Introgression – what’s that all about?

Introgression is lit ūüĒ• these days. While the idea has been around forever, there has been a lot of¬†interest in studying introgression in the last few years. Recently a¬†journal-club discussion on an article¬†(specifically this one ūüĎČ Kuhlwilm et al. (2016)) prompted me to write about this.¬†Introgression is nothing but the introduction of a new variant/allele into a population. This can occur through hybridization between genetically diverged populations of the same species or between closely related species.

Hold on a second now‚úč. If they’re two different species, how can they mix with each other? Aren’t different species by definition unmixable (well technically: two organisms are from the same species if they can interbreed AND produce a fertile offspring.)?¬†Ignoring all other complications around the term species (asexually reproducing organisms, I’m looking at you), speciation does not happen overnight. It’s not like one day a part of the population rebels and claims to be a different species (even Indian and Pakistan didn’t happen that quickly¬†ūüĎÄ). Truth is, we don’t reeeally understand how speciation happens (more on this and introgression in another post). Even in the classic, well-understood case of allopatric speciation (speciation due to geographic isolation), gene flow, though it slows down over time, continues to occur as the populations separate, making speciation rather fuzzy (quite literally, see Fig. 1). It may even occur some time after the populations have diverged quite a bit (something referred to as secondary contact). It is these two cases that introgressors¬†people who study introgression are often talking about.

OP-MOLB140159 2004..2017

Fig. 1: The species tree (blue line) is a measure of central tendency that captures the overall pattern of gene trees (fuzzy grey lines). Grey lines which span different species of bears (such as that between the Asian black bear and Sloth bear) are suggestive of gene flow from one species into another. Рfrom Kutschera et al. (2014)

So why is¬†introgression such a rage¬†now?¬†The idea has been around for a while, initially¬†used in experimental breeding, where a trait, such as disease resistance ūüĆŅ ūüźõ or cute fluffinessūüźē ūüźĺ would be introduced into a breeding line.¬†For a long time, it has also been discussed by evolutionary biologists who study naturally occurring plants and animals. One major reason it has become so popular in recent years is because the technology (cost effective high-throughput sequencing) and methodology (population genetic theory) have enabled us to harness genome-wide information from multiple individuals of¬†many closely related species, making it possible to study complex evolutionary histories. That, and¬†this¬†paper ūüĎČ ¬†Green et al. (2010).¬†In 2010, a team of researchers¬†sequenced the Neanderthal (or is it Neandertal?) genome and found that 1-4% of the genomes of non-Africans¬†are made up of Neanderthal sequences. This could only mean one thing: some hanky panky went down between Neanderthals and non-Africans as they came out of Africa. Mind.blown. ūüė≤ ¬†+ ūüí• = ūü§ē . Wait, what? Yeah,¬†the subset of human ancestors who left Africa made contact with Neanderthals and had a good ol’ time before Neanderthals went extinct.

ūü§Ē At this point maybe you’re¬†thinking: “Huh? How did that happen? Weren’t Neanderthals, or Homo neanderthalensis¬†a different species from¬†Homo sapiens.¬†It’s right there!”¬†Well, aside from the fact that the naming convention is man-made ūüôĄ, speciation is complicated, and not as clear-cut as the Biological Species Concept¬†makes it out to be.¬†Gene flow between genetically¬†diverged populations, while it may be evolutionarily prohibitive due to¬†pre- and post-zygotic barriers, is not only possible, but much more common than we thought. C’mon it’s not that crazy. After all, we’re well aware of the existence of hybrids such as mules and ligers.

introgrssion_models.jpg

Fig. 2: Map showing regions of contact among humans and archaic hominins

Following the Neanderthal finding,¬†researchers (a lot of the same people who were involved in the Neanderthal sequencing) also sequenced another extinct hominin, which they named Denisovans owing to the fact that it was discovered in Denisova Cave in Siberia Reich et al. (2010). They found that ~5% of the genomes of Melanesians derives its ancestry from Denisovans, suggesting interbreeding between Denisovans and ancestors of Melanesians (Fig. 2). In genetics-research time, this was a loooong time ago (the discovery, not the admixture). Since then, s***t has hit the fan for human introgression, with many studies showing admixture among human ancestors and¬†extinct hominins (Fig. 3), some of whom we haven’t even sequenced yet! (Hammer¬†et al.¬†(2011), Sokglund and Jakobsson (2011),¬†Pr√ľfer et al.¬†(2013),¬†Vernot and Akey¬†(2014), Sankaram¬†et al.¬†(2014), Lu¬†et al. (2016), Kuhlwilm et al.¬†(2016), Sankaram¬†et al. (2016)¬†to cite ¬†a FEW). For¬†geneticists and evolutionary biologists ūü§ė, this is an exciting time not only for sketching out human evolutionary history, but also for understanding speciation on a fundamental level and how we define ‘species’ in the first place.¬†Stay tuned for a post on this last bit: “Is geographic isolation important for speciation?” – or something cooler along those lines.

introgression_wtf.jpg

Fig. 3. Possible introgression events among humans and archaic hominins. The blue arrow shows introgression from an unknown archaic hominin species –¬†Kuhlwilm¬†et al.¬†(2016)

Next up: The stage is set – How do we detect introgression? I’ll talk about how we can draw inferences from even one or two individuals from a species (not-a-real-hint: not your everyday N= 1 problem). Also –¬†incomplete lineage sorting (ILS) explained. I literally can’t wait…

One thought on “Introgression – what’s that all about?

  1. Nate says:

    this intro to introgression is ūüĒ•ūüĒ•ūüĒ• ! Love the use of diagrams…makes life so much simpler. Looking forward to your next post ūüôā

    Like

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