Anthropology.net

Fellow blogger, Simon Greenhill of HENRY, and co-authors published a cool paper evaluating language evolution that just came out in today’s issue of Science. The premise behind the paper, “Languages Evolve in Punctuational Bursts,” is simple to follow. By comparing related versions, or homologs, of common words between the following language families: Indo-European, Bantu, and Austronesian, changes in languages can be tracked through the fate of certain words, just as mutations in key genes can tell a species’ history.

The team selected the homologous words from a Swadesh list, one of several linguistic lists of vocabulary where the words have “basic.” Swadesh lists are used is used in lexicostatistics, a way of quantitative language relatedness assessment as well as glottochronology, a method to assess and date language divergence dating. Swadesh lists were used in this study because they are changed very little over time and are rarely borrowed, making them good clues about how one language relates to another.

In my own head, I’ve built my own set of Swadesh lists and compared them to languages I’ve come across. I wish I thought about making some sort of formal study out of my observations. I guess Simon et al. beat me to the punch! Here’s a couple of examples from a cross Indo-European language family comparison that I’ve conjured up…. The words for father and mother in English, Spanish padre and madre, Farsi (Persian) pedar and madar. Despite many borrowings, English the much younger languages is much phonetically different from Latin languages in this example, and even more derived from the Farsi homologs.

Using this sort of comparative vocabulary data, Simon et al. were able to construct phylogenetic trees to show how new languages sprouted from root languages. Furthermore, applying the same mathematical models that showed that biological speciation can occur in bursts, to language to conclude that lineages with many “nodes,” or offshoots, change faster over time than language families that have few offshoots. And most of this acceleration occurs right around time the new languages separated from their ancestral lines.

I love these sorts of comparisons, especially because punctuated equilibria is fresh on my mind. As recent as last week has there been an explosion of discussion on punctuated equilibrium on Sandwalk, the Loom and Greg Laden’s blog. But anyways, I must hand it to Simon Greenhill and his coauthors who gracefully integrated an evolutionary biological concept into a linguistic anthropological scope. It really doesn’t matter whether the replicators are genes or words, the same approaches can be used to analyze the data and explain the model.

One last thing, do read Simon’s blog post describing his project and involvement as well as the Nature News coverage on the paper.

Atkinson, Q.D., Meade, A., Venditti, C., Greenhill, S.J., Pagel, M. (2008). Languages Evolve in Punctuational Bursts. Science, 319(5863), 588-588. DOI: 10.1126/science.1149683

If you don’t follow my other blog but are interested in tool use, I just blogged about gorillas who have been seen using clumps of grass and branches as weapons as well as the new research which links macaque tool use and mirror neurons at Primatology.net.

John Hawks also covered the macaque & mirror neuron linkage too, so check out his write up too!

I’ve got a couple pseudo-science, evolutionary psychological news bits to share with you. The first is coverage of Alan Harvey music evolutionary theory that he presented at the Annual Australian Neuroscience Meeting. From the article,

“[Alan Harvey] says music is not just a pretty sound, but also a way of communicating that is just as important as language… [and] music has been central to the evolution of the modern mind.”

I really can’t think of a way to go about proving that the ability to make and appreciate music has been positively selected in humans. In Harvey’s mind, the reason why we see music in all human cultures is indicative of its selective advantage. But that’s not convincing enough for me.

I’ve been thinking about ways to show scientific basis for this hypothesis. Perhaps comparing and contrasting activity in the auditory association area of the brain, the Wernicke’s area, in the temporal lobes of different non-human primates and humans from different cultural backgrounds subjected to music will elucidate how much more activity is required to process and associate music. Anyways, that’s just one possible experiment. The rest of Harvey’s thoughts are summarized in this 2006 transcript, “History of language and music in humans,” where he mentions the book, “The Singing Neanderthals.”

To be really honest, I know little about the music throughout human evolution. The aptly titled book, “The Origins of Music” or this paper, “Music, Cognition, Culture, and Evolution,” maybe a nice place to start informing myself of this topic. I think one of our frequent commenters, Victor Grauer, will do better justice if he decides to cover this news bit.

The next pseudo-scientific topic is about, “what evolution can say about why humans kill — and about why we do so less than we used to?”

