BS&M Does Dissertation Defenses

Congrats to Dr. Hlubik & Dr. Janiak!

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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.

Sarah_defense

And to Dr. Janiak: may your exoskeletons be chinitous and your copy numbers variable.

Mareike_defense

BS&M Gets Visitors: the Tapanuli Orangutan and Dr. Sarah Tishkoff

Expanding our understanding of diversity

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!

pongo_tapanuliensis
Welcome to the fam, Pongo tapanuliensis! (From Nater et al. 2017)

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.

Continue reading “BS&M Gets Visitors: the Tapanuli Orangutan and Dr. Sarah Tishkoff”

BS&M Gets Fancy with Metacommunity Ecology

Guest Blogger: Shauhin Alavi

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.

Click through for the table of jargon and references!  Continue reading “BS&M Gets Fancy with Metacommunity Ecology”

BS&M Does Bears?

A brief follow-up on the Cretan footprints

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):

Sunbear
Exhibit A (left): a sun bear foot. Exhibit B (right): a sun bear after it was recorded saying, “it was ME, it was ME ALL ALONG. Even my family – even my IMMEDIATE family bought it!”

 

Anthro News

#MeetAlesi

So, the big fossil news that the Leakey Foundation was teasing when last I posted? It was this:

Alesi_anterior view
Anterior view of the cranium of Nyanzapithecus alesi (Nengo et al. 2017)

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:

1) You don’t often find complete crania (the skull minus the jaw) of fossil apes. Typically, the bones at the back of the skull (the ones that form the brain case) break sometime before a fossil is found (if it’s found at all, which is a whole different issue). If you want to become a primate fossil, it takes specific circumstances and a lot of luck.

2) You really don’t find fossil ape crania in Africa dated to between 10-14 million years old. Alesi is it. Other fossil ape partial crania are known from this time period in Europe (Pliobates cataloniae at 11.6 mya and Pierolapithecus catalaunicus at 12.5-13 mya from Spain, and Rudapithecus hungaricus at 10 mya from Hungary, to name a few) and Asia (Sivapithecus indicus at 12.3 from Pakistan), which might say something about where fossil apes originated or it might either be the result of less digging having happened in Africa resulting in a deficient fossil record or the difficulty in identifying the earliest apes.

MioceneApe_crania
Pliobates (Alba et al. 2015), Pierolapithecus (Moya-Sola et al. 2004), and Rudapithecus (Begun et al. 2012). (Left to right)

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!

References
Alba, D.M., Almécija, S., DeMiguel, D., Fortuny, J., de los Ríos, M.P., Pina, M., Robles, J.M. and Moyà-Solà, S. (2015). Miocene small-bodied ape from Eurasia sheds light on hominoid evolution. Science350(6260), aab2625.

Begun, D. R., Nargolwalla, M. C., & Kordos, L. (2012). European Miocene hominids and the origin of the African ape and human clade. Evolutionary Anthropology: Issues, News, and Reviews21(1), 10-23.

Moyà-Solà, S., Köhler, M., Alba, D. M., Casanovas-Vilar, I., & Galindo, J. (2004). Pierolapithecus catalaunicus, a new Middle Miocene great ape from Spain. Science306(5700), 1339-1344.

Nengo, I., Tafforeau, P., Gilbert, C.C., Fleagle, J.G., Miller, E.R., Feibel, C., Fox, D.L., Feinberg, J., Pugh, K.D., Berruyer, C. and Mana, S. (2017). New infant cranium from the African Miocene sheds light on ape evolution. Nature548(7666), 169.

Ghost Lineages Ride Again: the Spit Edition

Guest Blogger: Mareike Janiak

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?

Fav_things_gif.gif

The new spit paper” by Duo Xu and her colleagues is titled “Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation” and is going to be published in the journal Molecular Biology and Evolution.

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:

regular_poodles

And then there’s haplotype E:

special_poodle

Yes, still a poodle, but also kind of…out there and unexpected.

So what’s the deal with haplotype E?

Continue reading “Ghost Lineages Ride Again: the Spit Edition”

Anthro News

Chimpanzee super strength!

Things around the blog have been a bit slow with BS&M on its summer hiatus (and me teaching an intensive summer human osteology course), but new anthro papers continue to come out!

What I’ve been reading:

Chimpanzee super strength!
Matthew O’Neill and colleagues tested the claim that chimpanzees are “super strong” relative to modern humans using a combination of actual chimpanzee muscle samples and computer modeling. Spoiler alert – they’re only about 1.35 times stronger than we are, and the reason for this has to do with both muscle fiber type and fiber length. Chimps have more “fast fibers” than we do, along with longer fibers, which the authors suggest make their muscles capable of greater maximum force output and power than ours. This might be beneficial for a large-bodied, arboreal primate. But not all arboreal primates have skeletal muscle dominated by fast fibers; O’Neill et al. also point out that the slow loris has, like we do, muscle that is mostly made up of slow fibers. And, based on their comparisons to other mammals, the authors suggest that our slow, short muscle fibers likely evolved within the hominin lineage, making them a unique characteristic of our group.

So what this means from an evolutionary perspective is that sometime over the last 7-8 million years, potentially coinciding with our shift toward obligate (full-time) upright bipedalism, the architecture of our muscles changed along with our skeleton. This is super cool because soft tissue anatomy isn’t preserved in the fossil record (except in certain rare, extreme conditions, and never in hominins) and this gives us a way to potentially investigate it. I also have some purely self-serving questions/ideas about how this relates to my own research interests, but I think I’ll stay quiet about them for the time being.

In other Anthro News: if you’re in the area and haven’t been, check out the Philadelphia Zoo. They’ve got some very cool primates (omg, red-shanked douc langur) and the Zoo360 Animal Exploration Trails are awesome. The family of gibbons was hanging out in one when I was there and watching the baby do its hilarious little bipedal run up close was incredible.

Reference
O’Neill, M. C., Umberger, B. R., Holowka, N. B., Larson, S. G., & Reiser, P. J. (2017). Chimpanzee super strength and human skeletal muscle evolution. Proceedings of the National Academy of Sciences, 201619071.