Anthropology.net

Monte Verde, Chile is a very interesting archaeological site. First discovered in 1976, the site is about 500 miles south of Santiago and has yielded artifacts of a small settlement of 20 to 30 people living in a dozen huts along a small creek. Aside from artifacts, a wide variety of midden has also been unearthed from the site indicating these people survived on extinct species of llama, gomphotheres, shellfish, vegetables and nuts.

In 1979, Tom Dillehay conducted radiocarbon dating of the bones and charcoal found at Monte Verde. The results were shocking at the time. The dating of the organic materials was at 14,000 years before the present. This conflicted with other archaeological evidence of the settlement of North America, such as the artifacts that supported Clovis theory… none of which had dates earlier than 13,000 years ago. To have people living in Chile 14,000 years ago would have meant that people arrived in the Americas earlier than 13,000 years ago. Lots of people rejected the radiocarbon dating because of it challenged the Clovis theory. It wasn’t until 1997 that archaeologists reviewed the evidence, visited the Monte Verde site, and approved of the date.

Since then, lots of other evidence, such as genetics and more artifacts have helped provide more understandings on the mode and tempo of the peopling of the Americas. I’ve covered some of the recent evidence. If you’re interested in reviewing them, check out this collection of blog posts related to the peopling of the Americas.

Today’s Science has published a new report from Monte Verde, authored by Tom Dillehay and others. The paper, “Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America,” announces the discovery of the remains of nine species of seaweed and algae found from hearths in Monte Verde. Radiocarbon dating of the layer yielded a date of 14,220 and 13,980 years ago… which is right in line with the 1979 dates.

The finding of seaweed and algae in Monte Verde is a curious one, and what makes this paper unique. See, Monte Verde is about 10 miles away from the ocean. The authors interpret that the seaweed and algae was of some value for the people of Monte Verde for them to haul it inshore… Perhaps it was used for food or medicine?

Who knows, really? What we can interpret from this evidence is that prehistoric people stuck to the shore. Sticking to the shore woulda made traveling throughout the Americas much more efficient, according to some scholars who subscribe to the coastal migration hypothesis. The general view of this hypothesis is that the early immigrants would have spread down the coast much faster than they could move inland because they could exploit familiar coastal resources more readily and get much of their food from the sea. Not much evidence has been found to support this hypothesis, partially because sea levels are 200 feet or so lower 14,000 years ago than they are right now. Any seaside sites would have been covered up as the ice melted after the last ice age. Finding seaweed from site like Monte Verde indicates that 14,000 years ago people relied on some sea life, and kept relatively close to the shore even though they established a rather permanent settlement inland.

From my personal experience with hiking the Santa Cruz mountains as well as working at an archaeological site in the Monterey Bay, I too have seen evidence that prehistoric peoples were relying heavily on sea life for food. Often, I’ve found mussel shells deep within the forest. I have also seen how people were regularly hunting fur seals from a rookery.

Dillehay, T.D., Ramirez, C., Pino, M., Collins, M.B., Rossen, J., Pino-Navarro, J.D. (2008). Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America. Science, 320(5877), 784-786. DOI: 10.1126/science.1156533

There’s a new PLoS ONE paper making the rounds in the press today. The research behind it fits the kinda stuff you may see on Dienekes’ Anthropology Blog and sometimes on GNXP… it is basically an investigation on the attractiveness of a symmetrical face. The paper is published open access, under the title, “Symmetry Is Related to Sexual Dimorphism in Faces: Data Across Culture and Species.” It comes from psychologists and anthropologists in the U.K. and the U.S.

This subject is extremely interesting. The face has many functions in social behavior — moods are assessed from emotions expressed on the face. The face also functions as a billboard, advertising the quality of the mate. More attractive faces are often thought to be higher quality mates. Both symmetry and degree of sexual dimorphism have been linked to affect the attractiveness of human face shape.

