Genetically identical mice develop individuality

One of the more interesting findings in behavior genetics is the fact that monozygotic twins (essentially genetic clones of one another) that are raised together (essentially in the same general environment) do not develop identical personalities. Clearly, this means that there is some sort of non-shared environmental factors that condition individuality. It is very difficult to pin these factors down in humans because we can't simply throw them into controlled experimental conditions and watch what happens (and rightfully so).

The journal Science has just published a fascinating study by Julia Freund and her colleagues that explores this issue with mice. What they did was take a group of 40 genetically identical female mice (well, about as identical as you can get; they were super inbred, but may vary by a handful of SNPs and/or VNTRs) and let them roam around an enriched environment for a few weeks. They were able to track their movements (in order to examine how "explorative" each individual was) and their hippocampal development (this part of the brain is thought to regulate behavioral plasticity). I'll let the authors pick it up from here (Freund et al. 2013: 758):

This study shows that adult neurogenesis, as an instantiation of brain plasticity, is linked to individual differences in experience among genetically identical individuals who live in a nominally identical environment. About one-fifth of the experiential effects on adult neurogenesis was captured by a measure of roaming through an enriched environment. This finding supports the idea that the key function of adult neurogenesis is to shape hippocampal connectivity according to individual needs and thereby to improve adaptability over the life course and to provide evolutionary advantage...[t]his is in line with the observation that behavioral treaits can be strongly influenced by external stimuli that vary between individuals or populations of individuals...

They continue (Fruend et al., 2013: 759):

Three months of living in a complex environment led to a massive magnification of individual differences in explorative behavior among genetically identical individuals over time, and these differences were related to adult hippocampal neurogenesis. The rich environment lost its "sameness" over time and gave way to the emergence of a personalized "life space" and a "mouse individuality," similar to what has been observed in humans for personality traits.

There has been a lot of discussion regarding cloning. Now, if you wanted to produce two absolutely identical people, think about all the factors you'd have to keep constant, and we're not just talking about minute changes in the intrauterine environment (temperature, etc.), but also all the experiences an individual will have over their lifetimes. Genetically cloning an individual may not be so difficult, but creating two identical human beings may be nigh impossible.

References:

Freund, J, Brandmaier, AM, Lewejohann, L, Kirste, I, Kritzler, M, Krüger, A, Sachser, N, Lindenberger, U, Kempermann, G (2013). Emergence of individuality in genetically identical mice. Science 340, 756-759.

The end of slavery and the Old South

I just finished Bruce Levine's book, The Fall of the House of Dixie: The Civil War and the Social Revolution that Transformed the South. Most of what I've read on the Civil War, while not ignoring the southern perspective, is typically written through northern eyes. I therefore found two things particularly interesting in Levine's book:

• Southern opinion was actually quite diverse on the question of succession and the war. The inevitability of succession was by no means shared by all southern whites, and there were several southern-based groups that actively fought against the Confederacy throughout the war. In fact, Robert E. Lee and other Confederate officers were forced to dispatch regiments from the regular army to help with home defense. 
• While most southern (and northern, for that matter) whites shared a common belief in white supremacy, only a select few at the top of the social hierarchy owned most of the slaves. This means that many of the soldiers fighting for the Confederacy were non-slave holders, and as the war dragged on many of these poorer folks developed a deep resentment for the planter elite. They began to wonder why they should fight such a destructive war to preserve an institution that they never had, nor likely ever would, benefit from.

Levine, in his BookTV lecture (you can also check out an NPR interview here), cites a recent national survey in which 50% of Americans polled "deny that slavery was the main cause of the U.S. Civil War." This view is even more prevalent among those below 30 years of age (nearly 3 out of 5). One of the key points of the book, and most of the contemporary sources appear quite clear on this, is that slavery was in fact a major, if not the major, impetus for the war. Other motivating factors, like the defense of state's rights or the maintenance of southern honor, while certainly important to some individuals, were largely concocted by elite slave owners to inspire the non-slave holding majority to participate, or drudged up years later to justify the war in a postbellum society hostile to slavery.

Although I didn't plan it this way, the North Carolina Museum of History is currently exhibiting an original copy of the Preliminary Emancipation Proclamation, which Lincoln issued in September of 1862 and warned the Confederacy of the Union's intention to grant freedom to slaves within areas still in active rebellion. My wife and I stopped by the exhibit yesterday, and two pages of the proclamation (they never have all seven on display at once), written in the hand of one of  Lincoln's secretaries (I would guess either John Hay or John Nicolay, although I have not been able to confirm this), are on display. The museum will also be showing North Carolina's original copy of the 13th Amendment that abolished slavery in the United States:

References:

Levine, B (2013). The fall of the house of Dixie: The Civil War and the social revolution the transformed the South. Random House, New York.

