The oldest known plague

New ancient DNA research has identified the bacterium Yersinia pestis, which causes the deadly and epidemic illness known as plague, in Chalcolithic and Bronze Age Central Eurasia, from Altai to Poland and the Caucasus.

S. Rasmussen, M.E. Alentoft et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell 2015. Open access → LINK [doi:http://dx.doi.org/10.1016/j.cell.2015.10.009]

Summary

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

The bacterium was yet unable to cause the bubonic form of the plague and could not spread by means of fleas either. Instead it probably caused pneumonic and spticemic plague and was propagated by coughing and sneezing, much like the flu. 

Figure 1

Archaeological Sites of Bronze Age Yersinia pestis
(A) Map of Eurasia indicating the position, radiocarbon dated ages and associated cultures of the samples in which Y. pestis were identified. Dates are given as 95% confidence interval calendar BC years. IA: Iron Age.
(B) Burial four from Bulanovo site. Picture by Mikhail V. Khalyapin. See also Table S1.

In spite of the hype, the prevalence of the plague was low: only 7 out of 101 samples tested positive for the bacterium, ranging from c. 2800 BCE (Altai) to c. 1000 BCE (Southern Azerbaijan, Iran). A 7% prevalence is still significant but it's also obvious that 93% of the people in the period studied did not die from the plague, so let's not exaggerate, alright?

The exaggeration is already seeded in the study with passages as this one:

These early plagues may have been responsible for the suggested population declines in the late 4^th millennium BC and the early 3^rd millennium BC (Hinz et al., 2012, Shennan et al., 2013).

Neither of the referenced studies (see here and here) deals with Eastern Europe, West Asia or Central Asia, and the analyzed dates only slightly overlap with the period in which Y. pestis is found, so I fail to see the logic. It is true that there could be a coincidence in the case of Little Poland, where both Y. pestis and a demographic decline are apparent c. 2000 BCE but in all other cases it really needs a good deal of imagination to make any association.

In any case, it is clear that even the most virulent plague ever known, the Black Death, only managed to make a dent in the European demography and its consequences were not those of demographic re-expansion of the less affected populations (Polish, Basques) but a double socio-economic transition in two phases:

1. The lack of manpower in the decades after the Black Death allowed the lower classes to renegotiate their situation in various ways. It was the period in which the feudal system was most dramatically eroded, with peasants gaining control on their farmed lands and lords losing large shares of their exploitative profits, while being forced to compete against each other for whom offered best working conditions to the now scarce farmers, who, legally or not, migrated from the worst places to the ones offering better conditions. 
2. A reaction by profit-jealous landlords that largely replaced farming by husbandry, which requires less manpower. A well known case were the English enclosures, which would, slowly but steadily, set the foundations of Capitalism.

This is explained by historian, actor and director Terry Jones in the following video:

So the consequences and context of these epidemics must be considered adequately and not distorted nor simplified unduly in the line of the infamous Guns, Germs and Steel book, which greatly exaggerates the consequences of natural epidemics and is one of the favorite books of Eurocentric reactionaries with a distorted and overly simplistic view of things. One of the "virtues" of the epidemic hype is that it somehow absolves the winners from their historical crimes, blaming them on nature almost alone: instead of genocide, they use these deformations of reality to blame the mass destruction of whole nations and populations, be them Neanderthals or Native Americans, on "natural causes". 

Hypocrisy!

Instead I wonder about the real demographic impact, not yet well assessed, of the epidemics, and also about the real socio-economic consequences of such demographic declines. Of course, they could have allowed for localized migrations in the aftermath of the epidemics (or whatever other causes of demographic declines) but they should also have favored at least short-term renegotiations of the social order in favor of the suddenly scarce working classes (farmers). This "upward mobility" and partial "leveling" of what was already in many cases a feudal-like caste society should have dramatic effects in the constitution of the nations of the Bronze Age, regardless of later re-adjustments and expansions, which one can imagine as an imperfectly cyclical process.

