The tall and long tales that elephants tell (also, ancient DNA never forgets)

The new paper on ancient DNA from elephants, mammoths and mastodons, A comprehensive genomic history of extinct and living elephants, is pretty cool. It leverages next-generation sequencing and ancient DNA, to reconstruct the demographic history of several species of elephants, extant and extinct.

The major core finding is that ancient DNA along with better data from extant species suggests that straight-tusked elephant of Europe (P. antiquus), which went extinct 50,000 years ago, seems to have been an evolutionary synthesis of sorts. A substantial portion of its ancestry as from a deeply diverged lineage of elephant. But another fraction seems to derive from a branch of the African forest elephants, in particular, the West African variety. Finally, earlier on there was also admixture with an Asian pachyderm related to the woolly mammoth.

You can see from the figure at the top that the divergence between these lineages is on the order of hundreds of thousands to millions of years.

This section from the conclusion is a huge takeaway:

Our genomic analyses of present-day and extinct elephantids revealed a history of multiple major interspecies admixture events. Evidence for gene flow among closely related mammalian species is not unprecedented. Examples include cases of unidirectional gene flow [e.g., from polar bears into brown bears (47), similar to the Columbian mammoth gene flow into woolly mammoths observed in our study]; emergence of admixed species [e.g., North American wolves with ancestry from coyotes and gray wolves (48), similar to the straight-tusked elephants in our study]; different extents of gene flow [e.g., between gray wolves and Eurasian/African golden jackals (49), and between bonobos and central/eastern chimpanzees (50), as in the case of straight-tusked elephants and west African forest elephants/woolly mammoths in our study]; extended periods of gene flow during the initial diversification of species [e.g., between eastern and western gorillas (39), Sumatran and Bornean orangutans (39), and the ancestors of humans and chimpanzees (39, 51), like those inferred from most pairwise species comparisons in our study]; and adaptive introgression [e.g., in the great cats of the genus Panthera (52)], which could have played an important role in the evolution of elephantids as well. Our results in elephantids thus add to the growing weight of evidence in favor of the view that capacity for hybridization is the norm rather than the exception in many mammalian species over a time scale of millions of years.

Big speciose mammal lineages seem to have hybridzed a lot. Should this surprise us? Probably not.

Placental Invasiveness Mediates the Evolution of Hybrid Inviability in Mammals:

A central question in evolutionary biology is why animal lineages differ strikingly in rates and patterns of the evolution of reproductive isolation. Here, we show that the maximum genetic distance at which interspecific mammalian pregnancies yield viable neonates is significantly greater in clades with invasive (hemochorial) placentation than in clades with noninvasive (epitheliochorial or endotheliochorial) placentation. Moreover, sister species with invasive placentation exhibit higher allopatry in their geographic ranges, suggesting that formerly separated populations in mammals with this placental type fuse more readily on recontact. These differences are apparently driven by the stronger downregulation of maternal immune responses under invasive placentation, where fetal antigens directly contact the maternal bloodstream. Our results suggest that placental invasiveness mediates a major component of reproductive isolation in mammals.

Monkeys and apes (including humans), have very invasive placentas. Afrotheria, somewhat less so. Placental invasiveness isn’t the only criteria to predict or gauge the viability of hybridization, but it’s a major one.

I’ve stated before that genomics didn’t really change our understanding in a qualitative way in relation to evolutionary biology. Yes, stupid arguments about selectionism vs. neutralism really don’t happen anymore because there’s a mad scramble for data, as opposed to rhetorical tactics. But, perhaps in the area of understanding speciation with regards to mammals genomics has really changed things. That is, it’s a lot more about reticulation and a lot less about bifurcation.

To a great extent the “biological species concept” (BSC), which to the general public is the scientific species concept, is mammal focused. If plant geneticists had the catbird seat I think we’d have a different view of what species were. As it is, that’s not what happened. Species are human constructs and reify a certain Platonic sense of categories and kinds. What genomics is showing us here is even in the “best case” circumstances of the BSC, in mammalian lineages, when evaluated over reasonable time spans species barriers are highly porous.

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17 thoughts on “The tall and long tales that elephants tell (also, ancient DNA never forgets)

  1. The real question is whether these taxonomic units should be called species at all. Or are they rather just subspecies or races of one biospecies? If animals do procreate successfully in the wild, they are races of one species.

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  2. The given example is perfect because it is a new hybrid race. To call the two mother races species is an oxymoron to me considerIng the living proof of their non-speciation.

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  3. Talk to me like I’m stupid…
    Can you explain (with additional examples) placental invasiveness vs. non-invasive placentas, both descriptively and functionally? Or point me to something like Placental Invasiveness for Dummies or The Idiot’s Guide to Placental Invasiveness? Strangely, wikipedia has no entry for these concepts.

    Hmm… I see that wikipedia does have a page on Placentation, but still…

    Talk to me like I’m stupid.

    All I can get from this article is that the difference has to do with how many layers of cells or tissues are between the embryo and the mother’s blood. (Following a link, I discover a line that I love, the opening line of the entry for Chorionic villi:

    Chorionic villi are villi that sprout from the chorion to provide maximum contact area with maternal blood.