I feel as if this topic has been talked about ad nauseam, so I really don’t know why I’m giving it special coverage. I guess its because I find the ‘homicide adaptation theory’ the article describes as a dumbed-down reiteration of game theory, the theory that says individuals will choose strategies that will maximize their return. Here’s what’s actually said of the the ‘homicide adaptation theory’ from the book “The Innate Mind,”

“The theory proposes that, over evolutionary history, humans have repeatedly encountered a wide range of situations in which the benefits of killing another person outweighed the costs — particularly when the assessed costs of murder are low, success is likely and other non-lethal options have been closed off.”

The article goes on to describe the violence we see in non-human primates and compare that to human violence behavior. There’s also a run down on the history of violence. Some discussion is given to concept, the culture of violence.

I think these two news bits aren’t incredibly insightful but they are interesting topics to think about. How can one go about explaining behaviors as beneficial adaptations? I don’t wanna rehash the argument behind sociobiology as an adaptionist program, because Lewontin did a great job addressing this shortcoming in sociobiological/evolutionary psychological thinking… But I can’t help but to think, why do these behaviors have to be considered through an adaptive framework? In other words, why can’t these behaviors just be features of being human?

Even though I read the classic 1975 Science paper by Mary-Claire King and Allan Wilson, where they demonstrated through comparative protein analysis, that chimpanzees and humans are genetically 99% identical, I was still shocked to read the results of the initial draft of the chimpanzee genome when it came out in September 2005. Like many others, I understand chimps to be the closest living relative of humans in the natural world. The similarities we share in behavior, morphology, personality, and culture are phenomenal… But to read that 96% of total the human genome is identical to the chimpanzee genome, well, I was floored with that statistic to say the least.

Since then, many studies have elucidated that the phenotypic differences between humans and chimpanzees are due to differential gene expression. The foremost study on this subject, that comes to my mind, is Yoav Gilad’s 2005 paper, “Expression profiling in primates reveals a rapid evolution of human transcription factors.” I would also check out important 2005 paper, “Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees.”

In the Gilad paper, he and his coauthors used novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously. Their study showed that as humans diverged from their ape ancestors in the last five million or so years, genes for transcription factors, which are proteins that control gene expression, were four times as likely to have changed their own expression patterns as the genes they regulate. So basically any small changes in the expression of these regulatory genes can have an enormous impact, because they influence the activity of their downstream gene product. I’m not one toot my own horn, but if you are still confused by this summary I apologize… I don’t have a better way to explain what and how differential gene expression is better than this comment I left in April 2007.

That being said, I’ve been wondering what causes differential gene expression for quite sometime. I know many different stimuli can activate and repress gene expression, from cell signaling to environmental shifts such as climate change or drought. But I wondered how differential gene expression can be manifested to cause such a massive difference between genetically similar humans and chimpanzees. Could it be due to the alignment of the moons of Saturn, or are there more tangible things… like diet, that cause differential gene expression?

Much of anthropology currently thinks that one of the identifiable human traits is a dietary divergence. That’s why I’ve kept a keen eye on the work of David Strait, who is investigating fossil morphology of early hominins to check out how changes in morphology and diet change go hand and hand. I’ve also been following Nate Dominy‘s work, which is much more applicable from a genetic perspective because he’s looking at genes such as AMY1, a salivary enzyme, and how humans have a different copy number compared to other primates. But by in large, my question has been unanswered.

Fast forward to today, when I catch this headline from PLoS One, “Human and Chimpanzee Gene Expression Differences Replicated in Mice Fed Different Diets,” in my RSS feeds. Before I even read the abstract, I thought to myself, “Wow, here it is… A paper to answer it once and for all.” You know you’ve heard the cliche phrase, we are what we eat… now it seems that a group of scientists from China have grouped up with Svante Pääbo, the man whose dominating anthropology authorship, to investigate how the different diets of chimpanzees and humans affect gene expression.

Because of logical and ethical issues, actual humans and chimpanzees were note subjected to experimental conditions and sacrificed to determine the differences in gene expression. Instead, four groups of six young mice were feed four different diets for two weeks. Here’s a summary of the diets given to the respective four groups. You’ll get a kick out of the last one.

1. Ye old mouse pellet diet, high in calories and proteins and heat processed to yummy goodness.
2. Veggie, fruits, and yogurt — similar to what captive chimpanzees get.
3. Human cafeteria food.
4. The Supesize Me diet. Yes, exclusively McDonald’s fast food.