Poverty directly damages brain development

Children that at early ages have similar or even greater gray matter than their wealthier peers, get stuck in a weaker development as they grow just for being poor. That is what a new study has found:

Jamie L. Hanson et al., Family Poverty Affects the Rate of Human Infant Brain Growth. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0080954]

Abstract

Living in poverty places children at very high risk for problems across a variety of domains, including schooling, behavioral regulation, and health. Aspects of cognitive functioning, such as information processing, may underlie these kinds of problems. How might poverty affect the brain functions underlying these cognitive processes? Here, we address this question by observing and analyzing repeated measures of brain development of young children between five months and four years of age from economically diverse backgrounds (n = 77). In doing so, we have the opportunity to observe changes in brain growth as children begin to experience the effects of poverty. These children underwent MRI scanning, with subjects completing between 1 and 7 scans longitudinally. Two hundred and three MRI scans were divided into different tissue types using a novel image processing algorithm specifically designed to analyze brain data from young infants. Total gray, white, and cerebral (summation of total gray and white matter) volumes were examined along with volumes of the frontal, parietal, temporal, and occipital lobes. Infants from low-income families had lower volumes of gray matter, tissue critical for processing of information and execution of actions. These differences were found for both the frontal and parietal lobes. No differences were detected in white matter, temporal lobe volumes, or occipital lobe volumes. In addition, differences in brain growth were found to vary with socioeconomic status (SES), with children from lower-income households having slower trajectories of growth during infancy and early childhood. Volumetric differences were associated with the emergence of disruptive behavioral problems.

Figure 2. This figure shows total gray matter volume for group by age.

The data is clear (for details of the localized frontal and parietal evolution see figs. 3 and 4). The question is: why does this happen? The paper attempts also to discuss that:

These results extend a consistent literature in rodents, non-human primates, and humans suggesting that early environments marked by stress or deprivation negatively influence brain development [65]–[69]. This emerging body of research has found differences in brain structure in portions of the frontal lobe, which fits well with the analysis presented here [68]. These findings suggest that aspects of low SES environments have important functional implications for children's health and adaptation [70], perhaps by influencing key features of central nervous system development. In regards to neurobiological mechanisms, the differences in volume we find are likely due to neuronal remodeling, rather than birth of new neurons (or neurogenesis) [27], [71], [72].

(...)

Candidate factors might include the effects of household resources, environmental stimulation, crowding, exposure to pathogens and noise, parental stress, and nutrition. It is also possible that pre-natal experiences affect brain development and reflect other disadvantages and risks related to poverty. Because humans are able to adapt to a range of environmental conditions, we must understand more about the level at which impoverished environments become toxic for children.

And quite suggestively in the introduction they mention as well that:

Conditions such as the variety and complexity of the stimuli in an animal's cage can influence different aspects of brain structure, including the number of neurons, glial cells, myelination, dendrites, synapses, and neurogenesis (for review, see Ref. [23]–[24]). 

The specific causes can be many but I'd dare say that "caging", i.e. the limitation of stimuli for living in smaller, impoverished, artificial habitats (including of course whatever limitations that the adults around them may have, such as low culture or emotional instability) is likely to be a key negative environmental factor for brain development.

On the other hand I can imagine that certain enrichment (cultural, health even technological, why not?) that has happened to our species in general in the last centuries, may be behind the so-called Flynn effect, which is that the measured IQ has been growing everywhere quite steadily. 

But in any case it is quite worrying that these social differences have such a big effect on the children and emphasizes the need to overcome them and to provide the best possible environment for the development of the future generations.

Was the grove snail Epipaleolithic livestock in Western Europe?

Cepaea nemoralis
(CC by Papa Lima Whiskey 2)

The problem of disjunct distribution of Western European species or, in this case, subclades of a single species is nothing new and has been startling biologists for almost two centuries already, with particular interest of Irish-Iberian, Breton-Iberian or just general Irish-continental disjunct relationships of various species (the so called Lusitanian distribution). Among them is the iconic strawberry tree (madroño in Spanish, found in Ireland but not Great Britain) but also a number of small land animals: the Kerry slug (found in NW Iberia and SW Ireland only), the Quimper snail (found in NW Iberia and Western Brittany) or the Pyrenean glass snail (found in the Pyrenees and Ireland).

There are also cases of subclades within an otherwise widespread species which show a similar pattern. In 2003, Masheretti et al. demonstrated that the Irish variant of the pygmy shrew had its greatest affinity with populations of Andorra, in the Eastern Pyrenees, from which they are descended.

This study illustrates a similar case but affecting the snail species Cepaea nemoralis (grove snail or brown lipped snail), whose Irish lineages are mostly derived from Iberian ones and in most cases from the Eastern Pyrenean haplogroup C.

