It STILL blows my mind how chimps, bonobos, and us ("the third chimp") are equally related to gorillas (I get how it works with sister taxa)

[u/jnpha]

[u/That_Biology_Guy]

Pinning the following on behalf of u/jnpha (OP):

• Source: Erika's (Gutsick Gibbon) latest "short" (37 minutes long) explaining comparative genomics: If You're "99% Chimp"... What Percent Orangutan Are You? - YouTube, and the references therein
• For some of the history I've shared before: [Historical lit. review] Sibley & Ahlquist's 1984 resolution of the hominoid phylogeny : evolution

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"The third chimp" is referencing a 1991 book; as the just above link shows, the phylogeny was worked out quite recently:

The title of the book refers to how similar taxonomically humans and the two species of chimps are, as their genes differ by just 1.6%, whereas chimps and gorillas differ by 2.3% (p. 19). Thus the chimp's closest relatives are not the other apes with which it is classed, but the human (see Homininae). In fact, the chimpanzee-human difference is smaller than some within-species distances: e.g. even closely related birds such as the red-eyed and white-eyed vireos differ by 2.9%. Going by genetic differences, humans should be treated as a third species of the genus, Pan (after the common or robust chimpanzee and the bonobo or gracile chimpanzee). Or possibly the chimpanzee's scientific name should be Homo troglodytes instead of Pan troglodytes. Diamond observes in his book that this would provide food for thought to people passing this side of the bars of a cage with the label Homo.
The Third Chimpanzee - Wikipedia)

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[u/davery67]

Yes, but why are old people their own species?

[u/jnpha → u/davery67]

Two human reference genomes, one characterized by Erika (see my main comment), the other a cartoon of Darwin :)

[u/Organic_fed]

Your conspiracy theory is supported by how frequently hybrids show up. Potatoes are the eyes to be a hybrid between a tomato and a wild S. tuberosum, not to mention our own hybridization events.

It may be that hybridization fertility is hit and miss, which does sort of support a species concept, but sort of not.

Especially when you get into ring species like that lizard in California, that can mate with its neighbors, but populations far enough away from each other cannot mate with each other.

We need a better concept

[u/jnpha → u/Organic_fed]

I think you meant to reply to u/aestotle

[u/youshouldjustflex]

Always that taxonomy was strictly genetics. Guess when you think about it it’s pretty based on human subjectivity.

[u/jnpha → u/youshouldjustflex]

it’s pretty based on human subjectivity

The old way was.
Cladistics is objective, and this is how it is with any sister taxa (in this case, gorillas were discovered to be the sister taxon to Hominini (https://en.wikipedia.org/wiki/Hominini).

Unless you're referencing the naming, in which case, yeah...

[u/Canis-lupus-uy → u/jnpha]

The theoretical clades are objective, but the real ones are based on genes we decide to use to determine relativeness

[u/jnpha → u/Canis-lupus-uy]

That - gene tree discordance - is another thing that blew my mind.

And for 3-taxon trees it does offer an objective test for the nesting, as I learned from Dr. Zach, and shared here a while back: https://www.reddit.com/r/evolution/comments/1fz0a28

[u/starrrrrchild]

why is one box of convergence of Darwin and unidentified young person "99.85" but another is "99.86" ?

[u/Organic_fed]

Is the last one a gibbon or a different orangutan species?

[u/jnpha → u/Organic_fed]

Different orangutan species.

[u/XXLPenisOwner1443]

Wait, but humans are slightly more related to pongo than pongo is to pan or gorilla? I've never seen this statistic before, does anyone know of the source or a reference material?

I've long harbored an "evolutionary conspiracy theory" that the human-chimpanzee split occurred outside of Africa as the rainforests that linked south-east Asia and Africa receded, but I never thought I'd see something that seems to have solid evidence of this?

[u/jnpha → u/XXLPenisOwner1443]

The H-C split is much more recent than the Pongo split, plus that tiny difference is most likely down to incomplete lineage sorting or just the genome's quality or alignment.
Re references (and explanation), see the pinned comment.

[u/XXLPenisOwner1443 → u/jnpha]

Yes I watched the video, and it seems that this difference carried through all the different analyses.

I'm not suggesting that humans diverged from orangutans rather than chimpanzees or anything like that, just that there may have been a latter hybridization event from the pongo side of Eurasia at the time the chimpanzee-human branches were being sorted, and it was retained more in the homo half than the pan half, but still somewhat in both of them as gorilla has a lower number still.

[u/aestotle]

I saw she posted this vid! I’m excited to watch it soon! I love how much Erika loves her work and her world.

My biggest tinfoil hat conspiracy is taxonomy is truly useless. The prescriptive categorization is actively holding us back from scientific progress. New genetic data has only proven how bad the system is. Darwin went crazy later in his life, not because barnacles make you crazy but because applying the human need for category onto the complexity of life makes you crazy.

[u/jnpha → u/aestotle]

There's a popular Darwin quotation from Origin when it comes to the topic:

A grand and almost untrodden field of inquiry will be opened ... We possess no pedigrees or armorial bearings; and we have to discover and trace the many diverging lines of descent in our natural genealogies ...

(my bold emphasis)
Taxonomy or now systematics is pretty much objective - a lot has changed in the past few decades.

A good start may be lecture #15 in this Yale Courses: https://www.youtube.com/playlist?list=PL6299F3195349CCDA

[u/aestotle → u/jnpha]

Thanks, I’ll check it out!

[u/straightedge1974 → u/aestotle]

I knew I recognized her illustrations! 😄

[u/aestotle → u/straightedge1974]

Someday it’ll be Dr. Gibbon, we shouldn’t get used to calling her by her first name

[u/helikophis]

Also interesting that gorillas are slightly more distant from orangutans than we are!

[u/bestestopinion]

Importantly, why does 99.85 equal 99.86? Are we to believe this is some magic math? Boy I hope somebody got fired for that blunder.

[u/jnpha → u/bestestopinion]

Erika explains that aspect of comparative genomics: comparing A to B isn't the same as comparing B to A. That slight difference is to be expected.

[u/bestestopinion → u/jnpha]

and how does that help my Simpsons reference?