Hi readers, long time no see! We’ve been slow getting back into the journal club swing of things after our winter break hiatus as we had ANOTHER Center for Human Evolutionary Studies guest speaker. Dr. John McGann (Psychology Department, Rutgers University) came by last Friday to give a lecture on the neuroscience of olfaction (or, put plainly, on how brains, genes, and your nose interact to process smells). It was super cool. Dr. McGann was an engaging speaker – I’d consider the myth that humans don’t smell very well to be thoroughly busted.
As I did for Dr. Bernard Wood’s guest lecture from last semester, I live-tweeted this one as well and have condensed it into a Twitter moment for your enjoyment. Check it out and let me know what you think of the format!
Today in BS&M we’ll be talking about the new modern Homo sapiens fossil material from Israel that suggests some humans left Africa earlier than previously thought. I’ll put a post together on that for y’all later this week.
Next Friday we have another guest speaker, Dr. Alan Rogers from the University of Utah, who will be talking about Neandertal and Denisovan ancient DNA. If you want to follow along with that in real-time (Friday, Feb. 9 at 3:30 pm EST) I’ll be tweeting it from the handle @CHES_Rutgers. Otherwise, expect a recap here!
Hey BS&M fans, thanks for sticking around. We’ve had fewer journal club meetings than usual this semester (and thus, fewer papers to blog about) thanks to a host of awesome guest speakers and, now, two successful dissertation defenses in as many months! Major BS&M congrats go out to Dr. Sarah Hlubik and Dr. Mareike Janiak, whose names you might recognize from their guest blog posts on mystery spit and Cretan footprints.
For the readers who aren’t in academia, the dissertation defense is the culmination of a person’s graduate student career. While the format varies from school to school, there tend to be some common elements. After a PhD candidate submits their written dissertation to their committee members (made up of their main advisor[s], department members with complementary areas of expertise, and an “outside” expert or two from another university), they schedule a time and place for a public “defense” of their dissertation (some schools call this a “Final Public Oral Examination”). For us at Rutgers, the defense itself is a 40-50 minute powerpoint presentation on our work, followed by questions from our committee, followed by public questions. The whole thing generally takes between an hour and a half and two and a half hours.
The dissertation defense is a stressful rite of passage that has been likened to a snake fight. It’s also incredibly rewarding for the fellow grad students in the audience, because, while we know generally what our friends are working on, we rarely get into the nitty-gritty details of it with them. The defense is an opportunity to celebrate their hard work and hear them get called “Doctor” for the first time (the novelty of which has yet to wear off for me, personally).
So, here’s a toast to Dr. Hlubik: may you find Prometheus in the Kenyan desert.
And to Dr. Janiak: may your exoskeletons be chinitous and your copy numbers variable.
This week’s BS&M blog takes on two new pieces of anthro news – neither of which we’ve actually had a journal club meeting about!
The first bit of news has been making waves all over the internet (as news tends to do, I guess): a third species of orangutan has been named! The newly designated Pongo tapanuliensis, or the Tapanuli orangutan, comes from the southernmost extent of the previously known Sumatran orangutan (Pongo abelii) range. P. tapanuliensis was named on the basis of morphological and genetic comparisons, which suggested that its skeleton looks subtly different from that of all other living orangutans (for example, in having relative broad upper canines and a relatively shallow face) and that it’s the oldest orangutan lineage (having split from the line leading to the other two species around 3.38 million years ago). Pretty cool!
While the naming of a “new” mammal species (especially one as large as an orangutan) is always exciting, there are a few potential issues to consider. First,P. tapanuliensis was named on the basis of a single (male) specimen and two genomes. It’s possible that there are other Tapanuli orangutan skeletons in museum collections that were not previously recognized as different from the northern Sumatran populations; this would be a something to look into, in the interest of increasing sample size. I’m also curious about what the skeleton of a female Tapanuli orangutan might look like. Second, Nater et al. estimate that there are already fewer than 800 Tapanuli individuals left. This (and splitting the Sumatran orangutans into two species) has implications for conservation. Is it worth it to prioritize saving the more endangered Tapanuli orangutan, which may already lack a population of viable size, or is it better to concentrate efforts on the Sumatran orangutan? A more optimistic view might be that this new species will attract attention (and money, which is ultimately what allows conservation efforts to happen) to the plight of orangutans generally. It’s impossible to know. Either way, the “discovery” of the Tapanuli orangutan expands our understanding of the diversity of our closest relatives – again, pretty cool!
