A peek: Natural selection reduced diversity on human Y chromosomes

In science we often get together with other scientists and present preliminary results before the publication of the manuscript.  I think that attending meetings is an excellent opportunity to learn what other people are working on, share the research that I am currently engaged in, and both give and receive feedback about the analysis and interpretations.

In this case, I presented a poster at the scientific meeting I attended, the 2013 annual meeting of the Society for Molecular Biology and Evolution, about work that was recently accepted for publication (expected to be published in January). I'm working on an accessible research blog post about this work. In the meantime, here is the description from the poster this summer, and the pdf version of the poster (you can also download the preprint version here):

Description

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

Wilson Sayres, Melissa; E. Lohmueller, Kirk; Nielsen, Rasmus (2013): Natural selection reduced diversity on human Y chromosomes. figshare. 
http://dx.doi.org/10.6084/m9.figshare.806296

The platypus is not a hybrid. But, these are still fun.

Speaking of hybrids, I was reminded that after my post about the platypus (check it out here), I received a lot of funny depictions of the platypus as a hybrid. Before I share, however, let's get one thing straight:

The platypus is not a hybrid.
The platypus is not a hybrid.

The platypus is not a hybrid.

Okay, now that we've gotten that out of the way, let's have some fun. Every time you see one, you can be the one to explain that the platypus belongs to a unique lineage of mammals that, while awesome, is not a beaver-duck hybrid (or maybe that's just what I'll do). Please share more in the comments.

From Tracy Heath, via the blog "Something that I like":

Venn diagrams were never so awesome.

From Clement Chow via cheezeburger.com:

Via cheezeburger. com

From a comment, via cheezeburger.com:

Via cheezeburger.com

From Clement Chow, artwork by styrofoamdiablo:

"Beaver+Duck-Eggo: Platypus" by styrofoamdiablo

From Clement Chow, from shirtwoot:

"Mystery of the Platypus Solved" from shirtwoot

From Jacob A. Tennessen (at OSU), the Platypus Trophy, which is awarded to either the Oregon Ducks, or the Oregon State Beavers, after their annual football game.

Platypus Trophy

Yes, you share a common ancestor with pigs, but it was a long, long time ago.

I was recently invited to comment on an Anthropology Network discussion on LinkedIn, where someone asked, "I'm wondering what this community's thoughts are about the theory that humans are a hybrid?" and linked to the blog post by Eugene McCarthy supposing that humans resulted from a hybridization event between chimpanzees and pigs. Because it is a private network, I'd like to repost, with some expansions, what I added to that discussion. But, let's just start off by clearing the air: 

Chimpanzees did not mate with pigs and produce humans.

Chimpanzee, by Ikiwaner (Own work), via Wikimedia Commons

Adorable piggy, by A R, via Wikimedia Commons

I am not a little piggy!

I was surprised that a group of anthropologists would even consider this a reasonable topic for discussion, but perhaps this speaks to the need for more cross-discipline communication. 

I find it distressing that the chimp-pig hybrid article dismisses the abundance of genetic evidence that provides no support for such a hypothesis of human ancestry. There are several scientific and logical flaws with the supposition that humans resulted from what must have been multiple matings between chimpanzees and humans. Also, please see an alternative discussion of this hypothesis by PZ Myers here, then another summary and discussion by ARTIOFAB here. 

1. Humans are genetically very similar to chimpanzees, and genetically distant from pigs
There are no regions of our genome where the genomic content more closely resembles a pig than a chimpanzee. If such a hybridization had occurred, we would, like we do with the Neandertal and Denisovan genomes, find regions where segments of modern humans are more closely related to pigs than any other species, but we do not. 

I really don't understand how anyone can look through images of pigs and think that we resemble pigs more than we do chimpanzees or bonobos:

Pan paniscus (bonobo) By Pierre Fidenci (http://calphotos.berkeley.edu), via Wikimedia Commons

2. Body hair has been lost independently in many mammalian lineages.
Yes, hairlessness over most of our bodies evolved in humans, but it did so independently in the human lineage. Similarly hairlessness independently (we call it convergent evolution) evolved in naked mole rats, manatees, and cetaceans (dolphins and whales). Rodents are actually more closely related, evolutionarily, to humans than pigs, but we don't see a naked mole rat - chimp hybrid theory because it is obviously ridiculous to the general public. The chimp-pig hypothesis is even more improbable. And, furthermore, many pigs have not lost hair on their bodies or faces.

Bearded Pig, by Art G. from Willow Grove, PA, via Wikimedia Commons

3. Chromosomal and genetic differences between chimpanzees and pigs preclude fertile hybrids.
The chromosomal differences between chimpanzees (48) and pigs (38) would preclude any chimp-pig zygote from developing, or even replicating properly. The author greatly over-exaggerates claims about the fertility of hybrids of sheep-goat hybrids (most are stillborn), and also misuses the term geep (which refers to a chimera of sheep/goat cells). The author also ignores the close evolutionary relationship of sheep and goats, where the chromosomes (and the breaks/fusions) can readily be mapped, where most of the gene content is still conserved among chromosomal regions. Such an identity of the order and orientation of gene content does not exist between chimpanzees and pigs, but is possible between the very closely related human and chimpanzee (all chromosomes are one-to-one, except for human chromosome 2, which is a fusion of two ancestral chromosomes that remained unfused in chimpanzee). 