In this study, subjects were given arrays of photos of 500 faces from people of European and African ethnicity as well as photos of non-human primates (macaques). About a third of the faces were male and the rest were females. The subjects were asked to judge for the most attractive face. The most attractive faces were then measured for symmetry. Symmetry was determined by measuring deviations from the midline, as well as measurements for the distance between the eyes. In total 6 measurements were made to assess bilateral symmetry.

The degree of sexual dimorphism was also measured. The distance between specific points, like the prominence of the cheekbone and ratios of the height of the jaw to the lower face height, lower face height to the face height and ratio of the width of the face to the height of the lower face were made. In all samples, symmetric males were ones who also had more masculine facial proportions and symmetric females had more feminine facial proportions. I’ve put up a figure that shows the highs and lows of attractive faces form their study.

These conclusions further validate the notion that sexual dimorphism and symmetry in faces advertise mate quality. I kinda have an issue with how the authors are phrasing their results — they had two ethnic groups in their study but conclude that symmetry & dimorphism is attractive in all cultures. It is very probably that other cultures also share this sentiment, but it is over-stretching the results to say that this reaction is evident ALL cultures and species based off of two ethnic groups.

I’m also not too sure how the authors justify that sexual dimorphism and symmetry in the face provides evidence that there must be a biological mechanism linking the two traits during development. This could be because I really don’t know much about evolutionary psychology. There is without a doubt something going on psychologically that makes people associate symmetry and dimorphic faces as attractive, how that translates to mate quality is highly debatable. On a related sidenote, I find the data about our ability to find attractive primate faces also very interesting, the authors suggest that,

“the signaling properties of faces are universal across human populations and are potentially phylogenetically old in primates.”

Which indicates that there’s been some sort of selection in the primate lineage that has predisposed us to associate symmetrical, dimorphic faces as attractive.

Little, A.C., Jones, B.C., Waitt, C., Tiddeman, B.P., Feinberg, D.R., Perrett, D.I., Apicella, C.L., Marlowe, F.W., Reimchen, T. (2008). Symmetry Is Related to Sexual Dimorphism in Faces: Data Across Culture and Species. PLoS ONE, 3(5), e2106. DOI: 10.1371/journal.pone.0002106

The latest edition of the anthropology blog carnival Four Stone Hearth is now up at remote central, so fell free to head on over and check it out.

The next and 41st 4SH will be at Our Cultural World, on May 21st.

So, I got my hands on that mouth watering Nature paper I mentioned a couple days ago. It is titled, “Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution,” and it is probably the biggest anthropology news of this week. I’ve read it and it is dense. It really shouldn’t be so dense because what the authors ultimately did was a cladistic analysis on 17 of the most complete hominin fossil skulls. What really makes this study different is in the traits they have quantified and compared for their study. I’ll do my best to translate it into plain English.

First, let me define the methodology behind this paper, cladistics, also known as phylogenetics, is a way to organize entities. It can be used to organize really anything — such as tools like hammers, wrenches, pliers, etc. In this case, cladistics was applied on hominin species. Cladistics ultimately organizes things based on upon their ’shared derived characteristics.’ Shared derived characteristics is an ambiguous term. It really means the traits that are seen in members of the same species, which are unique from other species, i.e. all orangutans have red hair whereas chimpanzees do not, making them different. When dealing with fossils, researchers can only compare and contrast measurements from the bones, such as the size of the brain case or the length of a bone.

I’ve written on several occasions how cladistic analysis works great for grouping different organisms that are really derived. It gets dicey when cladistics tries to resolve organization of organisms that show a lot of variation amongst between them, as seen in a recent discussion on H. floresiensis. The authors of this paper acknowledge this as a primary motivation for their research. They write,

“However, completion of cladistic analysis becomes problematic because, at lower taxonomic levels, most of observable variation is expressed as continuous changes of size and shape rather than in discrete identifiable structures.”

This problem arises when analyzing hominin fossils, especially fossils thought to be members of the genus Homo. All members of the genus Homo share a large number of derived morphological similarities, that make them different from australopithecines and other apes. What are they? A strictly bipedal adult stature and the largest brain size of all primates are a couple. But, because collections of Homo fossils show a lot of variation in the traits, it makes it difficult to validate such questions like if Homo neanderthalensis was more bipedal that H. heidelbergensis. This has made discerning what traits are unique to each species of Homo troublesome. The authors also acknowledge this. In their own words,

“these [discretization methods] disregard the continuous nature of many complex morphological traits.”