Adele J. Grindon & Angus Davison, Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pone.0065792]

Abstract

The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared “Lusitanian” history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.

The evidence gathered by this study is most readily visible in fig. 2:

While it is not the focus of this study, we see here two other cases of probable disjunct distribution:

• Hg D is found in Iberia, Ireland, small pockets in Britain and SW France but also in North and Central Europe.
• Hg F shows also disjunct presence in Cornwall, far away from the main cluster around the Bay of Biscay.

The authors of this and previous studies have suggested that this distribution may have to do with intentional transport (as livestock) in the process of the colonization of the Atlantic Islands in the Epipaleolithic. In support of this claim, there is enough fossil evidence of the snail in the island:

Fossil material indicates that this species has been continuously present in Ireland for at least 8000 years (Newlands Cross, Co. Dublin: 7600+/−500 BP Cartronmacmanus, Co. Mayo: 8207+/−165) [7], [8].

In other cases, such as the inedible Kerry slug, we may suspect unintentional transport and therefore we would be justified to imagine a later time frame for their arrival to Ireland, possibly in the Chalcolithic-Megalithic period, but the evidence for C. nemoralis is highly suggestive of intentional transport in the Epipaleolithic. We can therefore say that the humble grove snail was one of the first domestic animals of Europe, possibly second after the dog.

Puctuated equilibrium, speciation and everything else

I believe it is worth recommending the reading of this new review paper which discusses the various evolutionary theories en vogue, with emphasis in punctuated equilibrium, which is surely a very realistic model:

Jaroslav Fregg, Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution. Biology Direct 2013. Open access → LINK [doi:10.1186/1745-6150-8-1]

Abstract

Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.

Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation -- while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.

The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.

I don't dare to evaluate the paper but I do recommend reading it because it can help us to better understand what is going on when we talk of speciation, competition, evolution, dynamic equilibrium, etc. I picked up this quote:

Approximately 35% of the substitutions (20-70%, depending on the studied taxon) was shown to occur in brief periods of speciation. It is worth mentioning that we are not aware of how many speciation events actually occur in the studied, seemingly unbranched lineages. Therefore, the published estimates of speciation associated substitution rates represent only the lower margin of the real figures.

And the only figure, which illustrates how a highly diverse population/species can be stable and how evolution can happen and often does in bottlenecks instead:

Most punctuational theories of evolution, including the evolutionary conceptions of Wright, Mayr, Carson, Templeton and Flegr (for comparison see Table 1), suggest that sexually reproducing species respond evolutionarily to selection (are evolutionarily plastic) only during speciation. The mechanisms of this type of evolutionary behavior of sexual species suggested by the various theories differ, for a review see [1]. For example, the genetic revolution model [2] implicitly and the frozen plasticity theory explicitly [3] suggest that a species is evolutionary plastic when its members are genetically uniform, i.e. only after a portion of the original species has split off, skirted extinction for several generations, and then undergone rapid multiplication (Figure 1).

The paper uses the "open review" format, including commentaries from the reviewers and the replies by the author - this I find an interesting novelty which adds some value to the paper by pointing possible avenues for discussion or further research.

Hominid speciation: sudden or gradual?

It depends apparently: bonobos may have diverged quite suddenly while in other cases, including the Pan-Homo split, the process of speciation appears to have been more gradual.

Thomas Mailund et al., A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. PLoS ONE 2012. Open access → LINK [doi:10.1371/journal.pgen.1003125]

Abstract

We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

Did the human hand evolve for boxing (too)?

That is the intriguing conclusion of a new study:

Michael H. Morgan and David R. Carrier, Protective buttressing of the human fist and the evolution of hominin hands. The Journal of Experimental Biology, 2012. Freely accessible → LINK [doi: 10.1242/​jeb.075713 ]

