Are orangutans our closest living relatives? Part II

Ok, as the comment in my previous post pointed out to me, the question was raised by this new paper:

Evolution of the second orangutan: phylogeny and biogeography of hominid origins
John R. Grehan and Jeffrey H. Schwartz
Journal of Biogeography
Abstract

Aim To resolve the phylogeny of humans and their fossil relatives (collectively, hominids), orangutans (Pongo) and various Miocene great apes and to present a biogeographical model for their differentiation in space and time.

Location Africa, northern Mediterranean, Asia.

Methods Maximum parsimony analysis was used to assess phylogenetic relationships among living large-bodied hominoids (= humans, chimpanzees, bonobos, gorillas, orangutans), and various related African, Asian and European ape fossils. Biogeographical characteristics were analysed for vicariant replacement, main massings and nodes. A geomorphological correlation was identified for a clade we refer to as the ‘dental hominoids’, and this correlation was used to reconstruct their historical geography.

Results Our analyses support the following hypotheses: (1) the living large-bodied hominoids represent a monophyletic group comprising two sister clades: humans + orangutans, and chimpanzees (including bonobos) + gorillas (collectively, the African apes); and (2) the human–orangutan clade (dental hominoids) includes fossil hominids (Homo, australopiths, Orrorin) and the Miocene-age apes Hispanopithecus, Ouranopithecus, Ankarapithecus, Sivapithecus, Lufengpithecus, Khoratpithecus and Gigantopithecus (also Plio-Pleistocene of eastern Asia). We also demonstrate that the distributions of living and fossil genera are largely vicariant, with nodes of geographical overlap or proximity between Gigantopithecus and Sivapithecus in Central Asia, and between Pongo, Gigantopithecus, Lufengpithecus and Khoratpithecus in East Asia. The main massing is represented by five genera and eight species in East Asia. The dental hominoid track is spatially correlated with the East African Rift System (EARS) and the Tethys Orogenic Collage (TOC).

Main conclusions Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human–orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. The EARS and TOC correlations suggest that these geomorphological features mediated establishment of the ancestral range.

See also Humans More Related To Orangutans Than Chimps, Study Suggests at Science Daily.

Here they look at physiological features of apes and conclude that we, humans, look more similar to orangutans than the African apes.

Of course, this conclusion only flies if we discard the molecular evidence as artifacts.  The molecular evidence is pretty clear in putting us closer to chimps, then gorillas, than orangutans.

Quoting from the Science Daily piece:

Schwartz and Grehan contend in the Journal of Biogeography that the clear physical similarities between humans and orangutans have long been overshadowed by molecular analyses that link humans to chimpanzees, but that those molecular comparisons are often flawed: There is no theory holding that molecular similarity necessarily implies an evolutionary relationship; molecular studies often exclude orangutans and focus on a limited selection of primates without an adequate “outgroup” for comparison; and molecular data that contradict the idea that genetic similarity denotes relation are often dismissed.

“They criticize molecular data where criticism is due,” said Malte Ebach, a researcher at Arizona State University’s International Institute for Species Exploration who also was not involved in the project but is familiar with it.

“Palaeoanthropology is based solely on morphology, and there is no scientific justification to favor DNA over morphological data. Yet the human-chimp relationship, generated by molecular data, has been accepted without any scrutiny. Grehan and Schwartz are not just suggesting an orangutan–human relationship—they’re reaffirming an established scientific practice of questioning data.”

Personally, I put more faith in the molecular data, but then I don’t know that much paleontology…

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Are orangutans our closest living relatives?

John Hawks: Are orangutans our closest living relatives?

No

My answer would be “it depends” and “some places, yes”, but that answer is a bit more complex…

We’ve been working on the orangutan genome sequence the last year – the genome paper will probably be submitted in a few months and we have a few companion papers on our work on it – and we think we have evidence that some places in the genome humans are closer related to orangutans than chimps (our closest living relatives) and gorillas (our second closests).

So as species, no orangutans are not our closest living relatives – chimps and gorillas, in that order, are closer related to us – but the picture is slightly more complex than this if we look at individual nucleotides in our genome.

It has to do with gene trees vs species trees and so called incomplete lineage sorting.

It is well known that we are mainly closest related to chimps, but quite a large fraction of the genome we are actually closer related to the gorilla. Check e.g.

We think we see the same for humans and orangutans, but to a much lesser degree of course.

Our paper is still in a rough draft, so I won’t say more about it here…

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Solid state quantum computers

Researchers have built the first solid state quantum computer. Only two qubits, but it’s a start.  If it scales, at least there is really no option of just sticking a lot of two bits together to get more with these quantum computer beasts; you need quantum states and that is where the tricky part is, and the quantum bus they use here might be a way to achieve this.  I don’t know enough physics to have any opinion on this, though… if someone does, please enlighten me!

Quantum computers are really cool because they, in some applications, works like non-deterministic computers: when an algorithm like a search needs to make a choice in where to search next, it can go both ways and doesn’t have to first look one place and then the other like a deterministic computer (like all the computers we have today).  So it can explore an exponential search space in polynomial time.

When people talk about NP (non-deterministic polynomial) problems that is what they usually mean.  Problems where a non-deterministic algorithms can solve the problem in polynomial time, but where we do not know any polynomial time algorithms to solve it using a deterministic algorithm.

A lot of optimisation problems of practical importance falls into this category.  Today we use all kinds of heuristics to solve these problems – usually sub-optimally – so even if we can only solve some of those kinds of problems with quantum computers, it is hard to overestimate how important quantum computers can become if we ever manage to build large ones.

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Last two weeks in the blogs

Due to exams and such, I didn’t put up my list last week, so here you have it for the last two…

Astronomy and cosmology

Blogging

Epidemiology

Genomics

Intellectual Property

Programming

Research Life

Statistics

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