I’ll get to what that really means later in the next paragraph, but first let me also outline another related shortcoming in using cladistics to figure out what’s going on within Homo. See, in the process of trying to find discrete traits in each fossil hominid, researchers have often relied on quantifying multiple traits and presenting them as a univariant measurement. According to the authors, this “disregards the multivariant and geometric nature of form.”

Yesterday, I shared a perfect example of this problem — Yoel Rak identified several traits in the Neandertal mandible thought to be unique to them. He was pownced upon for disregarding that the Neandertal mandible size may have increased as a function of the expanding skull. This problem is not isolated to just Rak, it seems to be prolific within paleoanthropology. Functional traits are often separated from developmental traits, when in fact they are really integrated. The authors address ‘a logical approach’ to overcome this problem,

“treat integrated features as a single phylogenetic complex, and to treat the complex as if it were an independent character.”

The authors applied their approach, selecting four measurements of the skull that integrate functional and developmental traits. The four measurements the authors quantified are the flexure of the cranial base, facial retraction, neurocranial globularity, and the shape and position of the masticatory apparatus. If you’re curious to see exact what these measurements are, the authors provided a figure that illustrates them. I’m putting it right below this paragraph. These traits are believed to be constrained to evolve in a coordinated fashion, rather than independent from one another.

17 skulls were analyzed. John Hawks expressed beef with the sample size, but they are all very complete skulls. Folding in incomplete specimens woulda relied on inferring more missing measurements — which I don’t particularly think is the most conservative approach to figuring out hominid evolution. The 17 skulls are A.L. 444-2, Sts 5, KNMER-406, OH 5, SK 48, WT 17000, KNMER 1813, KNMER 3733, Zhoukoudian, D2700, Steinheim, Kabwe a.k.a. Broken Hill 1, Atapuerca 5, Gibraltar 1, La Chappelle-aux-Saints, and La Ferrassie 1. A skull of a gorilla, chimpanzee, and modern human were also included in the analysis.

In any cladistic test outgroups must be established. Since we know gorillas and chimpanzees existed before the emergence of hominids, they were considered part of the outgroup — or the ancestral form to compare and constrast shared derived characteristics. Australopithecines, like members of the genus Paranthropus (KNMER-406, OH 5, SK 48, WT 17000) and Australopithecus (A.L. 444-2, Sts 5), were also considered in the outgroup because the scope of this study was to resolve the phylogeny of Homo. To reiterate, the function of establishing an outgroup in phlyogenetics is that the outgroup branched from the parent group before the other two groups branched from each other. Respectively, the ingroup (all the Homo skulls) are more closely related to each other than any single one of them is to the ‘outgroup.’

Casts of the skulls were digitized and the measurements were made. A Procrustes analysis was applied to normalize the data, removing variations in translation, rotation and scaling that woulda occurred in digitizing them. The statistical test used was a principal component analysis (PCA), a test that simplifies the variation described by many variables into a few. I kinda see a flaw in this, PCA has often been criticized for quantifying multiple traits and presenting them as a univariant measurement… a concern the authors raised in their introduction.

Anyways, two phylogenetic trees were constructed from the PCA, one applying a maximum parsimony algorithm and another applying a maximum likelihood algorithm. The parsimony algorithm organizes data based upon the premise of having least number of evolutionary changes. Maximum likelihood algorithm is much more statistically viable, it focuses on integrating probability — the normal distribution of a certain variable. Both trees constructed from the data were similar, differing only in the relative position of H. sapiens in relation to the complex H. erectus, H. ergaster, and H. rhodesiensis.

