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Science

Scientists Unveil 'Unified Genealogy of Modern and Ancient Humans' (vice.com) 75

Posted by BeauHD from the genome-sequencing dept.
Scientists have unveiled the largest human family tree ever created, a shared ancestry that is woven out of more than 3,600 individual genome sequences that date back more than 100,000 years, providing an unprecedented glimpse into the deep past and complex present of our species. Motherboard reports: The immense family tree was stitched together from existing datasets and contains modern genetic information from around the world as well as samples from extinct human relatives such as Neanderthals and Denisovans. Scientists led by Anthony Wilder Wohns, who conducted the research while earning a PhD at the University of Oxford's Big Data Institute, were able to confirm major events in human history from this integrated framework, such our species' migration out of Africa, while also encountering surprises about past populations that will require more research to understand. The outcome is a "unified genealogy of modern and ancient humans" that demonstrates the power of computational methods "to recover relationships between individuals and populations as well as to identify descendants of ancient samples," according to a study published on Thursday in Science. Though this particular study is focused on humans, the team noted that the same approach could be used for almost any other species.

One of the innovations of study is a new algorithm that can more efficiently collate all this information into a single genealogy or tree sequence. By revealing relationships between individuals and populations of humans that stretch back deep into our prehistory, the approach mapped out 231 million ancestral lineages of our human family over time, as shown in the [video here]. The findings confirmed the timing of many migrations that are known from archaeological evidence, but there were a few unexpected implications in the data as well. For instance, the new family tree hints that humans first arrived in North America 56,000 years ago, much earlier than is currently estimated, and points to human migration to Papua New Guinea a full 100,000 years before the earliest documented evidence of habitation in that region. These tantalizing results do not necessarily mean that those migration timelines should be pushed back, but they do offer a compelling avenue of research going forward.
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Scientists Unveil 'Unified Genealogy of Modern and Ancient Humans' More

Scientists Unveil 'Unified Genealogy of Modern and Ancient Humans'

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  • That was weird and hard to interpret. Why show it backwards in time? I'd get a lot more out of it if the video showed human migration from Africa out to the world rather than shrinking back to the start.

    • Why is this a data visualization fail, and not a perspective fail? And what is it you think you might have gotten out of it had it ran backwards, that you didn't get the moment you realized it was moving into the past?

    • Re: (Score:1)

      by Tablizer ( 95088 )

      > hard to interpret. Why show it backwards in time?

      Because Donald ordered everyone to "go back to where you came from!"

  • Ancestors distinct 56kya. Not in the americas. Slashdot, vet these posts, this sounds like a copy paste from a major news site who also got it wrong.
    • Not what it looks like to me.
      Looks like distinct ancestors at 50k generationa ago, and first predicted arrival in the Americas of ~56kya.

    • Re:Read the article (Score:4, Informative)

      by RockDoctor ( 15477 ) on Saturday February 26, 2022 @08:43AM (#62305867) Journal
      We're both big enough, old enough and ugly enough to know that reading news sites about science is an utter WOMBAT (Waste Of Money, Brains And Time). Go directly to the paper and read what was actually said, and don't bother listening to someone else's misunderstanding.

      Paper [biorxiv.org](unpaywalled).

      • Thank you- I was looking for that. Admittedly, I gave up quickly after hitting the paywall.

        The actual paper does, at least, explain the 56kya pre-Last-Glacial-Maximum finding of an ancestral line in the Americas:

        At 56 kya, some ancestral lineages are observed in the Americas, much earlier than the estimated migration times to the Americas.

        This effect is likely attributable to the presence of ancestors who predate the migration and did not live in the Americas, but whose descendants now exist solely in this region; the same effect may also explain the ancient ancestors within Papua New Guinea.

        Thus confirming, TFA, actually did have it correct.

        • Yup. I have access to Science, hence my original comment. I already had read TFA.
          • Then I'm curious why you made such a comment.
            TFA said, "hints that humans lived there"
            THP says, "likely attributable"

            THP doesn't disagree with TFA, as there are in fact hints at such a thing, though the paper gives its opinion on what the more likely explanation is.
            That being said, there's evidence of pre-LGM habitation of the Americas that there isn't good explanation for yet, so it's also possible that it's exactly what it looks like.

