart-news/we-choose-friends-who-are-genetically-similar-us-180952050/ https://www.smithsonianmag.com/smart-news/we-choose-friends-... "I like your genes: People more likely to choose a spouse with similar DNA" https://www.sciencedaily.com/releases/2014/05/140519160716.htm https://www.sciencedaily.com/releases/2014/05/140519160716.h...
- trhway 5y agoi think that also can be interpreted as "it is the modern human and Neandertals hybrid which happened to be the winning combination that took over the planet" or "interbreeding with Neanderthals is what saved modern humans after the genetic bottleneck of 70K year ago" or "the modern humans who didn't bred with Neandertals got selected out".
- themgt 5y agoThis seems to explain the technique they're using to study this: Ancestral recombination graph (ARG) inference (2) is a powerful starting point for such an analysis. An ARG can be conceptualized as a series of trees, mapped to individual sites, over phased haplotypes (chromosomes) in a panel of genomes. Ancestral recombination events, or sites at which chromosome segments with different histories were joined together by historical recombination, form boundaries between trees. Each ancestral recombination event manifests as a clade of haplotypes, all of which descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree (3). ARGs are complete descriptions of phylogenomic datasets and present for recombining genomes what single trees present for nonrecombining genomes, i.e., a complete description of their genetic relationships. We run [our ARG] SARGE on a panel of 279 modern human genomes, two high-coverage Neanderthal genomes, and one high-coverage Denisovan genome. Using the resulting ARG, we map Neanderthal and Denisovan ancestry, ILS, and the absence of both across modern human genomes. We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where *one or more humans* has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome. It sounds like a fancy graph-based Venn diagram of the genome overlap between different groups comprising sets of individual genomes. I'm still not 100% clear on their definition of "human-unique" - i.e. are these regions where all 279 sample human genomes are identical, or maybe all 279 had one or more modern versions of the allele vs. any of the samples still having an ancestral version? They go into detail on some specific genes: Several patterns emerge when considering genes with high-scoring human-specific mutations, and we highlight some of these key findings. Gene ontology terms related to mRNA splicing, processing, and export are enriched in genes with high-scoring mutations (table S7). Of these, we find a regulatory mutation affecting one—LUC7L3—that is somewhat tissue specific (tau, a measure of tissue specificity scaled from 0 to 1 = 0.713), most highly expressed in cerebellar tissue, and annotated to be involved in splice site selection. Its paralog LUC7L and the gene KHDC4, both of which also have high-scoring (top 50th percentile) regulatory mutations, are involved in the same process. In addition, the gene NOVA1, which harbors a nonsynonymous mutation in the top 95th percentile of our score distribution (Fig. 5C), is a neuronal splicing factor that regulates splicing of genes involved in synapse formation within the brain (43). Which makes it sound like maybe yes, all modern humans have the "new and (hopefully) improved" version of these genes while no ancestral samples did. https://advances.sciencemag.org/content/7/29/eabc0776 https://advances.sciencemag.org/content/7/29/eabc0776
- deleted 5y ago[deleted]
- neonate 5y agohttps://archive.is/Rs62D https://archive.is/Rs62D
- nobrains 5y ago7% of DNA is a lot of DNA.
- warent 5y agoWas just thinking this is actually a much higher percent than I originally thought
- cblconfederate 5y agoHow does that compare to other species
- lkrubner 5y agoIt does raise the question of "us" versus "them". But who was "them" really? It's clear there were some stupid humans: homo habilis home erectus homo naledi It's clear there are some smart humans: homo neanderthal homo denisovan homo sapien And it's clear there are some that we are not yet sure about, in particular: homo heidelbergensis But what about: homo antecessor If you could wave a magic wand, and summon them now, it's likely that Sapiens, Neanderthals, and Denisovans could learn each other's language and have a conversation. But would we be able to have a conversation with Heidelbergensis? So the question comes up again, as strong as ever, who was the first smart human? We used to think they were Sapiens, now it is seems likely the first really smart humans came before Sapiens, and we are just one of several smart humans. There was a species of humans that was unique to southern easter Africa, they had the largest skulls of any known human species, a recent article in the New York Times quoted one scientist saying they all would have been as smart as Albert Einstein. (I just searched for the article on Google and NYT but could not find it, it was an article that ran within the last 2 years.) In an ideal world we could find more DNA samples, and eventually figure out what the DNA is trying to tell us, but DNA doesn't last 2 million years, so we will never have the full DNA story of humans, going all the way back to homo habilis. So we are left looking at the clues and wondering, "When did us begin?"
- MichaelZuo 5y agoThe evolution of ‘anatomically modern humans’ was almost certainly a continuous change over many tens of thousands of generations. The assignment of arbitrary cutoffs and categories doesn’t really map onto reality well, as you’ve shown. Of course it’s difficult to accept that for every generation prior they were simply less ‘human’ and more ‘ape like’ all the way back to the first bipedal generation in sub-Saharan Africa. Because the implication is that our 10000th great grand parents were less human than we are, and their 10000th great grand parents were even less so, and so on until they were literally apes, or proto-apes to be more precise.
- lkrubner 5y agoCan you have continuous change when you have isolated populations who are facing different environmental pressures, which are pushing them in different directions? "Continuous change" suggests a story with a narrative, an outcome that grew naturally from the initial trends, rather than being frequently convulsed by contrary trends in a world that saw multiple reverses of global climate trends during various periods of glaciation interrupted by inter glacial periods.
- deleted 5y ago[deleted]