    D’oh! Of course. I knew that!)

    Anyway, what I gather is that rodents & “higher order” primates can be more distinct genetically and still produce viable (fertile?) hybrids than other mammalian species such as carnivores, ruminants & many marine mammals. Anything else? The placentation article does not mention pachyderms? What kind of placentation do they experience?

    Thanks

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  4. Can you explain (with additional examples) placental invasiveness vs. non-invasive placentas, both descriptively and functionally? Or point me to something like Placental Invasiveness for Dummies or The Idiot’s Guide to Placental Invasiveness? Strangely, wikipedia has no entry for these concepts.

    there’s less immune rxn i think to ‘foreign’ fetuses if u have a very invasive placenta. that’s why hybridization is easier.

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  5. What if the Humans of today had epitheliochorial or endotheliochorial placentation? Would they be able to mix?
    I think that this placentation study is fascinating and sheds much light on the issue.
    But I differ with your conclusion, Razib. To me, this is an idicative that very distant species of invasive placentation mammals can still breed – as opposed to your interpretation that the fact that they can interbreed somehow render their genetic differences “meaningless” (for the lack of better word).
    As you have said, you’re a lumper.
    To me, for instance, the fact that a Neanderthal and a Sapiens could interbreed doesn’t change the fact that they were different species. To you, the fact that they interbred means that they weren’t different species.

    If anything, this placentation study supports both my views and yours, depending on the angle.

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  6. as opposed to your interpretation that the fact that they can interbreed somehow render their genetic differences “meaningless” (for the lack of better word).

    don’t reinterpret what i said. i haven’t, and wouldn’t say genetic differences are meaningless. why did you use quotes?

    that’s just a dumb opinion.

    To you, the fact that they interbred means that they weren’t different species.

    i don’t have a strong adherence to the BSC. you’re really misunderstanding what i’m saying. species aren’t that important to most evolutionary geneticists.

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  7. I used quotation marks precisely to make the word loose – I’m not quoting you with them. In English-speaking countries they are mostly used as a “literal” device, but elsewhere they are also used to express ambiguity.

    Now, about this:
    “species aren’t that important to most evolutionary geneticists.”
    They aren’t to me either – but someone has to classify the differences when they are clearly there. Like, saying that the Neanderthal and Sapiens were the same? Or same enough? They weren’t, thus classify them as different.
    The fact that they interbred wasn’t because they were close (apart from both being offsprings of the Heidelbergensis), but maybe due to a placentation device.

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  8. Concerning Neandertals: We still dont know whether all first generation hybrids of both sex were completely healthy and fertile. There are different intermediate states of speciation.
    My guess is they were not at all.

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  9. i think you are flipping the order of the evidence here. what i noticed a long time ago is that on mammalian time scales the divergence btwn neanderthals and modern humans wasn’t that distant (500 to 1 million K, though now we’re converging on 750K or so). the fact that the placentals were invasive changed my priors so that i was even more skeptical of no-hybridization.

    as for whether they were a separate species, that depends on the lineage. if hybridization was a criterion for plants than there’d be a lot fewer species.

    so would a neanderthal have ‘human rights’ today? i think probably. so i’d call it the same species.

    now, a paleontologist is focused on morphology. so they go differently….

    (unless you studies species evolutionary geneticists generally shrug at species scientifically)

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  10. heterogametic breakdown – could you comment on the recent horse paleogenomic paper? The Przewalski horses have 66 chromosomes and the rest of the horses have 64, and they estimate that the modern horses have about 3% admixture from the Przewalski horse Botai ancestor, and it’s mostly female-biased (as in, no Botai Y chromosomes remain, but most of the modern horse mtDNA clades have already been there in the Botai horses)

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  11. so i haven’t read it yet. it’s cool. but i guess i wasn’t as surprised as a lot of people cuz i’ve read in this area and have some familiarity with equine genetics.

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  12. The horse domestication paper is potential a big deal for your “real favorite horse”, the South Asia genetic prehistory, because it’s likely one of the signature events in the PIE expansion, and because its authors already bragged about having cool results with the human aDNA from the same Botai site. So it’s where animal species interbreeding and human migration prehistory are coming together.

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  13. They may be overselling it, but this is verbatim:
    “another kind of DNA might help them in their work—ancient human DNA that details migration and population patterns from that time. Indeed, they already have some evidence from unpublished studies. But Outram is keeping quiet about that work. “My mouth is zipped for now.””
    http://www.sciencemag.org/news/2018/02/ancient-dna-upends-horse-family-tree

    The Botai ancient DNA to date wasn’t autosomal, was it?

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  14. No expert here, but I think if you view BSC as a tends-to-work concept rather than something that creates a bright-line rule that absolutely excludes organisms outside of the group, then it’s pretty descriptive. Even bacteria have mostly-separate lines of descent.

    This viewpoint wouldn’t be surprised about new species arising from hybridization, with hybrids either disappearing, following their own separate path or, rarely, the hybrids possibly reuniting and swamping out the original species. In the last alternative, BSC didn’t work the way it usually does, but maybe we shouldn’t expect it to always work that way.

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