After the two weeks, the mice were killed and the expression levels of brain and liver tissue was analyzed and compared. Right off the bat, no significant expression difference was noticed in brain tissue between the mouse, veggie, and cafeteria diets. Only did the Supersize Me diet affect brain gene expression!. Whoa, does that mean human and chimpanzee brains operate similarly? Likely, we know the brain utilizes glucose for metabolism… so long as you’re getting a source of carbohydrates, the brain should be functioning more or less just fine. But high fat diets affect the hippocampus, and polyunsatturated fatty acids hamper learning. All the differences in gene expression was observed in the liver, the organ that makes a lot of metabolites and stores glycogen storage.

The second observation was that the cafeteria and McDonald’s diets have indistinguishable expression differences. They clumped these two diets together, and compared them to the mouse and chimpanzee diets. When comparing the human diets to the mouse diet, no significant overlaps of expressed genes were observed. That’s probably because the human diet induces a much different effect on mouse liver genes. When comparing the human diets to the chimpanzee diet, a total of 117 different genes were expressed, specifically upregulated in the human diet. The expression level of these 117 genes was compared between orangutans and chimpanzees, who have much similar diets, and it was noted that they also have a similar expression level. In other words, the human diet causes 117 genes to turn on.

What’s really cool, and what really ties into a paper I reviewed a couple days, is that the authors found out that the promoter regions and the amino acid sequence of these 117 upregulated genes evolved faster than other genes. The authors suggest,

“…that changes in dietary regimes may have caused some genetic adaptations in the human and chimpanzee genomes. That dietary changes can result in genetic adaptations is illustrated… It is conceivable that certain dietary changes in human evolution, such as increased nutritional quality and a reduced need for detoxification due to the introduction of cooking, have caused a relaxation of selective constraints on diet-related genes.”

The indistinguishable expression differences seen in the livers of mice fed the cafeteria and McDonald diets is one of the most intriguing observations. Could some commonality in the diets, such as cooking, be causing this similar expression pattern? Possibly. Does that mean the advent of cooking food caused hominids to turn a major evolutionary corner about 1.9 million years ago? I’m sure Harvard professor, Richard Wrangham, would like to know, he’s the one that proposed in his 1999 paper, “The Raw and the Stolen. Cooking and the Ecology of Human Origins,” that cooking tubers is linked to changes in body size and tooth size that separated Homo erectus from earlier australopithecines (also something Strait is looking at!).

The 33rd edition of the anthropology blog carnival Four Stone Hearth is now up and running at Greg Laden, and comes with this recommendation from Greg…

This is an exceptionally outstanding set of posts for this or any carnival. I’m sure you will enjoy visiting and reading each and every one of these submissions.

He also includes the following information…

Welcome to the Four Stone Hearth Blog Carnival #33, ‘specializing’ in the four fields of anthropology. The previous edition of 4SH can be found at Testimony of the Spade, and the next edition will be hosted by Our Cultural World. The main page for Four Stone Hearth has additional information on the carnival, and you can submit entries via Blog Carnival.

Happy reading…

Today, I used Athena, a web app that lets one check out and compare promoter sequences in Arabidopsis, for my Functional Genomics class. You can check out the Bioinformatics publication that announces this cool tool, if you want. But I must admit it is not really applicable to the rest of this post… the only reason I bring it up is because it influenced what I’ve been thinking about the whole day: promoters and how they effect gene expression and ultimately phenotype, especially since last week I wrote up an overview on how mutations in the promoter sequence of the dopamine gene has serious behavioral ramification.

Promoters are often neglected parts of the genome. They are critical areas that contain landing spots for other proteins that control gene expression. These regions are upstream of genes, but their location isn’t always fixed at an exact spot. Sometimes they are 2,000 bases upstream or more, and other times they are just a couple bases from the start codon.