I’ve put the both figures of the tree on this post for you to evaluate. The top figure, a, is the parsimony tree and the bottom figure, b, is the likelihood tree. The coding may not be very straight forward… basically the recipe for deciphering the coding is the first capital letter represents the genus and the next three lower case letters represent the species. If you have any questions with that, comment here, and I’ll do my best to help you out.

The results aren’t very surprising. H. habilis is the ‘founder’ of the Homo clade. The press went wild over the conclusion Neandertals are distinct lineage from the H. erectus-sapiens lineage, which is misleading — we already have a lot of evidence supporting that. Something that’s worth pointing out is that H. heidelbergenis is more related to Neandertals than the H. erectus-sapiens group, which kinda makes sense, no H. erectus specimens have been found east of Turkey, to my knowledge, indicating that a group of Homo were unique to Europe, prior to the influx of H. sapiens — which could have been H. heidelbergenis.

Both trees show some curious organization in the australopithecines, they fail to form a monophyletic group, which is another hot debate in paleoanthropology. This indicates the australopithecines are paraphyletic. Both trees show that Australopithecus africanus is sister group of the genus Homo. This ain’t a very surprising conclusion because A. africanus was gracile and more like Homo… it is thought to have been a direct ancestor of modern humans and this kinda confirms it.

Even though the conclusions we’re Earth shattering, I do want to point out that the scope of this paper was not to totally reorganize our understanding of human evolution. In fact, they advocate for us to be more cautious in considering what we measure, factoring that some traits need to be considered as modules. It is still possible to recover and reconstruct relevant phylogenetic signals from these modules. In their own words,

“valuable phylogenetic information is recovered from data sets that consider independence on a developmentally and functionally basis, and which preserve the multivariant and continuous nature of complex phenotypes.”

González-José, R., Escapa, I., Neves, W.A., Cúneo, R., Pucciarelli, H.M. (2008). Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution. Nature DOI: 10.1038/nature06891

A summary of Yoel Rak’s talk at the last month meeting of the Paleoanthropology Society in Vancouver, Canada has surfaced in a National Geographic news article from several days ago. Yoel Rak and William Hylander analyzed the anatomy of the Neandertal face and inferred what that coulda meant as far as Neandertal dietary behavior. Did they take quaint bites like a sophisticated aristocrat or were they ruthless wide mouth ogres? If you read the title of this post you’d know the answer to that.

Rak presented his findings, specifically focusing on how the forward-positioned molars and an unusually large mandibular notches allowed Neandertals to gape widely. I’ve put up a photo of La Ferrassie 1 to you right. La Ferrassie 1 is a Neandertal skull found in 1909 in France that shows both traits.

“The scientists believe the large space behind Neandertals’ molars created a geometry that allowed them to take extremely large bites… perhaps an adaptation to the size of the food Neandertals ate, the researchers said.”

This sort of conclusion reeks of adaptionist story telling. I remember reading a similar study that analyzed the form of a horse’s mouth and concluded that it is perfectly adapted to eat apples. Just silly to think of selection and adaptation this way. Anyone one else who shares this sentiment will also appreciate Alan Mann’s snarky commentary, which really drives home the ridiculous nature behind this study. Mann said,

“They didn’t have to put a whole [animal] leg in their mouths.”

The news article goes on to express Mann’s opinion, on how the gape size expanded as a function of brain expansion.

“What has changed is the architecture that we begin to see in modern humans, where the face and the braincase have different kinds of structural relationships…This has produced a change in our ability to open our mouths.”

Recently, I introduced related studies that showed how Neandertals may have eaten plants and how form may not equal function in regards to hominin mastication anatomy. I have some concerns with both studies, but that doesn’t mean they don’t provide applicable criticisms towards Rak and Hylander’s conclusions on Neandertal dietary behavior.

Scientific American has a news piece explaining the implications of one of the new studies on the human genome that I reported on last week. In a nutshell, the news piece explains how the identification of 250 new regions throughout the genome impacts the current human reference genome… raising concerns that reference genome may be faulty—and that there may actually be yet-to-be-uncovered genes missing from it.