Congress and NSF face off

The chairman of the House Committee on Science, Space, and Technology, Republican Lamar Smith of Texas, has recently prepared a bill entitled "The High-Quality Research Act" that aims to revise the criteria by which the National Science Foundation would award grants. According to ScienceInsider, the new bill would:

require the NSF director to post on NSF's website, prior to any award, a declaration that certifies the research is (1)...in the interests of the United States to advance the national health, prosperity, or welfare, and to secure national defense by promoting the progress of science; (2)...the finest quality, is groundbreaking, and answer questions or solves problems that are of utmost importance to society at large; (3)...not duplicative of other research projects being funded by the Foundation or other Federal agencies.

The bill is being proposed in response to several social science grants that were identified as a waste of tax-payer money. I am in agreement with arstechnica's John Timmer who, in response to points (2) and (3) of the bill's criteria, argues:

The other two requirements, however, completely misunderstand both basic research and the role of the National Science Foundation. Basic research is largely about exploring the unknown; by definition, it's almost impossible to tell which areas of research will end up being groundbreaking of have commercial applications. And the NSF is specially tasked with funding basic research and science education.

Should NSF and other government funding agencies be required to justify their decisions? Absolutely. But who is best qualified to judge the merit of these projects? I'd say the hard-working, anonymous reviewers who have expertise in each particular field. I'll be keeping an eye on this...

Neandertals on TV

Just a quick note to let readers know that PBS is premiering two documentaries on Neandertals tonight, both of which highlight the very latest science on these extinct humans. One is called "Decoding Neanderthals" and focuses on the new genetic and archaeological data, while the other is part of PBS's "Secrets of the Dead" series and focuses on the forensic-type information gleaned from Neandertal fossils. I've seen a bit of the "Decoding Neanderthals" show (you can view it for free on PBS's website), and it appears to be pretty good.

Can you scan that fossil for me?

Jean-Jacques Hublin, the director of the Department of Human Evolution at the Max Planck Institute for Evolutionary Anthropology, recently commented in the journal Nature on the need to provide free (or at least affordable) access to digital data for paleoanthropologists. Hublin discusses microCT data of hominin fossils in particular, and the Leipzig team just recently released quite a bit of free digital material for the hominin fossils from Kromdraai, South Africa (Skinner et al., 2013).

The question of access has always been a thorny one in paleoanthropology: on the one hand you have the research teams that spend months (even years) recovering the fossils and the museums whose responsibility it is to protect their country's heritage, and, on the other, researchers and educators who would like access to the materials to carry out additional research and teaching. I think open access to data is a good idea in principle, now its just a matter of convincing researchers and museums to open up! Easier said than done. Once you publish a study, the data are, after all, available, but many researchers are hesitant to publish their raw data because they may still want to carry out additional analyses before anyone else (and why not?). In other cases, its simply a matter of data management capabilities and expertise rather than any stinginess.

References:

Hublin, J-J (2013). Free digital scans of human fossils. Nature 497, 183.

Skinner, MM, Kivell, TL, Potze, S, Hublin, J-J (2013). Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of Human Evolution 64, 434-447.

Early hominin meat-eating and expensive tissues

I actually was not aware of its publication until I came across it on John Hawks's weblog, but Joseph Ferraro and his coworkers have come out with a detailed taphonomic analysis of the faunal remains from Kanjera South, an important Oldowan site from Kenya that dates to about 2 million years ago. Their abstract does a nice job of summarizing the significance of the site and the study's findings (I guess this is what abstracts are supposed to do, after all; Ferraro et al., 2013: 1):

The emergence of lithic technology by ~2.6 million years ago (Ma) is often interpreted as a correlate of increasingly recurrent hominin acquisition and consumption of animal remains. Associated faunal evidence, however, is poorly preserved prior to ~1.8 Ma, limiting our understanding of early archaeological (Oldowan) hominin carnivory. Here, we detail three large well-preserved zooarchaeological assemblages from Kanjera South, Kenya. The assemblages date to ~2.0 Ma, pre-dating all previously published archaeofaunas of appreciable size. At Kanjera, there is clear evidence that Oldowan hominins acquired and processed numerous, relatively complete, small ungulate carcasses. Moreover, they had at least occasional access to the fleshed remains of larger, wildebeest-sized animals. The overall record of hominin activities is consistent throughout the stratified sequence - spanning hundreds to thousands of years - and provides the earliest archaeological evidence of sustained hominin involvement with fleshed animal remains (i.e., persistent carnivory), a foraging adaptation central to many models of hominin evolution.