While their locations vary, they all contain cis-acting elements which are areas of the DNA that have binding sites for proteins called transcription factors. The transcription factors have specific binding sites, and they latch onto the area that best matches their specificity. Based upon what other specific binding sites are located in the promoter, a whole cohort of proteins form a complex that recruits polymerase to being transcribing the gene and expressing it. All the components of the complex need to be present for polymerase to do its thing, which expands the flexibility of the expression and regulation of genes. The following illustration documents tones down this complexity with just the basic role of a transcription factor:

Basically, all I want you to appreciate is that promoter sequences are critical to understand gene expression and regulation. They are effectively the on and off switches that begin transcription of a gene into a product. Now, if you’re still confused and angry with why I’ve dumped all this molecular biology on your tired Monday night eyes, don’t blame me.

Blame the early online PLoS Genetics release that inspired me to introduce you to the wonderful world of promoters, enhancers, gene expression and gene regulation. See with a title like this, “Differential Allelic Expression in the Human Genome: A Robust Approach to Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression,” I just had to pass the goodness onto y’all.

In a nut shell, the article is important because it confronts one of the biggest mantras going around and offers an explanation that shifts the meaning behind the mantra. The mantra goes something like this, “Humans are genetically 99.9% identical.” Part of the mantra, is true, because we’re more or less genetically identical in the genes that code for proteins. And most of these protein encoding genes make proteins that are important for basic cellular functions, which we all need. But, that’s about all the mantra has going for it.

Our differences are manifested by many different genetic anomalies, from SNPs within exons to repetitive sequences. But a lot of our phenotypic differences come about from the different patterns in which our otherwise homologous genes are expressed or regulated. And the DNA the ares of the promoter that effect gene expression and regulation, and make us different, are neglected and not analyzed because linkage/association mapping of gene expression is notably costly and is a hell of a lot of work. In this new paper, a new method is described with all of the catch phrases that excite many molecular biologists, such as “robust” and “high-throughput” ways to,

“directly measure differences in allelic expression for a large number of genes using the Illumina Allele-Specific Expression BeadArray platform and quantitative sequencing of RT-PCR products. We show that this approach allows reliable identification of differences in the relative expression of the two alleles larger than 1.5-fold (i.e., deviations of the allelic ratio larger than 60:40) and offers several advantages over the mapping of total gene expression, particularly for studying humans or outbred populations. Our analysis of more than 80 individuals for 2,968 SNPs located in 1,380 genes confirms that differential allelic expression is a widespread phenomenon affecting the expression of 20% of human genes and shows that our method successfully captures expression differences resulting from both genetic and epigenetic cis-acting mechanisms.”

Effectively what this paper describes is a way to sequence and screen promoter regions of a lot of human genes, to see and compare what’s in them. With an understanding of the allelic differences that are represented in the promoter region of a gene of a population, we can begin to see how different combinations of transcription factors being to alter gene expression and phenotypic differences, and why humans are so diverse.

One more video to share with you, this time it is an advertisement for a type of machine called a thermal cycler, that I’ve been using a lot for last five months. And by a lot I mean I’ve used one almost every day to run a super top secret set of PCR reactions for a project I’m working on.

A thermal cycler just a really accurate fancy pants oven and refridgerator. What is loaded inside, are tubes full of nucleic acids and a reaction mix, which amplifies the nucleic acids with polymerase enzymes as it heats and cools.  Anyways, this video (somewhat comical and corny) is made by a Bio-Rad, a biotech company that has tried to make a viral video to promote their new line of 1000 Series thermal cyclers. Gotta hand it to them for being one of the first science companies out there to explore a new type of advertisement.

Seems like to today is turning into the film Fridays that I always looked forward to early on in my education. You probably deserve a break from this week’s blogging. This video that I’ll be sharing with you has many flaws, but it is a creative way to visualize the evolutionary processes. I don’t particularly appreciate how little to no effort was made to show the Cretaceous–Tertiary extinction event nor the dearth of mammalian evolution, instead they literally fast forwarded millions of years of evolution to show an ape walking bipedally in the trees… which is a somewhat dangerous interpretation.

Anyways, its flawed but it is entertaining, especially since I brought up limb evolution during the Devonian. The video also gets plus points because it plays a favorite Nine Inch Nails song of mine,

If you read the overview on limb evolution that I wrote yesterday, I think you maybe interested in watching this 51 minute conversation between Carl Zimmer and Neil Shubin that the Panda’s Thumb pointed too.