Human Genome Project assembled this reference genome I am referring to in 2003. The reference genome is an amalgamation of sequences from four people (two men and two women) and still has gaps in it. I look forward to seeing if amendments will be made to the reference genome based upon these findings. If you think about it, it is gonna be a really big challenge to assemble a more complete reference genome. To recap the conclusions of the study,

“The researchers identified 1,695 instances of structural variations, 800 of which had not been previously reported. Fifty percent of the regions affected by these mutations showed up in more than one of the people studied. Forty percent of the 525 regions found to be missing from the reference genome were due to copy number variations, which means that a crop of yet-to-be-discovered genes may be hiding within them.”

With so many variants floating around, both large ones like copy number variations and small ones like SNPs, the reference genome must be assembled with the most common sets of alleles. That’s gonna take a lot of work, the genomes of many people from different ethnic backgrounds will need to be sequenced, assembled and folded into the current model.

The press is running some mouth watering news on an upcoming Nature paper that provides ‘a new, simplified family tree of humanity.’ I’m really interested in this topic, especially figuring out just how bushy our phylogeny is. See, there has been what I consider misguided movement growing within hominin systematics. One where features from a small sample size of fossils has lead researchers to consider them unique enough name lots of new species, all under the guise of diversity. The only ’success’ this movement has had has been in complicating the evolutionary history of humanity.

I’m extremely concerned about this problem because not only does it make teaching and explaining human evolution more challenging, but also raises ethical concerns if people are just naming new species to make a name for themselves. Often times that stuff gets weeded out in critiques and reanalysis, but there are so many different species names floating around that it is hard for anyone not verbose in hominin nomenclature to figure out who’s who.

All that being said, I hope you realize that reading any new approach to simplifying human evolutionary history will be extremely refreshing. I’ve tried to track down the paper in Nature’s advanced issue section, but it ain’t there yet. Soon, I hope. In the meantime, all we have to review is the AFP release on the topic.

The lead author is Rolando Gonzalez-Jose, from the Patagonian National Centre at Puerto Madryn, Argentina. It seems like the thesis of this paper is that facial traits do not appear out of the blue but result from continuous change. Ahh, sounds like a punctuated equilibrium debate. He argues that, specimen that have relatively minor changes in features as compared to others should not be automatically held up as representing a new species. Well, no duh.

In order to establish this, Gonzalez-Jose used a new analytical approach on 3D images of 17 hominid species, with a gorilla, chimp and modern human thrown in. The approach focused in on measuring the similarities and differences on a particular set of fundamental yet long-term changes in skull shape. Using computational methods, the skulls were compared on four variables,

1. The roundness of the skull
2. The base of the skull
3. The protrusion of the jaw
4. The facial retraction, or in other words the position of the face relative to the cranial base

Organizing the outcome of the measurements into a phylogenetic tree, reportedly reveals a clearer view on the evolutionary history of humans and their ancestors. Some conclusion reported are messages we’ve read time and time again, such as this one result: Neandertals are declared “chronological variants inside a single biological heritage.” Again, I don’t have the paper, so I’m going on what was said in the press release.

It should be noted that the source can’t spell ‘phylotogenic’ correctly. I don’t know if that’s any indication on how trustworthy this report is because I know I have a lot of typos and grammatical mistakes here, but I’m not full time reporter. As a professional news outlet, I expect them to catch mistakes like that when reporting science.

This coming Wednesday, May 7^th, will mark the 40^th edition of Four Stone Hearth, the anthropology blog carnival that began life here at Anthropology.net – so if you have anything you’d care to contribute to this next edition, you can send it via submit@fourstonehearth.net or instead to remote central, the hosting blog this time round.

In brief, Science has published three news pieces that you maybe interested. They are all reports of what was presented at the American Association of Physical Anthropologists meeting a couple weeks ago. The first, “Snapshots From the Meeting,” is a summary of the conference, where Ann Gibbons and Elizabeth Colutta discuss, ‘the evolution of gliding, the divergence of Homo habilis and H. erectus, and Neandertal speech.’ The last topic is something I covered, so you may wanna read a more professional overview.