Summary

The derived proportions of the human hand may provide supportive buttressing that protects the hand from injury when striking with a fist. Flexion of digits 2–5 results in buttressing of the pads of the distal phalanges against the central palm and the palmar pads of the proximal phalanges. Additionally, adduction of the thenar eminence to abut the dorsal surface of the distal phalanges of digits 2 and 3 locks these digits into a solid configuration that may allow a transfer of energy through the thenar eminence to the wrist. To test the hypothesis of a performance advantage, we measured: (1) the forces and rate of change of acceleration (jerk) from maximum effort strikes of subjects striking with a fist and an open hand; (2) the static stiffness of the second metacarpo-phalangeal (MCP) joint in buttressed and unbuttressed fist postures; and (3) static force transfer from digits 2 and 3 to digit 1 also in buttressed and unbuttressed fist postures. We found that peak forces, force impulses and peak jerk did not differ between the closed fist and open palm strikes. However, the structure of the human fist provides buttressing that increases the stiffness of the second MCP joint by fourfold and, as a result of force transfer through the thenar eminence, more than doubles the ability of the proximal phalanges to transmit ‘punching’ force. Thus, the proportions of the human hand provide a performance advantage when striking with a fist. We propose that the derived proportions of hominin hands reflect, in part, sexual selection to improve fighting performance.  

I wouldn't dare to comment much but for what I have read in the paper, it looks plausible, notably because it is indeed significantly efficient versus the open hand (as much as 3x) and because chimpanzees can't do it... but australopithecines could. 

However I can also imagine this development as a side-effect of other adaptive uses of the hand, such as grabbing a spear, which is no doubt a much more daunting weapon than a naked fist... in most cases at least.

Fig. 2

Ice and "complex organic materials" on Mercury's poles

This is one of those perplexing astronomical news that make history and I can't but mention. US scientists have found, with the help of scout satellite MESSENGER,  that not just suspected Mercury's polar water ice (in shadowed craters) is indeed that but also that confusing dark regions around it are complex organic materials, possibly darkened by the intense solar radiation that bathes the small inner planet. 

The team found that the probe's reflectance measurements, taken via laser altimetry, matched up well with previously mapped radar-bright regions in Mercury's high northern latitudes. Two craters in particular were bright, both in radar and at laser wavelengths, indicating the possible presence of reflective ice. However, just south of these craters, others appeared dark with laser altimetry, but bright in radar.

This confused scientists for a while but eventually they realized that the puzzling regions actually hold water ice at a meter's depth into the soil, where the heat of the sun can't reach so easily. 

Radar-reflectant regions (ice) show in yellow

The most interesting part however is that the astronomers are almost certain now that the dark material must be complex organic matter, darkened by the extreme solar radiation.

Is there life in Mercury? 

Source: Science Daily.

Ref studies: 

1. David A. Paige, Matthew A. Siegler, John K. Harmon, Gregory A. Neumann, Erwan M. Mazarico, David E. Smith, Maria T. Zuber, Ellen Harju, Mona L. Delitsky, and Sean C. Solomon. Thermal Stability of Volatiles in the North Polar Region of Mercury. Science, 29 November 2012 DOI: 10.1126/science.1231106
2. Gregory A. Neumann, John F. Cavanaugh, Xiaoli Sun, Erwan M. Mazarico, David E. Smith, Maria T. Zuber, Dandan Mao, David A. Paige, Sean C. Solomon, Carolyn M. Ernst, and Olivier S. Barnouin. Bright and Dark Polar Deposits on Mercury: Evidence for Surface Volatiles. Science, 29 November 2012 DOI: 10.1126/science.1229764

Elephant hair density helps cooling

The low density of elephant hair has been demonstrated to help cooling:

Conor L. Myrvhold. What Is the Use of Elephant Hair? PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047018]

At low densities, hair has almost no effect on air flow and does not trap an insulating air layer near the skin, but the extended hair acts as a pin fin that increases thermal exchanges with the surrounding air. Thus, as the hair density decreases from that of very furry animals, a break-even point is reached where the hair function switches from an insulator to a heat exchanger. This break-even point occurs at a density of about 0.3 million hairs/m² [26] for thick hair covers with creeping flow in between (recall that 1500 hairs/m² is about the maximum density of elephants). For comparison, the hair density of the human head is about 2 million hairs/m² (see Methods and Discussion S1).

These heat dispersal properties were already known for plants (leaf hair, cactus' spines) but it is the first time to be demonstrated for an animal, more specifically a mammal like us. 

Figure 1. Pictures of elephant hair on the top of the back of an Asian elephant, (A) and an African elephant’s head (B).

The presence of hair on elephants was first noted by van Leeuwenhoek [30]. Photos taken by Conor L. Myhrvold in the Woodland Park Zoo, Seattle, Washington, from outside of the elephant enclosure, with permission from the Zoo.