One of the hallmarks of human evolution, aside from our bipedalism and extraordinarily large brains, are our forelimbs… especially the famed prehensile thumb. Our forelimbs, or arms, are extremely flexible compared to a quadruped. For example, because of the shallowness of the ball and socket joint that connects our humerus to our scapula, our arms can rotate 180 degrees. A special thank you to our arboreal tree swinging ancestors. But our arms aren’t that different from other organisms. Actually, if you’ve spent any time reading your basic biology textbook, you probably have come across a common illustration which compares the human forelimb to forelimbs of other organisms, such as the bat, whale, etc.

In these illustrations, you are supposed to see how the bones that make up a bat’s wing are structurally analogous to both human hands and seal flippers, due to the common descent of these structures from an ancestor that also had five digits at the end of each forelimb. The bones of the bat wing are proportionately different from a human’s arm, but they still share the major components such as the humerus, radius, and ulna. These illustrations are ultimately meant to document that a lot of homology exists in the basic vertebrae body plan and establish the fact that all vertebrates share a common evolutionary ancestor.

Based off of papers such as this 2006 Science publication, we’ve come to understand that the structural homology is due to the activation and expression of several critical genes that regulate development. One of them is called sonic hedgehog or SHH, named after a favorite video game of the researcher who discovered the gene. When there are mutations in SHH, limbs do not develop normally, as illustrated in the collection of skeletons from the various mutant stocks to the right. The forelimbs of the top represent normal development with the presence of SHH. In the absence of SHH signaling, forelimbs are mutated as seen in the bottom.

Comparing the SHH sequence between organisms have shown that it is a highly conserved gene, found with little difference in species as diverse as arthropods and mammals. In 2006 we also saw another paper that figured out the molecular evolution of SHH is relatively accelerated in primates, when compared to other mammals. And SHH is even more accelerated in the human lineage. Since SHH is a gene expressed during and for development, such findings implicate SHH as a potential contributor to the evolution of primate and human specific morphological traits.

Anyways, where I’m trying to go with this is that we see a conservation in limb development, both genetically and phenotypically. Neil Shubin, a professor of anatomy at Chicago University also investigated this phenomenon and published his findings in his book, “Your Inner Fish: A Journey into the 3.5 billion-year History of the Human Body“, which explores the links between humans and their most ancient forebears.

He’s analyzed the tiktaalik fossil, which is supposed to represent a transitional species of fish to amphibian. By the way, the tiktaalik discovery was announced also in 2006 by Shubin and colleagues. In his comparisons, he sees that ours wrists and unique opposable thumb, even the shape of our skulls, can be traced to origins in the tiktaalik. Shubin also found out that the tiktaalik fossil displayed similarities to the human shoulder, elbow, and forearm.

“When we study the structure of these joints to assess how one bone moves against another, we see that tiktaalik was specialized for a rather extraordinary function – it was capable of doing push-ups,” writes Shubin.

Separately, Shubin has found that modern-day fish carry genes allowing for the growth of wrists, hands and fingers. These are now “switched off” so the digits never develop in the fish.

Such findings cast doubt on the assumption that hands are a more recent evolutionary step than fins. Instead, fins may have developed as an improvement on hands.

The research also supports the argument that the majority of the human genome developed 500m years ago and is shared with most living creatures.

One of the factors that makes living forms different is the ability to switch off certain genes while retaining them in the genome.

An alternative approach is to adapt similar genes to different purposes. Some of the genes involved in the evolution of human vision and hearing play an active but very different role in the metabolism of jellyfish.

I feel that excerpt was awfully simplistic, but I want to bring to attention what I’ve bolded. The second statement, the one that says the majority of the human genome developed 500,000,000 years ago is an extraordinary but not nearly as controversial statement as the first one. We know that genes like SHH and the HOX genes are conserved… and being eukaryotes, many of the genes that encode for basic functions of the cell are conserved.

But where Shubin is paraphrased, saying fish have the developmental genes that pattern for wrists and fingers but don’t express them, is ballsy. Furthermore, saying limb patterns that makes up a hand developed before fins is even more of a contentious statement. It is reminiscent the curve ball Aaron Filler’s threw us in his human ancestor for the apes hypothesis, because the current understanding is based upon fish with fins gave rose to amphibians that have more hand-like forelimbs than their fishy ancestors. I’d like to know what genes Shubin has identified as inactivated in fish for the development of hands, wrists, fingers in fish are. But unfortunately the source article doesn’t mention them. I guess I gotta buy and read the book.