On that note, you may also wanna check out, “Australopithecus Not Much of a Nutcracker,” which is directly related to research on Paranthropus boisei’s diet I reported on a couple days ago. The piece is a bit more thorough though, providing a summary of the,

“different analytical methods suggest that robust australopithecines didn’t eat hard nuts and seeds routinely as had been thought, and that robust and gracile hominids actually ate similar fare.”

Last but definitely not least is an interesting news piece on the paleohistory of tuberculosis. In the news report, Ann Gibbons discusses how DNA, coming from early humans were infected with strains of Mycobacterium tuberculosis, prior to the emergence of pastoralism. This suggests that humans were the primary vector that transmitted the disease to bovids and other animals and not vice versa. This kinda shakes up the hypothesis that Razib has been thinking about — that importance of vitamin D was selected as an important immune system component after the Neolithic revolution, when humans began to be pastoralists and agriculturalists.

All three news pieces are short and sweet, a total of three pages long. Check’em out.

Gibbons, A. (2008). AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS MEETING: Tuberculosis Jumped From Humans to Cows, Not Vice Versa. Science, 320(5876), 608a-608a. DOI: 10.1126/science.320.5876.608a

Gibbons, A. (2008). AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS MEETING: Australopithecus Not Much of a Nutcracker. Science, 320(5876), 608b-609b. DOI: 10.1126/science.320.5876.608b

Gibbons, A., Culotta, E. (2008). AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS MEETING: Snapshots From the Meeting. Science, 320(5876), 609-609. DOI: 10.1126/science.320.5876.609

Two similar papers published the latest issues of Nature and Genome Research do high-resolution analyses of the structure of the human genome. They differ in methodology, but have some cool conclusions. The Nature paper, “Mapping and sequencing of structural variation from eight human genomes,” created libraries of 4 African, 2 Asian, and 2 European genomes. From these libraries they created thousands of clones to figure out if there are structural variations in genomes of these eight individuals from diverse geographic ancestry.

The Genome Research paper, “Scanning the human genome at kilobase resolution,” used ditag genome scanning (DGS) to analyze the human genome in high resolution. This method is really similar to serial analysis of gene expression (SAGE), in that genome is fragmented, each tag is ligated with a marker, and a sequencing technique (454 in this particular study) is used ultimately to determine the origin of the fragment in genome. The authors of this paper report that their method was strong enough to provides a kilobase resolution for studying genome structure. DGS is also highly specific and can cover a lot of the genome. Downstream applications of DGS are to validate assembled genomes but also to compare genome similarity and variation in normal populations.

Both methods are able to identify genomic abnormalities like insertions, inversions, deletions, and translocations, much better than current technologies. But why is this all important to anthropology? The Nature paper shows how they were able to find 525 new insertion sequences that are not present in the human reference genome. These new insertion sequences are shown to be variable in copy number between individuals, which ultimately make for 525 new ancestry inherited markers. Furthermore, when the authors of the Nature paper sequenced their clones they were able to find an additional 261 structural variants which reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome.

One last point, most ancestry inherited markers have been SNPs, but more recent research on the human genome has shown, however, that larger-scale differences like the copy number variations (CNVs) and others screened in these two papers, may account for a great deal of genetic variation among individuals.

Got race?

Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N.A., Tsang, P., Newman, T.L., Tüzün, E., Cheng, Z., Ebling, H.M., Tusneem, N., David, R., Gillett, W., Phelps, K.A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J.D., Korn, J.M., McCarroll, S.A., Altshuler, D.A., Peiffer, D.A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D.A., Mullikin, J.C., Wilson, R.K., Bruhn, L., Olson, M.V., Kaul, R., Smith, D.R., Eichler, E.E. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature, 453(7191), 56-64. DOI: 10.1038/nature06862

Chen, J., Kim, Y.C., Jung, Y., Xuan, Z., Dworkin, G., Zhang, Y., Zhang, M.Q., Wang, S.M. (2008). Scanning the human genome at kilobase resolution. Genome Research DOI: 10.1101/gr.068304.107