Mailund on the Internet

I just read this post by John Hawks this morning over my morning coffee.  I totally agree with this sentence:

Many years ago, I got used to the fact that paleontologists and geneticists live in separate realities.

and I find this quite disturbing.

I’m one of the geneticists trying to figure out the ancestry of apes and trying to date the speciation events, and I just cannot read the paleontology papers.  Well, I can read them, but I really don’t understand them, so I often end up just scanning for estimates of speciation times without being able to judge how they come about.

Just last week I tried to figure out the divergence time between humans and orangutans to relate it to the estimates we get in the orangutan genome project.

For example, following a reference from another paper I read this one that, according to the first paper was supposed to give a lower bound on the speciation of 18 million years ago.  First I just scanned the PDF for “18″ but the units where “18″ appear are mm so not exactly what I was looking for.  So I tried actually understanding the paper… I probably failed, ’cause as far as I understand it it gives an upper bound of 20 million years ago.

Scanning the supplemental information of the first paper I then found that they use the 18 mya both as an upper and a lower bound, depending on which table you look at, and that just makes it that more confusing.

As a side remark, here I agree with John Hawks again:

After quoting from their online supplement (once again, grumbling that the essential details are hidden online where nobody reads them!)

I hope that it is an upper bound, since a lower bound would be very inconsistent with our genetic estimate, but I just wish I could be sure I understood the paper…

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238-242=-4

I read this paper in bed yesterday before going to sleep:

Doubts about complex speciation between humans and chimpanzees

Presgraves and Yi, Trends in Ecology & Evolution 2009

Abstract

Two patterns from large-scale DNA sequence data have been put forward as evidence that speciation between humans and chimpanzees was complex, involving hybridization and strong selection. First, divergence between humans and chimpanzees varies considerably across the autosomes. Second, divergence between humans and chimpanzees (but not gorillas) is markedly lower on the X chromosome. Here, we describe how simple speciation and neutral molecular evolution explain both patterns. In particular, the wide range in autosomal divergence is consistent with stochastic variation in coalescence times in the ancestral population; and the lower human–chimpanzee divergence on the X chromosome is consistent with species differences in the strength of male-biased mutation caused by differences in mating system. We also highlight two further patterns of divergence that are problematic for the complex speciation model. Our conclusions raise doubts about complex speciation between humans and chimpanzees.

Complex speciation between humans and chimpanzees

You might remember the Patterson et al. paper in Nature back in 2006, that argued for a complex speciation of humans and chimps: An early separation between the two, followed by a hybridization and then the extinction of one of the species ancestral to the hybrids.

The arguments for this theory were 1) large variation in divergence time along the autosomal chromosomes and 2) a much more recent divergence of the X chromosome compared to the autosomes.

Wakeley then argued that 1) at least didn’t need any complex speciation history.  The variation in divergence is actually as would be expected just from variation in coalescence times along the chromosomes, assuming a reasonably large effective population size of the human/chimp ancestor species.

As for 2), the coalescence process alone cannot explain the recent divergence of X chromosomes.  We do expect a more recent divergence of X chromosomes than autosomes, since the effective population size of X chromosomes is 3/4 of that of the autosomal chromosomes, but the divergence of the X chromosomes is less than what can be explained by this.

This could either be explained by selection on the X chromosome (which essentially reduces the effective population size and thus leads to a reduced divergence) or by the difference in mutation rate between males and females that would affect the X chromosome differently than the autosomes (reducing the difference between the two).

It is well known that there is a bias in mutation rate between males and females, having to do with the average number of genome replications per generation in males and females, respectively.  The details I won’t go into here (although they are pretty important for the post, the post would just get too long and I don’t want to loose the readers who already know this … I might write about it in a separate post another day…)

Anyway…

Selection is probably not likely.  It would require a pretty uniform selection across the X chromosome.  The male-biased mutation explanation sounds more reasonable.

A problem with both explanation, though – Patterson et al. argued in their reply – is that this weird pattern in X is only observed between human and chimp and not between human and gorilla (or chimp and gorilla).

If mutation-rate differences alone could explain the observed data, we would expect a consistent value for from the human–chimpanzee and human–gorilla divergence data, but estimates of are significantly different (P = 0.001). A high value of also cannot explain other important features in Table 1: the near-absence of sites on chromosome X that cluster humans and gorillas or chimpanzees and gorillas; or why human–gorilla divergence should not be reduced on chromosome X (such a reduction would be expected if high male mutation rate were responsible for low human–chimpanzee genetic divergence on chromosome X).

Lineage specific male biased mutation rate

The Presgraves and Yi paper argues that male biased mutation rate can explain the pattern after all.

True, the low divergence on X is only observed between humans and chimps and not between humans and gorillas, but if the strength of this bias is larger on the human and chimp lineages than on the gorilla lineage it could still be an explanation.

Chimps are very promiscuous, humans somewhat less so, while gorillas are polygynous.  This affects sperm production so chimps produce most sperm per ejaculation, gorillas the least and humans again inbetween.

With more sperm produced in humans and chimps than in gorillas, it is therefore conceivable that the mutation bias is stronger in chimps and humans than in gorillas.

So they estimate this bias per lineage and get exactly that result: the bias is strongest in chimps, intermediate in humans and weakest in gorillas:

With different male-biased mutation rate in the lineages, with much less bias in gorillas, there is nothing strange in a reduced divergence on X chromosomes between humans and chimps than between humans and gorillas.

Voilà!  No more need for a complex speciation history!

At least until the next paper…

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1. Presgraves, D., & Yi, S. (2009). Doubts about complex speciation between humans and chimpanzees Trends in Ecology & Evolution DOI: 10.1016/j.tree.2009.04.007
2. Patterson N, Richter DJ, Gnerre S, Lander ES, & Reich D (2006). Genetic evidence for complex speciation of humans and chimpanzees. Nature, 441 (7097), 1103-8 PMID: 16710306
3. Wakeley J (2008). Complex speciation of humans and chimpanzees. Nature, 452 (7184) PMID: 18337768
4. Patterson, N., Richter, D., Gnerre, S., Lander, E., & Reich, D. (2008). Patterson et al. reply Nature, 452 (7184) DOI: 10.1038/nature06806

231-236=-5

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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181-179=+2

Another week has passed, so here is my round-up of the posts I liked last week…

Apes

• Orang-utan study suggests that upright walking may have started in the trees (Not Exactly Rocket Science)

Genetics