The second bit of anthro news is also about expanding our understanding of diversity, but this time of our own genome.
Last week, I instigated my fellow BS&Mers into veering a little off the beaten path, and convinced everyone to discuss a recent Ecography paper that took a metacommunity approach to studying shape variation in rodents. Metacommunities are sets of communities linked by the dispersal of more than one species. Community scale studies are largely lacking across evolutionary anthropology, and given that many extant primates (and probably fossil hominins) fit nicely in the metacommunity framework, this seemed like a good opportunity to explore the potential applications of this approach to anthropological questions.
The paper was met with mixed reviews within our group. Part of the problem was that not everyone was familiar with some of the metrics and analyses (and jargon) utilized in the metacommunity framework. Namely, community weighted means (CWM), principal coordinates of neighborhood matrices (PCNM), principal coordinates of phylogenetic structure (PCPS), and redundancy analysis (RDA). Admittedly, the paper was not written in the most accessible way. For anyone that might be interested in reading this paper, see the table at the end of this post for my best attempts at explaining these (at least for our group) commonly unfamiliar concepts.
One talking point amongst the BS&Mers was whether we actually learn anything new by zooming out to the metacommunity level. A few people (mostly from the B&S contingent of our group) argued that we don’t necessarily need the added complexity of communities to study how environment influences shape variation, and that this is easily done at the species level. I personally believe that looking at variation in community level indices (like CWM) allows us to look at very large scale evolutionary relationships that we might miss at the species level. By scaling up to metacommunities, we are acknowledging (after accounting for phylogeny) that all members of the ecological community are subject to the same environmental variables, and therefore the same selection pressures. Understanding how the mean trait value for the entire community varies with the environment gives us a starting point when trying to understand function.
Another interesting talking point amongst the BS&M crowd was whether or not the paper should have been rooted in some hypotheses. Some of us expressed dissatisfaction at how function was implied throughout the paper, yet there were no hypotheses given for how shape should vary with respect to environmental variables. I actually think that in this case, not having explicit expectations was a bit refreshing. I certainly wouldn’t have considered some of the traits that the authors found to vary significantly with environment.
One thought I was left with after reading this paper was that I wish the authors had included community weighted variance (CWV) in their analysis. Having a measure of variance would at least tell us if a particular trait is worth considering in the first place. It would have also been nice to have incorporated a model averaged phylogeny (sensu 10ktrees).
BS&M ended with a very productive brainstorming session about how to extend this framework to primatological and anthropological questions. I think it would be interesting to use remotely sensed measures of canopy structure to see how morphology varies across primate metacommunities. I also think it would be important to use this framework to uncover how neutral and niche processes shape primate communities. Others proposed extending this framework to studying how various measures of social organization may affect primate trait evolution at the metacommunity level. And of course, we couldn’t resist discussing how we might extend this framework to studying trait evolution across fossil hominin communities. A fair bit of the hominin discussion was how to surmount the palimpsest nature of the hominin record.
Overall the BS&M crew seemed receptive to the approach presented in the paper and acknowledged the importance of the complexity inherent at the metacommunity level.
BS&M returned this past Friday and, alas, I couldn’t attend. Luckily, the discussion centered on the Cretan footprints paper that guest blogger Sarah Hlubik covered in our last post, so you guys aren’t missing out on sweet, sweet new paper coverage.
What apparently went down on Friday was a lot of talk about bears. Were there bears in the area during the Miocene? Yep and yep. Can bears walk upright? Yep! What do bear tracks look like? Like this (according to one site, anyway). Does this mean we need to change our name to Bears, Stones, and Monkeys?