Mapping of human and chimpanzee chromosomes, by JWSchmidt, from Wikimedia Commons

4. Fossil evidence can account for all of humans ancestry to the human-chimp common ancestor.
At what point in time would this have occurred? Certainly not the present. We have fossil evidence of modern humans, ancient humans, ancient hominids, ancient apes, ancient monkeys, and so on. Science can account for the progression of humans from our shared ancestor with chimpanzees, and even further back. At no point in history do the fossils of ancient humans in any way resemble the fossils of ancient pigs. 

5. Modern species share common ancestors, they did not beget each other.  
Modern humans did not evolve from modern chimpanzees any more than modern chimpanzees evolved from modern humans (that is, not at all). Fossil evidence suggests that the chimp-human common ancestor looked a lot more like a modern chimpanzee than it did a modern human, suggesting many more physical changes along the human lineage, but the modern chimpanzee has also experienced changes since our most recent common ancestor together, approximately 6 million years ago. Both humans and chimpanzees share a common ancestor with pigs about 90 million years ago.

6. Domesticated pigs and chimpanzees do not live in the same locations. 
Pigs (with reduced body hair) were domesticated in East Asia and in Europe. Chimpanzees live in central Africa. They live on different continents. They did not ever have the opportunity to get busy. Wild boars can be found in northern Africa, but this is still quite far from where chimpanzees live, and if they do overlap in range, it is only a very recent occurrence.

Wild Boar, by Volker.G (Own work), via Wikimedia Commons

7. Why hasn't an experiment been done? 
You could attempt each of the possible combinations (chimp sperm with pig eggs, and pig sperm with chimp eggs) and test the viability. It it works, we can have this discussion. If not, this guy needs to stop spouting nonsense that detracts from the real science being done.

By David.Monniaux, via Wikimedia Commons

Pumpkins

Little Bear picked out a pie pumpkin at the store last week. She helped me clean out the guts, and wash the seeds. The first thing we made with it was toasted pumpkin seeds:

Delicious toasted seeds. 

Then, I peeled the pumpkin and we boiled it.

Boiled fresh pumpkin.

And puréed it.

Pureed fresh pumpkin - so bright!

I made a pie crust using whole wheat flour and vegetable shortening.

Whole wheat crust.

And looked up a recipe for eggless pumpkin pie (because we were out of eggs at home). I found this one, but used half the sugar.

Ready to bake eggless pie.

It took nearly twice (yes, twice) as long to bake, which makes me high suspect our oven (will have to buy an oven thermometer soon). I don't think it is because of the reduced sugar, but that might have contributed.

But, it turned out to be pretty tasty. I prefer the consistency of pumpkin pie with eggs (more custard-like), but this was a wonderful eggless/vegan option.

Thoughts on scientific publishing, from someone without tenure, or a Nobel prize.

There has been a lot of heated discussion about recent Nobel prize winner, Randy Schekman's article, "How journals like Nature, Cell and Science are damaging science".  In it he argues that these types of journals preferentially publish science that is sensational over science that is important.

Of course they do.
Of course Nature, Cell, and Science choose to publish articles that they think are both scientifically accurate and going to be read by a lot of people. NCS have a brand to promote, and an audience to cater to that expects exciting articles of broad interest. I like to read or skim through articles that aren't in my own field in Science. They have no reason not to publish the articles that will bring in the most readership, and every incentive to seek out the "hottest" research topics.

I have no problem with a journal choosing to publish only a certain kind of research (chemistry, physics, biology, evolution, and so on), or choosing to publish articles that they think will bring in the most readership. It only becomes a problem when the quality of the science is overlooked in favor of the sensationalism. Publishing inaccurate science should not be tolerated.

The real problem.

Schekman argues that part of the problem with "high impact" journals that choose to prioritize flashy results over real scientific advances is that hiring, tenure, and promotion committees view publication in these journals as a measure of the scientific merit of a paper. I don't see this as a problem with the flashy journals, but in the people who assume publication in such a journal should be equated with scientific excellence.

As a postdoc on the job market, I am acutely aware of this, and worried about it. You'll note from my publications that I don't have a single NCS paper. I'm pretty sure that not having those NCS papers has/will hurt my prospects this year. I hope that some schools will still recognize my ability to do good science, to conceptualize projects and bring them to completion, and to successfully mentor students, and will offer me a position despite the lack of NCS-publications. Perhaps foolishly, I do believe there are departments that value science more than the journal where it was published. And, with the development of more detailed, and manuscript-specific, metrics, including downloads, citations, shares, page views, and saves, I think it will be easier in the future to dispense with using journal IF as a measure of scientific merit.