I searched online for hair density on human body (the question we all have in mind, right?) and I could only find a commercial reference (I'd appreciate a better one if you know one). Still it seems that the hair density on tights and legs (and therefore probably on most of the body) in humans is 50 hairs/cm², what translates as 0.5 million hairs/m², somewhat (but not a lot) above the threshold mentioned above.

I'd dare suspect that this means that human body hair (vellus) is for most people thermally neutral but then I wonder how it works with sweat, which is a key part of our tropical thermo-regulatory natural design. Elephants and plants do not sweat (although they do get wet on occasion), so it may well work somewhat different for them.

That seems to be an interesting challenge to explore.

Latest genetic news (links)

Anthropological and genetic news have been piling up in this strike journey. I'm not sure if I will be able to address all as they may deserve so I'm listing them here in very quick review.

My apologies because I meant that the "links" format would be over but if people overseas (and in some cases also in Europe) insist on working in the general strike journey and publishing things all around, all I can do is this (or risking not even doing anything at all).

Chimpanzee enterotype variation is just like ours. 

Even if our genomes have diverged the microscopic environments we host in our guts are almost exactly the same, with three different types depending exclusively on diet.

Andrew H. Moeller et al., Chimpanzees and humans harbour compositionally similar gut enterotypes. Nature Communications, 2012. Pay per view ··> LINK [doi:10.1038/ncomms2159]

Abstract

Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called ‘enterotypes’, each of which is overrepresented by a distinct set of bacterial genera. Here we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.

A more detailed review can be found at John Hawks' Weblog.

Fig. 1 (a) Left chimpanzee enterotypes, right human ones

High altitude adaptions in Ethiopia

Research on Ethiopian genetic nuances with a Basque name as lead researcher:

Gorka Alkorta Aranburu et al., The genetic architecture of adaptations (sic) to high altitude in Ethiopia. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref. code: arXiv:1211.3053 [q-bio.PE]]

Abstract

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo. 

H/t: Haldane's Sieve. 

An extensive review can be found at Ethio Helix (where else?)

Pig and boar genomes and evolutionary history

Martien A.M. Groenen et al., Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012. Open access ··> LINK [doi:10.1038/nature11622]

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Fig. 3 - reconstructed/estimated demographic history of boars

Less obvious strategies in long term evolutionary co-adaption

Interesting read on how competition can cause the formation of deep evolutionary valleys or gorges from which it is most difficult to exit and are therefore evolutionarily stable.

Eric Chastain et al., Defensive complexity and the phylogenetic conservation of immune control. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref code: arXiv:1211.2878 [q-bio.PE]]

Abstract

One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change by the opponent. To study how this can be done, we construct an evolutionary game between a controller that must process information, and an adversary that can tamper with this information processing. In this game, a species can foil its antagonist by processing information in a way that is hard for the antagonist to manipulate. We show that the structure of the information processing system induces a fitness landscape on which the adversary population evolves. Complex processing logic can carve long, deep fitness valleys that slow adaptive evolution in the adversary population. We suggest that this type of defensive complexity on the part of the vertebrate adaptive immune system may be an important element of coevolutionary dynamics between pathogens and their vertebrate hosts. Furthermore, we cite evidence that the immune control logic is phylogenetically conserved in mammalian lineages. Thus our model of defensive complexity suggests a new hypothesis for the lower rates of evolution for immune control logic compared to other immune structures. 

H/t: Haldane's Sieve.

Genetics and psychology in relation to heroin use and abuse

Ting Li et al., Pathways to Age of Onset of Heroin Use: A Structural Model Approach Exploring the Relationship of the COMT Gene, Impulsivity and Childhood Trauma. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048735] 

Abstract

Background

The interaction of the association of dopamine genes, impulsivity and childhood trauma with substance abuse remains unclear.

Objectives

To clarify the impacts and the interactions of the Catechol -O-methyltransferase (COMT) gene, impulsivity and childhood trauma on the age of onset of heroin use among heroin dependent patients in China.