            • ...the new family tree hints that humans first arrived in North America 56,000 years ago, much earlier than is currently estimated...

              That is why. That is not what the article says, nor the commentary on the article. It's what a major news site said, probably because they employ journalists who are scientifically illiterate.

            • But TFP doesn't say suggest that humans inhabited the Americas before 56kyr, or that they inhabited the Americas pre-14kyr (or whatever the currently accepted date for the Patagonia archaeology is; I don't follow the subject), or even, strictly, pre-1776 (though there are paper records that may contradict the 1776 occupation hypothesis). What the genetics suggest is that there were people living in (approximately) NE Siberia around 56kyr, but their only descendants today are providing blood samples in Centr

  • Hopefully it can tell me how genetics inexorably made me an overweight, lazy alcoholic, and how I had no hand in the matter.

    • Hopefully it can tell me how genetics inexorably made me an overweight, lazy alcoholic

      Genetics predicts that obesity is more likely if your ancestors come from a non-agricultural society. Asians have been eating rice for millennia, are genetically adapted to a high carbohydrate diet, and have the lowest rates of obesity.

      Alcoholism is more common if your genes come from ancestors without access to alcohol, such as Native Americans or indigenous Australians.

    • Lewis and Mortimer from. âoeTrading Placesâ making their usual $1.00 bet about genetics bs environment.

    • Your problem is that you chose the wrong parents.

  • Who's family is it that they traced back so far? It must be a significant percentage of extant humans. I recall a study years ago where they traced mitochondrial DNA that linked a common ancestor that lived a few thousand years ago with much of the population of modern Europe. Kinda makes war look stupid.

    • We're all related, back to at the least the origin of multicellularity (let alone radial versus bilateral symmetry) if not further. This is just adding a bit more detail to recent events.

      Regardless of which, the only purpose of war, ever, has been to remove resources from our more distant relative and apply them to closer relatives (including, if you wanted them, future relatives). That hasn't changed since ... I can't remember if the oldest archaeological evidence of organised warfare was 14kyr or 40kyr a

      • I'd argue that that's a too-reductive view of war as it actually happens. One thing we've seen again and again in history is that the most successful war-makers are those who are able to create war-making communities out of non-relatives.

        It's great in theory if you can limit your resource-maximization to those who are related to you closely enough that they stand out from the 99.9% of identical DNA and 98%+ of genetic variation in you that's shared across multiple regions of the world, but if you try to

        • Looking back a couple of generations ... did any of the European royal families of robber-baron descendants have any member less closely related than second cousin? Inbred bunch of legalised bastards that they are. Relatively successful by your metric (and their own).

          And of course, they used cruder (and cheaper) metric of relatedness then the relatively expensive on of genealogy. Speaking the same (approximate) language as you was an adequate measure of relatedness for the recruiting sergeant. Except, of c

          • It's interesting how much time and money those inbred European royals spent fighting each other, isn't it? There's no closer bond than fighting alongside your brother... and there's no greater enemy than a brother you're fighting against when you both want the throne.

            Gang slang and gang colours are basically the template for transcending relatedness in war. You can build a unified fighting force around speaking a language and flying a flag. Maybe add a song in there for everybody to sing, and you've go

            • and there's no greater enemy than a brother

              Fundamental biological resources theory (what is behind the calculations of statistical evolutionary theory) is that your most severe competition will come from the organisms most closely related to you. The most severe competition to a zebra (or lion) isn't the lion (or gut parasite, for the lion), but their respective siblings. To mis-quote Tennyson, "nature red in tooth and fratricide".

              • Or, for a different take, there is Haldane's aphorism that "I wouldn't lay down my life for a brother, but I would for four first cousins or eight second cousins". Many people think it was a joke, but Haldane had done the sums and was dead serious.

                • Haldane said he would lay down his life for two brothers or eight cousins. Family conflict in evolutionary theory, as I understand it, didn't really get started until Trivers.

                  However, despite Haldane working out the sums, what I've noticed about evolution and behaviour is that evolution rarely finds the theoretically perfect solution. Instead, it settles on whatever good-enough solution comes along and gets the job done. It is prone to settling on local maxima.