It seems the BS&M crowd is fairly skeptical about the claim of bipedal primate footprints in the Miocene, but loves them some possible bearpedality (thanks for that one, Fred). Personally, I’d love to see the authors find some body fossils of any potential candidate track-maker – and if it’s a primate, even better!
Until next time, I leave you with this (credit to Alex Pritchard):
So, the big fossil news that the Leakey Foundation was teasing when last I posted? It was this:
BS&M Blog readers, meet Nyanzapithecus alesi, a new 13 million-year-old Miocene ape from Kenya. HOW COOL IS THAT?!
I will tell you how cool. VERY COOL. I’m biased (as always – because I pick the things I want to write about for the blog, which are things that I think are very cool), but seriously. There are a bunch of reasons this discovery is awesome, like:
3) You also rarely find infant material in the primate fossil record. (Yes, I know, the Taung Child is an exception to this rule, too.) Infant bones are smaller and more fragile than those of adults, which makes them even less likely to fossilize and be recovered later.
Alesi is also awesome, simply by virtue of being a Miocene ape (my Miocene bias is definitely showing). The Miocene (23-5.3 mya) often gets called a “planet of the apes” because there was a huge diversity of hominoids (the fancy taxonomic group name for apes, including us, is Hominoidea) that lived through Europe, Africa, and Asia at that time. Which is SUPER AWESOME because they were “experimenting” with different types of locomotion at that time (which is totally my jam), but also makes it really hard to tell our potential ancestors from our side-branch cousins. A classic problem for people who work on Miocene apes is that they have ape faces and monkey bodies, and the field disagrees about which is more important (the face or the body) for figuring out who is related to who. Hopefully one of the authors of the Alesi paper (shout out to Kelsey Pugh!) will be able to work some of these relationships out with her dissertation research.
My final thought/question (for now) on Alesi is: the authors suggest that gibbon-like features evolved in parallel several times in different branches of the hominoid lineage – why couldn’t these features be ancestral, rather than derived? If that was the case, it would just require that a different set of facial features evolved in parallel instead. So why the gibbon-like ones and not the other ones?
That’s all for now! Hopefully BS&M will be back on September 8th – catch you then!
Darcy asked me to write a guest post on “the new spit paper” and it shows that she knows me well. Saliva? Salivary proteins? Functional genetic variation in those proteins? Possible interbreeding with mystery hominins? The microbiome?
The authors looked at genetic variation in a gene called MUC7, which codes for mucin 7, a protein that is only found in saliva. In an earlier study, they found that the number of times a specific part of the MUC7 gene is repeated varies across different primate species. In gorillas it is repeated only 4-5 times, while vervet monkeys have 11-12 repeats. Humans have 5-6 repeats, but the gene hadn’t been thoroughly investigated in our own species, which is where the current paper comes in.
One known function of mucin 7 is to bind with bacteria in the mouth, so one question the authors asked is whether genetic variation in MUC7 correlates with the type of bacteria found in a person’s mouth. Using data from the Human Microbiome Project the authors found that people that have more similarity in the MUC7 gene also have more similar bacterial profiles (microbiomes) – but only around the mouth. While this is an interesting result, it creates more questions than it answers! Do these different bacterial profiles provide an adaptive benefit? And if so, for what? In what context is it better to have one over the other? Is it dependent on pathogens in the environment or maybe on diet? Lots of great avenues for future research!
But the authors also found something else when they were looking at MUC7 variation across people, something very curious. As expected, they found a number of different patterns of MUC7. These patterns are called haplotypes and they appear as time goes by and (mostly benign) mutations accumulate along the gene. Generally these haplotypes were pretty similar to each other, but (and this is the weird part!) one of them, haplotype E, was totally different.
Most of the MUC7 haplotypes were like these poodles, small differences but all clearly poodles:
And then there’s haplotype E:
Yes, still a poodle, but also kind of…out there and unexpected.