Methods

202 male and 248 female inpatients who meet DSM-IV criteria of heroin dependence were enrolled. Impulsivity and childhood trauma were measured using BIS-11 (Barratt Impulsiveness Scale-11) and ETISR-SF (Early Trauma Inventory Self Report-Short Form). The single nucleotide polymorphism (SNP) rs737866 on the COMT gene-which has previously been associated with heroin abuse, was genotyped using a DNA sequence detection system. Structural equations model was used to assess the interaction paths between these factors and the age of onset of heroin use.

Principal Findings

Chi-square test indicated the individuals with TT allele have earlier age of onset of heroin use than those with CT or CC allele. In the correlation analysis, the severity of childhood trauma was positively correlated to impulsive score, but both of them were negatively related to the age of onset of heroin use. In structure equation model, both the COMT gene and childhood trauma had impacts on the age of onset of heroin use directly or via impulsive personality.

Conclusions

Our findings indicated that the COMT gene, impulsive personality traits and childhood trauma experience were interacted to impact the age of onset of heroin use, which play a critical role in the development of heroin dependence. The impact of environmental factor was greater than the COMT gene in the development of heroin dependence.

Emotional care or neglect of young children decisive for brain size, intelligence

An image says more than a thousand words. And in this case the image is a brain scan... or rather two side by side:

Both brains belong to 3-years-old children

... the child with the shrunken brain was neglected and abused by its mother, and the child with the larger and more fully developed brain was raised in a loving, supportive home and was looked after by its mother...

This is not just about IQ or head size, which may vary at least largely because of this type of environmental causes, but about everything in life, including emotional and social intelligence and the general ability to carry on with a normal, well integrated life (or become human waste). 

The first years of life are critical for all our development and parental love, very specially that of our mothers, is probably more important than almost anything else.

Source: Medical Daily.

East Asian oaks in the Ice Age

It may sound botanically erudite but it is also of great relevance in order to better understand the ecology and geography of people living in East Asia in the Upper Paleolithic. Hence worth mentioning here.

Dongmei Chen et al., Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047268]

Abstract

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (NST = 0.751 > GST = 0.690, P < 0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s F_S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

 
Maybe most interesting of all is this map: 

Figure 5. Ecological niche modelling.

Predicted distribution probability (in logistic value) is shown in each 2.5 arc-min pixel, based on the palaeodistribution modelling at present (0BP) (a) and at the last glacial maximum (LGM) (21KaBP) (b). The distribution of river systems on the exposed East China Sea during the LGM was drawn from Shota et al. (2012). Occurrence records of Q. variabilis at present are also plotted as black points in the maps.

Much more data for those interested in the genetic details can be found in the paper. 

Gut microbes can be decisive in fat accumulation

Credit: Image created by Ivana Semova, PhD

Certain gut microbes, known as Firmicutes, whose abundance varies from individual to individual, seem to be critical in fat absorption in the stomach and may be a major cause behind the obesity pandemic.

So far this has only been tested in zebrafish (a model organism not so different from us) but there are previous studies in humans that do suggest that the abundance of these microbes may be critical for us too. If so, it would explain how the long-term diet and not just the short-term one affects weight because the abundance of these bacteria would mostly be affected by long term trends, beginning in childhood.

Ivana Semova, Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish. Host & Microbe 2012. Freely available at the time of this citation ··> LINK [doi:10.1016/j.chom.2012.08.003]

Main source: Science Daily. 

Adaptionism (humor)

From the often great comic strip (cum video theater) Saturday Morning Breakfast Cereal:

Complex speciation process of polar and brown bears?

Actual modern hybrid

According to new research, polar and brown bears could have diverged as long ago as 4-5 million years but have been hybridizing intermittently since then, specially as ice sheets receded in interglacial periods as today's.

In fact we know that they do it nowadays.

While some clades of brown bear, notably the Admiralty Islands (but also French ones) are more closely related to polar bear by mitochondrial DNA,  by overall nuclear DNA they fall wholly within the brown bear clade. That's because, mtDNA-wise polar bears are a subset of brown bears, while by nuclear DNA they are more clearly distinct.

The authors propose that this implies mtDNA introgression from brown bear into polar bears, up to the point of total displacement of the native polar bear lineages, but of course it may also be that some of their calculations are totally wrong. After all molecular-clock-o-logy is not rocket science, not at all and a total lineage replacement by just occasional inter-breeding seems a most unlikely event with the laws of probability in hand.