This research team has been working hard out a Kanjera for many years now, and its really nice to see a comprehensive analysis of the faunal material from the site (we'd been getting tantalizing hints in various publications and presentations for some time).

Before we proceed, let me summarize the state of affairs just prior to these latest data. The 1.8 Ma time marker that Ferraro et al. mentions refers to the burst of evidence for meat-eating that emerges almost exclusively from Olduvai Gorge in Tanzania. One site in particular, the very well-known Level 22 at the gorge's FLK locality (also known as the Zinjanthropus Floor), dates to about 1.84 Ma and preserves thousands of fossils, many of which bear clear indications of hominin butchery. Now, up until a few years ago, it was thought that the animal bones from many of the other sites from Beds I and II of the gorge (ca. 1.9-1.2 Ma) were also largely the result of hominin activity. However, my colleagues and I showed that there are really only two sites, the previously mentioned FLK 22 from Bed I, and the site of BK, in upper Bed II (about 1.3 Ma), that are largely the result of hominin butchery (Domínguez-Rodrigo et al., 2007, 2009; Egeland, 2008; Egeland and Domínguez-Rodrigo, 2008). Now, we're not saying that hominins weren't at the sites; they certainly made, used, and left stone tools at these locations, but they were not doing a lot of meat-eating. There are a couple of other Oldowan sites here and there with some evidence for butchery, but if we ignore FLK 22 for the moment, good evidence for lots of meat-eating (or, to use Ferraro et al.'s term, "persistent carnivory") really doesn't pick up until much later, perhaps about 1.5 Ma.

What does all of this have to do with expensive tissues? Well, researchers have come up with several well reasoned, and very popular, human evolutionary models based ultimately on the shift to meat-eating. To start, brains and guts are very expensive tissues: one does a lot of thinking and the other does a lot of digesting, both of which take up good amounts of energy. If you start eating more meat, which is nutrient dense and easy to digest, you can divert energy from the guts to develop bigger noggins. Other possible correlates of a diet based increasingly on meat would be increased range size (carnivores, and other animal that eat high quality, easy to digest foods, tend to have larger ranges) and unique life histories (extracting nutrients using technology, and hunting with technology in particular, are difficult things to learn, and you don't want to die before you learn how to do them well, so perhaps we've evolved extended life spans to fit this need). People have traditionally seen the evolution of Homo erectus, with its bigger brain, long, lanky legs, and ability to leave Africa to colonize parts of Eurasia, around 1.8 Ma as great evidence for these shifts. Ok, all well and good, but, to use an old phrase: where's the beef? In other words, where is the evidence for sustained meat-eating just before and as H. erectus was evolving? Other than a single site, FLK 22, there really wasn't much...until now.

This is what makes the Kanjera evidence so important. I'm not sure it completely quashes my reservations (after all, we still only have two sites with good evidence for regular meat-eating between 2.6 Ma, when stone tools were first invented and used to butcher carcasses, and 1.5 Ma), but it is a good start.

References:

Domínguez-Rodrigo, M, Barba, R, Egeland, CP (2007). Deconstructing Olduvai: A taphonomic study of the Bed I sites. Springer, New York.

Domínguez-Rodrigo, M, Mabulla, AZ, Bunn, HT, Barba, R, Diez-Martín, F, Egeland, CP, Egeland, AG, Yravedra, J, Sánchez, P (2009). Unraveling hominin behavior at another anthropogenic site from Olduvai Gorge (Tanzania): New archaeological and taphonomic research at BK, Upper Bed II. Journal of Human Evolution 57, 260-283.

Egeland, CP, Domínguez-Rodrigo, M (2008). Taphonomic perspectives on hominid site use and foraging strategies during Bed II times at Olduvai Gorge, Tanzania. Journal of Human Evolution 55, 1031-1052.

Ferraro, JV, Plummer, TW, Pobiner, BL, Oliver, JS, Bishop, LC, Braun, DR, Ditchfield, PW, Seaman III, JW, Binetti, KM, Seaman Jr, JW, Hertel, F, Potts, R (2013). Earliest archaeological evidence of persistent hominin carnivory. PLoS ONE 8, e62174.

