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):

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!”


Hominin Trackways in the Cretan Miocene?

Guest Blogger: Sarah Hlubik

An in-press paper, available in the Proceedings of the Geologists’ Association on Aug. 31, describes trackways dating to 5.7 mya on Crete (shown in this post’s lead image, from Gierlinski et al. [2017]). This places them just before the Messinian Salinity Crisis, when the Mediterranean dried up, global climates were nice and warm, and the planet really did belong to the apes. A potential hominin trackway (let’s be real, any trackway at all) from this time period is WAY COOL for a couple of reasons:

1. Tracks do not preserve very well. Ever go walking along the beach and look behind you to see your footprints washed away by the next wave? Yeah, me too. Most footprints made in the dirt, sand, or mud, are going to be washed away or destroyed by other individuals, or simply smoothed over because there is so much water in the sediment. For tracks to preserve, they have to dry out a bit, and then be covered pretty quickly by sediment that is a little different in texture or that won’t end up squishing together with the underlying layer. So tracks at all are always really cool, and offer a glimpse into environments and animal communities that we generally don’t see.

2. The Miocene gets called the Planet of the Apes because of the intense radiation of apes that happened during that time period (23-5.3 mya). We know some about the vast array of species that must have occupied the Old World at that time, but there is a lot we don’t know (again, see how to become a fossil), and what we don’t know may have been living on ancient Crete and walking, at least some of the time. Suspensory locomotion evolved sometime during this period (see Pierolapithecus, Dendropithecus, and Dryopithecus), and many later Miocene apes were highly orthograde (which just means they sat upright). Today, suspensory locomotors include gibbons and orangutans, and these (also orthograde) apes are able to walk on two legs over the ground, so it isn’t outside the realm of possibility that a highly orthograde ape had to move across a relatively open, albeit somewhat gooey, landscape and did so on two legs.

Cheezburger animals monkey trees jungle GIF

3. Footprints can tell us a lot about who made them, even if they can’t tell us definitively who made them. Footprints can give us clues about how many toes, or digits, are on a foot, whether the toes had nails, hooves, or claws, and the overall shape of the foot. We can determine the direction individuals were walking, and get a general idea of a minimum number of individuals within a group (to an extent –preserved footprints should represent individuals who are walking over the landscape at roughly the same time, but who can say if they were there together). In this case, the authors claim that the footprints show a foot that resembles ours with all the toes, even the big toe, together, but without claws or a defined arch. Because of this, the authors claim that an original (basal) member of the Hominini clade (our own branch of the family tree) made these tracks, and suggest that whatever it was eventually gave rise to whatever we are now.

I’m not convinced, but I am certainly intrigued. At 5.7 mya, it post-dates early potential basal members of our lineage (Sahelanthropus and Orrorin) residing in Central and Eastern Africa, where current evidence overwhelmingly supports hominin evolution in savannah environments. Crete is a long way from any of these places, even if the Mediterranean Sea wasn’t a factor, and there are no Miocene ape fossils found particularly close to the trackways site. That doesn’t mean these footprints don’t belong to Miocene apes, but it makes it harder to argue that it was definitely an ape and not, say, a bear. Especially given the vast array of apes inhabiting the Planet of the Apes, I don’t have a problem with the possibility that more than one Miocene ape stood up to get across a flat surface, but it would be nice to point to a fossil close by in time and space and say, ‘Hey, it’s probably that guy!’.

Gierliński, G.D., Niedźwiedzki, G., Lockley, M.G., Athanassiou, A., Fassoulas, C., Dubicka, Z., Boczarowski, A., Bennett, M.R. and Ahlberg, P.E. (2017). Possible hominin footprints from the late Miocene (c. 5.7 Ma) of Crete?. Proceedings of the Geologists’ Association.

Sarah Hlubik is a PhD candidate in the Department of Anthropology at Rutgers University. She works on early hominin control of fire at Koobi Fora, Kenya.

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?


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:


And then there’s haplotype E:


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.

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.

A Mini-Post & Anthro News

Hominin herpes, European apes, and a fossilized spine

Sometimes a lot of cool stuff happens between BS&M meetings. In an effort to keep up with the constant flow of science and to tide you over until our next discussion, we’re going to try to post mid-week mini-blogs and links to what we’re reading during the week.

This week, Google alerted me to another instance of possible between-species hanky-panky in the fossil record. In a new analysis, Underdown and colleagues attempted to figure out the most likely pathway through which humans got genital herpes (HSV2) from the ancestors of chimpanzees. Yes, you read that right. The closest relative of human HSV2 is not HSV1 (oral herpes), but ChHV1 (the chimpanzee version of herpes). The authors suggest that these two viral lineages split from one another between 1.4 and 3 million years ago, and that either Homo habilis got “proto-HSV2” from the ancestor of modern chimps and gave it to Paranthropus boisei, who then passed it on to Homo erectus, or P. boisei got it directly from the ancestor of modern chimps and transmitted it to H. erectus. (H. erectus is generally considered directly ancestral to Homo sapiens, which is why the virus only has to make it to that species to end up in us.)

Before things get too weird, I want to point out that the authors don’t think that the interspecific hanky-panky went down between either H. habilis or P. boisei and a member of the population of ancestral chimps. They suggest that hunting or scavenging meat from infected chimpanzees would have likely been enough to pass the virus on to one of the hominins, probably via chimp blood coming into contact with an open wound during the butchery process. Once “proto-HSV2” made it into H. habilis or P. boisei, however…


Anyway. HSV2 now joins HPV (from Neanderthals) and body lice (from some archaic form of Homo) as evidence of ~close~ contact between humans and our hominin cousins (Reed et al. 2004, Pimenoff et al. 2017). The coolest thing about all of this research is that it’s not based directly on fossils or on ancient DNA; you can use things like the evolution of viruses to tell us about our own evolution. Awesome.

Read on for links to what we’ve been nerding out over this week and the references for the herpes paper.
Note: the featured photo is the OH5 cranium of Paranthropus boisei (credit:

Continue reading “A Mini-Post & Anthro News”