My impression is in fact the opposite: that the nuclear differentiation should have happened after that of the mtDNA but that molecular-clock speculations obscure this fact. But whatever. I may also be wrong, of course but I just can't accept molecular-clock-o-logy as evidence of anything - doing that is pseudoscience.

Ref. Webb Miller et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. PNAS 2012. Open access. [Early edition link, DOI: 10.1073/pnas.121050610] 

See also: Buffalo University press release, Science Daily.

Phylogenetic labyrinth... or molecular-clock fanaticism?

Update: PConroy mentions (see comments) a previous study (Current Biology 2011, Science Now article), which states that there is even closer mtDNA affinity between extinct Irish brown bears and modern polar bears than these have with the Alaskan ABC islander ones.

Neanderthals as leather-crafters

Fig. 1

A new study finds that some peculiarities of adult Neanderthal skeletons may be the product from repetitive scrapping:

Colin N. Shaw et al., Neandertal Humeri May Reflect Adaptation to Scraping Tasks, but Not Spear Thrusting. PLoS ONE 2012. Open access.

Abstract

Unique compared with recent and prehistoric Homo sapiens, Neandertal humeri are characterised by a pronounced right-dominant bilateral strength asymmetry and an anteroposteriorly strengthened diaphyseal shape. Remodeling in response to asymmetric forces imposed during regular underhanded spear thrusting is the most influential explanatory hypothesis. The core tenet of the “Spear Thrusting Hypothesis”, that underhand thrusting requires greater muscle activity on the right side of the body compared to the left, remains untested. It is unclear whether alternative subsistence behaviours, such as hide processing, might better explain this morphology. To test this, electromyography was used to measure muscle activity at the primary movers of the humerus (pectoralis major (PM), anterior (AD) and posterior deltoid (PD)) during three distinct spear-thrusting tasks and four separate scraping tasks. Contrary to predictions, maximum muscle activity (MAX) and total muscle activity (TOT) were significantly higher (all values, p<.05) at the left (non-dominant) AD, PD and PM compared to the right side of the body during spear thrusting tasks. Thus, the muscle activity required during underhanded spearing tasks does not lend itself to explaining the pronounced right dominant strength asymmetry found in Neandertal humeri. In contrast, during the performance of all three unimanual scraping tasks, right side MAX and TOT were significantly greater at the AD (all values, p<.01) and PM (all values, p<.02) compared to the left. The consistency of the results provides evidence that scraping activities, such as hide preparation, may be a key behaviour in determining the unusual pattern of Neandertal arm morphology. Overall, these results yield important insight into the Neandertal behavioural repertoire that aided survival throughout Pleistocene Eurasia.

The tasks that experimentally cause the same kind of asymmetry are hacking, pushing and pulling, while actions related to spear thrusting actually seem to reinforce the left side. The authors think that the repetitive nature of the task, which takes a very important work time investment in modern studied populations from Africa and the Arctic, may have been decisive in the development of the deformations.

Scrapers are incidentally the most common tools found in Neanderthal sites all across West Eurasia.

Of course it could well be that Neanderthals were mostly left handed for some odd founder effect of their species or even cultural bias. This possibility is also considered by the authors although it is not their primary hypothesis. 

Some Mousterian scrapers (source)

Echoes from the Past (Feb 12)

Some more links for you. 

I'm also lifting the temporary comment moderation filter, hopefully lessons have been learned and no more such measures will be needed. Thanks for your patience.

Prehistory of Europe

Pileta: Más sobre Unas focas pintadas por neandertales podrían ser la primera obra de arte...[es] - Salaman mentions that lack of economic resources do not allow to research further by the moment the possibility that the Nerja seals could have been drawn by Neanderthals. 

Pileta: Catalogan pinturas de Altamira que son 15.000 años más antiguas que los bisontes[es] - Some Altamira paintings are found to be 15,000 years older than the famous bisons. This may make them the oldest rock art in Europe (with permission of Nerja and comparable to Grotte Chauvet). No images of the early Aurignacian art are available yet but it is coincident with a trend to reclassify European rock art as of earlier age and Aurignacian period, as discussed here, but mostly not as early as in this case (before 30 Ka BP).