Archaic humans versus giant hyenas in Pleistocene Europe

María Patrocinio-Espigares and her colleagues have published an interesting study claiming to have identified evidence for competition between archaic humans and giant hyenas for access to a mammoth carcass from a site in Spain dated to over one million years ago. The site, Fuente Nueva-3, is found near the southern Spanish village of Orce, which is an extremely rich area for early Pleistocene fossils, including those of hominins. In fact, Fuente Nueva-3 and a nearby site, Barranco León, dated to 1.3 and 1.4 million years ago, respectively, currently preserve the oldest well accepted evidence for hominin occupation in all of Europe.

The excavations at Fuente Nueva-3 have been ongoing for well over a decade, but this paper reports on a partial skeleton of Mammuthus meridionalis, a species of mammoth, found in association with a few stone tools and, intriguingly, some coprolites (that is, fossilized poop). The materials were deposited near the edge of an ancient lake, and the authors argue that the mammoth (an old female) probably died of natural causes. The skeleton is relatively complete; only the legs and the head are missing.

Photo (A) and map (B) showing the distribution of mammoth bones, stone tools, and coprolites from Fuenta Nueva-3 . From Espigares et al. (2013: Figure 4).

Butchery marks (cutmarks from stone knives and percussion marks and notches from breaking open bones for marrow; although, some of the so-called percussion notches look a lot like the carnivore-created notches I've seen from modern assemblages) and tooth marks are pretty common on many bones from levels above and below the mammoth skeleton, but none whatsoever have been discovered on the mammoth bones in question. Nevertheless, the authors contend that the carcass was butchered by hominins, who removed the legs for consumption elsewhere, and later partly consumed by giant short-faced hyenas (Pachycrocuta brevirostris; they do not, however, tell us how they know the coprolites are those of a hyena).

I suppose this is possible. The authors correctly note that proboscideans are so big, and are covered by so much tough soft tissue, that butchery and tooth marks are unlikely to be inflicted. Pachycrocuta, though, as a recent paper by many of the same authors tells us, was about one-and-a-half times bigger than modern spotted hyenas and probably better adapted to bone-cracking than any other mammal that ever existed (Palmqvist et al., 2011) so, if anything would have left tooth marks on a mammoth-sized carcass, you would think it would be Pachycrocuta. I'll let the authors summarize their thoughts (Patrocinio-Espigares et al., 2013: 122; see the drawing by the very talented Mauricio Antón below for a reconstruction):

The Upper Archaeological Level of Fuente Nueva-3, dated around 1.3 Ma, provides the oldest evidence of a probable competition between Homo and Pachycrocuta, the two major bone-modifying and accumulating agents during early Pleistocene times in Europe. The evidence lies in the finding of an incomplete skeleton of M. meridionalis surrounded by 34 coprolites and 17 lithic artifacts. The skewed spatial distribution of these elements, the physical characteristics of the coprolites and the absence of the elephant limbs and cranium suggest that both hominins and hyenas scavenged the carcass of this megaherbivore, following a sequence of consumption in which the hominins arrived first, dismembered and transported the limbs, and probably also the cranium, and later the hyenas consumed the rest of the elephant carcass.

Original caption: Reconstruction of the possible sequence of interaction between hominins (A) and hyenas (B) during the exploitation of the carcass of M. meridionalis. From Patrocinio-Espigares et al. (2013: Figure 7). 

These conclusions are all based on indirect evidence (stone tools that may or may not have been used to butcher the animal, coprolites that may belong to hyenas that may have fed on the carcass). Either way, this does bring up the interesting issue of how hominins and carnivores interacted: were they competitors on the landscape for carcasses? Was this competition direct (i.e., fighting over access to carcasses) or indirect (one removing edible carcasses from the environment that the other in turn could not exploit)? Researchers have in fact suggested that competition from large carnivores went a long way towards preventing hominin populations from permanently colonizing Eurasia until after 600,000 years ago or so.

References:

Palmqvist, P, Martínez-Navarro, B, Pérez-Claros, JA, Torregrosa, V, Figueirido, B, Jiménez-Arenas, JM, Patrocinio-Espigares, M, Ros-Montoya, S, De Renzi, M (2011). The giant hyena Pachycrocuta brevirostris: modelling the bone-cracking behavior of an extinct carnivore. Quaternary International 243, 61-79.

Patrocinio-Espigares, M, Martínez-Navarro, B, Palmqvist, P, Ros-Montoya, S, Toro, I, Agustí, J, Sala, R (2013). Homo vs. Pachycrocuta: earliest evidence of competition for an elephant carcass between scavengers at Fuente Nueva-3 (Orce, Spain). Quaternary International 295, 113-125.