Gene genealogies vs population splits

Genes have genealogies, just as populations do. Usually, a gene’s  genealogy is the same as that of its species.  For example, turtles have their own versions of hemoglobin, and the common ancestor of those turtle hemoglobin genes is some ur-turtle  hemoglobin ( or is it turtle ur-hemoglobin ?) a long time ago.  This is a stochastic thing: it happens when only a single version of a gene survives – after that occurs, gene trees and population trees match, at least until the next split.

But it ain’t necessarily so, especially in cases where two species separated rather rapidly, or when the splitting populations are large – even more so when populations haven’t yet speciated at all.  When the gene tree conflicts with the population tree, we call it incomplete lineage sorting.  For example, gorillas split off before humans and chimpanzees separated, but some of the human genome (  ~30% ) is more similar to gorillas than it is to chimpanzees.   So, gene trees don’t match species trees very well  among humans, chimps and gorillas – although they do just fine between, say, humans and bears.

How much lineage sorting would you expect from human populations that have been  separated for, say 100,000 years? 250,000 years?  Close to zero.  Hardly any. So, can you use the fact that  human gene genealogies do not match apparent human population splits to prove those splits never happened – that there  had always been lots of gene flow between far-distant populations, say between sub-Saharan Africa and Siberia?  Presumably using magic carpets?

You could, but only if you were a bird-brain.

 

 

 

 

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12 Responses to Gene genealogies vs population splits

  1. Coagulopath says:

    The important detail seems to be that evolutionary processes work unevenly across the genome, and at multiple speeds. A percentage of human DNA is actually more similar to that of gibbons than to chimpanzees.

    I have a hunch that horseshoe crabs might be genetically closer to their ancestors 300 million years ago than more recent splits like spiders and scorpions.

  2. engleberg says:

    Since evolution happens at the speed of reproduction, the split between gorilla, chimps, hominids should have happened while all three were still bush babies breeding like rabbits. Before some bush babies evolved to giants, and some to giants with fat heads- us. A genetic profile of all existing bush babies would tell us more.

  3. Citizen AllenM says:

    Just to warm the memory of Harpending:
    https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0194862&type=printable

    “Judging from molecular-genetic data on lactase persistence,however, the consumption of fresh milk,at least, appears to have first begun to have an impact on the protein balance of individuals around 4,000 years ago.”

    Big advantages to those with better diets are mentioned later in the formation of early elites…lol.

  4. dearieme says:

    “but only if you were a bird-brain”: in this field I suppose it would be ideal if one could confidently distinguish (i) the unavoidably birdbrained, (ii) the wilfully birdbrained, and (iii) the pretend birdbrained.

    • gcochran9 says:

      In this case, Kevin Bird, i & ii.

      • JamesH says:

        I never found his use of Templeton convincing but what do you think of more recent papers such as this https://www.biorxiv.org/content/10.1101/416610v2 regarding gene flow between human populations?’
        Furthermore, ,more and more papers seem to recently come out that attempt to decouple links between phenotype and genetic ancestry, emphasize (potential at times) admixture and criticize the tree model in humans.
        Not to mention the Rutherford,Coop et al, arguments that we are all so recently related etc.

        • gcochran9 says:

          The Templeton stuff was all wrong – the time scales for ILS are long ( coalescence times). Bird doesn’t know jack: he got a mercy pass on the popgen part of his orals. He can’t even understand how reaction to a new thing in the environment can be heritable. He’s so dumb he’s Amy Harmon’s go-to guy.

          Make me miss Commies like Botvinnik or Kolmogorov or Vatutin.

          Look: local adaptation happens unless there is a lot of gene flow, on the order of the selective advantage in question – often as large as 1% a generation (which would drop Fst to near zero). Fst is not near zero, so this didn’t happen., nor would such massive population flows ( every generation) have been feasible, back in the day.

          And local adaptation doesn’t take forever: there are cases that look like it has happened in as little as a thousand years. Which theory says is possible.

          David Reich knows all this, and he’s not my sock puppet. He’s smart, and doesn’t really like being dishonest.

          Coop has a brain, but he’s a jerk, and I think dishonest. I say “jerk” because of that big letter that he originated, signed by many geneticists, condemning Nick Wade: such letters are supposed to be published in Pravda.

          • JamesH says:

            Thank you for the reply!

            Templeton also uses ML-NCPA to validate his results, a method mainly used and defended by him, which has been criticized a lot from what I have read.

            To my knowledge, the main inter-“racial”/continental gene flow events that have occurred before the Holocene were between different African groups, some between Europeans and East Asians (ie Villabruna) (or so it seems so far) and a back flow migration to Eastern Africa and the Yoruba (excluding the mixture of the groups that came to form the main populations today, which have still been largely isolated to each other as David Reich writes in his book).
            And it seems that most of it came from “pulse” admixtures, not continuous gene flow (and a quantitatively low amount as well).

            I am wondering if it is also possible that a lot of shared genomic variants or inferred gene flow, are at least partly due to recent events (ie colonization and the Age of Discovery).

            However are there not issues with interpreting Nm from Fst in natural populations?

            As for Coop, I have no doubt he is smart but definitely seems biased a bit, as every time I ran across his work it is a variation of papers like this (https://www.genetics.org/content/210/1/33.) or discrediting PGS.

  5. Palamas says:

    Will real science and honest discussions on the topic only exist once (the larger global) groups revert back to ethnostates, if that even occurs? What’s amusing is that you won’t see the Chinese caring about people’s feelings as they grow (imperially).

  6. Flemur says:

    As David Bowie might say, “Gene genealogy, let yourself go, whoah.”

    )Sorry, I’ll take my meds next time.)

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