                  Birds, for example, should theoretically

                  • *(There's an intriguing alternative idea from Roughgarden that some birds allow laying in each others' nests as a sort of cooperative "don't put all your eggs in one nest" mutual insurance, but I'm not sure how much support that idea has gathered.)

                    Ascribing "intention" in evolution is hard, but one example of a "good enough" solution is the behaviour of male ostriches, who (if I've got this right) set up nest sites, and allow females to lay their eggs there "in return for" mating ; if, some days later the s

                    • Interesting examples, thanks!

                      I think the extreme example I've heard of male brooding is in black swans, where something like a quarter of pairings are male-male. They'll get a female to lay eggs, then chase her away so they can raise the offspring. That doesn't really have much to do with what we're talking about, but I think it's interesting anyway. :-)

                    • Corollary to the ostrich example : unsurprisingly, female ostriches generally (only) can support developing one egg at a time. Whether they indulge in sperm storage, or need a "new" insemination after each egg is laid, I don't know. I infer the latter, from the male behaviour, while a "sperm storage" strategy would have led to males developing "mate early" and cloacal plug strategies. ... Ah, plugging the combined reproductive and excretory duct in order to "keep your sperm in there" would probably have dra

                    • Interesting question about how long speciation in humans would take.

                      I'd suggest that polydactyly wouldn't be enough, since it wouldn't produce reproductive isolation in the presence of horny-enough humans. And, as the Neanderthal and Denisovan cases suggests, humans are pretty horny.

                      Another thing that slows down human speciation, I think, is our very low level of genetic diversity compared to most other species. As Craig Venter put it, "We are all essentially identical twins." There just isn't much s

                    • Interesting question about how long speciation in humans would take.
                      I'd suggest that polydactyly wouldn't be enough, since it wouldn't produce reproductive isolation in the presence of horny-enough humans.

                      The polydactyly example is just a marker for whatever selection trait is chosen in addition to "being a preacher", so you can - at least initially - distinguish those who might become a priest from those who can't. You could just as well choose to teach the priestly caste a language distinct from the com

                    • All good points, and I've enjoyed the discussion, thanks!
                    • The time limit before the discussion gets archived is annoying. I'd have to RTFM to find out how long it is, but I suspect it's looming.

  • Where do they fit in? Geneticists seem to flip back and forth between them being a seperate species or a seperate race from us. I always thought if 2 creatures could successfully breed and have viable offspring they were the same species and given alll humans other than africans have neanderthal blood in them this was clearly the case.

    If thats no longer the definition of a species where does that leave various breeds of dog. Are they seperate species? A chihuahua and a great dane look a damn site more diffe

    • Yep. Domestic dogs are the same species, different brewing yeast are the same species. Humans have always intermingled. Get in touch with the Neanderthal in you and get down with your bad self.

    • Re:Neanderthals (Score:5, Interesting)

      by MightyMartian ( 840721 ) on Saturday February 26, 2022 @08:20AM (#62305823) Journal

      The species definition is much fuzzier than that. In part, the notion of "species" is an artificial construct, a convenience necessary for categorization. For instance, a ring species is a species that has a wide territory, where each population of the species can interbreed with the next one, but the populations at the far ends cannot. Are the members of populations at the far ends different species, or the same species?

      It's possible that Neanderthals and modern humans had somewhat different mating signals, in which case even if conception was possible, it was fairly rare for Neanderthals and moderns to interbreed. Or perhaps it was more difficult for conception to occur, so that even though sex was common, producing viable and fertile young was uncommon. Barriers to interbreeding, whether they be biological, behavioral, or geographical, are usually what taxonomists use to determine whether two populations are a different species or not, but successful interbreeding in many cases isn't a binary "yes" or "no", but sometimes along a continuum with related species. For instance, coyotes and wolves are continued a separate species because of fairly significant differences in mating behaviors, and yet there is some gene flow between wolf and coyote populations (the so-called red wolves are basically descendants of wolf-coyote interbreeding). However, it appears such interbreeding isn't all that common, so taxonomists usually consider them to be separate species, and further, at least so far biologists can tell, wolves and coyotes only interbreed when a population is under stress, and there may not be many viable opportunities for mating with their own species.

      • Mod parent up!