Don't get me wrong, I'm not naive. I know I'm not going to be considered at some institutions because I don't have publications in the NCS journals. While "luxury" journals are valued at "luxury" institutions, it is also important to remember that "luxury" institutions (as pointed out over at Telliamed Revisited) can also be used inappropriately to infer quality of a person and their research. Case and point: I was told on an interview, "It would be really great for our department to hire someone from Berkeley, like you." Ugh. Nothing to make you feel frustrated with the system like thinking you may have been recruited solely because you came from University A instead of University B.

So where does that leave us?
Tenured, well-known, professors have been chiming in on the issue, but will that affect how I proceed with my scientific trajectory. I am confident that any position I advocate cannot be attacked on the basis of, "I've already made it." I can assure you, in this tumultuous academic job environment, I have not "made it". At this stage in my career these are the four things regarding scientific publishing that are important to me:

1. Scientific papers, results, and datasets should be publicly accessible.
2. Classifying research by field is useful.
3. There is value in peer review (pre and/or post).

4. Reviews should be public.


1. Scientific papers, results and datasets should be publicly accessible
For me, the most important aspect of publishing my work is that it should be publicly accessible and reproducible. Nearly all journals now offer an option to pay (sometimes a prohibitive amount) to allow papers to be freely available, and many are requiring data to be submitted with publication. Assuming I have all the funding in the world (ha!), where will I submit?


2. Classifying research by field is useful.

Well, I'll submit wherever I think the audience for my paper will be the best. I tend to find new publications through google scholar and pubMed searches, but on occasion, I'll scan through the recently published articles in journals with a focus that is near my discipline. So, as an early-career scientist, I will publish in journals that are in my field, or through venues where my work can be classified (tagged, labeled) in broad categories, so people who weren't already looking for my specific paper might find it.

3. There is value in peer review (pre and/or post)
I have found peer-reviewed comments to be immensely valuable for my accepted manuscripts. Sometimes this delayed publication for months, and I didn't always agree with the reviewer comments, but that doesn't mean the process itself was worthless. I don't think that the current system is the best, but I also don't think it is terrible. One of the challenges with the peer review process is the huge lag time between submitting a manuscript and it finally being published. Most journals don't have a good way around this. One option would be to go with a system like F1000 or PeerJ, where manuscripts can be archived and immediately available upon submission.


4. Reviews should be public.

For journals with pre-publication peer review, I wish that all papers were published with the pre-publication reviewer comments. I think it would be immensely valuable to see what other scientists thought of the work before it was published. For all work, I think it will be beneficial to have a single location where post-publication comments can be collected, reviewed, and published. This would likely need to be monitored in some way to prevent it from turning into a free-for-all by trolls. 

So, will I publish in Nature, Cell or Science? 
I don't know.

But, I can tell you that I know better than to judge the value of a paper, or a scientist, by the journals they're published in, and that is where we have to start. 

Why sequence the manatee genome?

By Gaylen Rathburn, via Wikimedia Commons

I was excited to learn today that there is genome sequence for the West Indian manatee (Trichechus manatus)!! A friend wondered why I was so excited, asking, "Is it evolutionarily interesting?"

Well, first off, I've always been fascinated with manatees: they are so defenseless, and yet grow so large that they are rarely predated on. They are, however, especially susceptible to human-made water vessels. I am excited for their genome because I've always loved them. But, they are also pretty evolutionarily awesome.

1. Manatees are more closely related to elephants than they are to dolphins or whales.
The manatee and the bottlenosed dolphin are approximately 100 million years diverged from each other. The manatee is classified under the Afrotheria, which also includes elephants, hyraxes, and aardvarks, while the dolphin is classified as Laurasiatheria, which also includes the red panda, hippos, horses, rhinoceros, and bears. You can click on the links above for more detailed lists of the species included in each group.

Although about 100 million years separate manatees from dolphins, the manatee and elephant are only separated by about 61 million years. Unlike dolphins, but like elephants, manatees have toenails:

By Fritz Geller-Grimm, via Wikimedia Commons

2. Manatees convergently (independently) evolved the ability to live under water
Unlike other mammals that live primarily in the water (whales and dolphins), the manatee (and dugong) does not breath air through a blowhole on top of its head. Instead, manatees breath through their nostrils. How cool is that?

By Rusty Clark from Merrit Island FL via Wikimedia Commons

Additionally, manatees independently evolved flippers and wide tails.

Manatees also convergently lost most of their hair (although this isn't unique to water-dwelling mammals as many terrestrial mammals lost most of their hair too, including pigs, naked mole rats, and humans). I wonder whether similar genes are involved (disrupted?) to result in the loss of hair across these mammals?

3. Manatees have a much lower metabolic rate than expected for their body mass.
Manatees are fairly sedentary, and have a low metabolic rate (0.36 times the predicted rate for placental mammals). Dolphins have a much higher metabolic rate, but a similar expected lifespan as manatees (approximately 50-60 years, to my understanding). So, it will be fascinating to investigate how genomes differ between fspecies with similar generation times, but very different metabolic rates.