        E.O. Wilson defines Species broadly as well.

        If they can't reach each other to breed then they are a new species, even if progeny would be viable otherwise.

        So when I travel to Japan, I'm a new species of human compared to being in Seattle! Weird right?

        But when you look at intermixing populations from Japan and Seattle over time it makes more sense. You can see the diversification and mixing. Then it's not so weird.

        Food for thought.

        • If they can't reach each other to breed then they are a new species, even if progeny would be viable otherwise.

          So when I travel to Japan, I'm a new species of human compared to being in Seattle! Weird right?

          Since you traveled to Japan then the two groups CAN reach each other. Japanese resident in the U.S. were interned back 80 years ago so they reached your area. So same species by that definition.

          Now if we were in communication with a biologically identical species in another star system then by this definition they would be a different species. I would disagree with that definition.

    • To amplify what MightyMartian said, there are many different definitions of species; by one count, 7 major definitions with 27 variations. It's because "species" as a category is a rough-but-useful heuristic. It maps what happens in nature to a concept, but it can't map perfectly, so people have come up with different imperfect mappings for different purposes.

      What they are using in this research is a concept which is much closer to what is actually happening on a DNA level: An ancestral recombination gr

    • I recommend reading Mildford Wolphoff & Rachel Caspari's Race and Human Evolution. It's quite interesting. Before I read it, I thought that the Out of Africa theory was set in stone. However, the authors argue that the various early hominids (e.g. homo erectus) are not distinct species but were able to interbreed with homo sapiens. This would include neanderthals. More extreme versions of the Out of Africa theory assume that homo sapiens slaughtered all the neanderthals, while moderate versions, along w

      • This paper stands in direct opposition to everything you are citing. Sure thereâ(TM)s likely contribution to the Homo sapiens genome from outside of Africa, eg homo eructus or Neanderthals. But the overwhelming majority of our gene pool originated in Africa, likely East Africa, and that is where most of it came from tens of thousands of years ago. There are multiple lines of evidence for this, including genetic, linguistic, and archaeological data. One only needs to look at the age and prevalence of ar

        • Speaking as a linguist, I doubt that "the number of languages and their variety" tells us anything about the origins of humanity. On the rest of your points, I have no reason to doubt what you say.

    • Re: (Score:2)

      by hey! ( 33014 )

      "Species" are a convention that exists purely for scholarly convenience; in nature there are no sharp divisions between closely related species. There are plenty of closely related "species" that can produce fully viable offspring. Even if you tried to use that as a supposedly objective criterion, you'd still be stuck with an exercise in line drawing lines since moderately divergent populations can produce viable offspring with somewhat reduced fertility -- which may have been the case with H sapiens and H

  • They released the data months ago, before the paper came out, and just for fun I generated 24 hours of video [youtube.com] mapping where all of the genetic variants on chromosome 22 have been found in current human populations.

    • Oh, and I also made this graph [wikipedia.org] for Wikipedia from the data.

      What you're seeing on the graph: The vast majority of genetic variation in any individual human comes from a pool that's shared in multiple regions of the world. 99%-99.5% of the genetic differences between a Frenchman and their French neighbour comes from the same pool of genetic variants that define the difference between that Frenchman and someone from China. We are a well-mixed stew.

      • Oh, and note that I'm talking about genetic variation only. We are all 99.85-99.9% completely genetically identical. Of the 0.1-0.15% of differences between us, it's 99-99.5% of those differences that are found in multiple regions of the world. (For Africa and Oceania that 0.1-0.15% is made up of 98% differences that are shared with other regions rather than 99-99.5%; in Africa because it retained a larger pool of genetic variation than the group that left Africa, and Oceania because it was isolated for

  • Probably some advertising javascript requirement or something. Just download https://www.science.org/doi/su... [science.org] from the source website to get a simple MP4 and a PDF caption. Who needs some third-party advert-ridden data-thief to view an MP4 and read a PDF?

    If you don't have a subscription to Science, the paper is on BioArXiv at https://www.biorxiv.org/conten... [biorxiv.org]

    It's easier to see what is happening if you run the video at about a quarter speed (can Vimeo do that? I've no idea - I don't have an exception for

  • ...when doing their family tree on genealogy websites.

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