Neanderfollia[cat] offers us some interesting maps of the MP-UP transition in Europe: 

• Mapa de jaciments Chatelperronians (Chatelperronian sites)
• Mapa de jaciments Aurinyacians (Aurignacian and Proto-Aurignacian, but not Bohunician, sites)

Prehistory of South Asia

AIOC: Lithic continuity & innovation in Holocene South India - D. Fuller introduces a new paper (ppv) on the Holocene industries of India (pictured below).

AIOC: Sourcing the 'lost Saraswati' river: new geological evidence - the same author, discusses how the lost Saraswati river does not match the Holocene geology of the subcontinent but could correspond with that of the Pleistocene.

AIOC: A widening range of textiles on Harappan trading ships

Paleodiet

How to feed a pregnant Neanderthal (AVRPI) - the almost always interesting archaeologist Julien Riel-Salvatore discusses several papers on the apparent myth of high protein Paleolithic diets.

Genetics

Max Planck Institute Leipzig | A High Coverage Denisovan Genome - The Denisovan genome is available for all to explore (the researchers however request courtesy if used for academic publication).

Ultraconserved regions of the genome do not seem to have any particular importance:

PLoS Genetics: Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila (open access).

Linguistics

Il tente de décrypter l'ADN de la langue basque (SudOuest)[fr] - Basque cultural journalist Hasier Etxeberria prepares a documentary on the various theories on the origins of the Basque language. 

Psychology and Biology

Brains may be wired for addiction

Preference for fatty foods may have genetic roots

Why do cells age? Discovery of extremely long-lived proteins may provide insight into cell aging and neurodegenerative diseases

Tiny primate 'talks' in ultrasound - our distant Pinoy wild cousin, the tarsier, is not as silent as was thought, they just talk in ways we can't hear.

What elephants want: Ranging and raiding in Asia and Africa | EveryONE  - elephants in fragmented habitats need more land, they also follow the lead of the old ones when raiding crops.

Echoes from the Past (Feb 2)

Lots of links that I think of interest but I do not have time, knowledge or enough discipline to deal with in greater detail.

Truly sorry about the format (or lack of it); I'm drowning in information.

Middle Paleolithic

Olduvai Geochronology Archaeology project

PLoS ONE: Why Levallois? A Morphometric Comparison of Experimental ‘Preferential’ Levallois Flakes versus Debitage Flakes (open access)

Pigmento de ocre neandertal de 250 mil años de antigüedad[es] (ochre pigment used by Neanderthals some 250,000 years ago), also: Neanderthals used red ochre much earlier than previously thought

Levallois core and flake (replica)

Neanderthals and their contemporaries engineered stone tools, anthropologists discover, also Modern flint expert 'reverse engineers' Neanderthal stone axes - and says our ancestors were clever, elegant engineers 

La Cueva de Nerja podría albergar las pinturas más antiguas de Europa[es] Nerja Cave (Andalusia) holds which are possibly the oldest rock art of Europe (which must be of Neanderthal-made if the dates are correct). Also: Las pinturas rupestres más antiguas del mundo podrían tener 43.000 años de antigüedad y ser obra del Hombre de Neandertal según unas nuevas dataciones de Nerja[es] and Cave paintings in the Nerja Caves are much older than thought and also Más sobre el sensacional descubrimiento de la cueva de Nerja[es].

Neanderthal-made rock art?

Upper Paleolithic & Epipaleolithic

El joven de la cueva del Mirón fue enterrado hace 18.500 años[es] (the young man of El Mirón cave, Asturias, was buried 18,500 years ago)

Una sentencia da la razón a Zeleta S.L. y pone en peligro a Praileaitz[es] (tribunal puts Praileaitz cave, Basque Country, at even more risk)

Neolithic & Chalcolithic

Diverging Trajectories? Forager-Farmer Interaction In the Southern Part of the Lower Rhine Area and the Applicability of Contact Models (Luc Amkreutz) - Academia.edu (you need an academia.edu account to view, very interesting anyhow)

Archaeologists uncover oldest evidence of ploughing in Czech lands

Russian fish trap findings

Halladas en Rusia trampas de pesca de más de 7.500 años de antigüedad[es] and 7500 years old traps found in Russia and Complex Fish Traps Over 7,500 Years Old Found in Russia.

Diversidad LBK y relaciones entre Neolíticos y Cazadores-Recolectores[es] (LBK diversity and relationships between Neolithic and hunter-gathererer peoples).

Modelos generales del Neolítico versus datos arqueológicos[es] (general modeling of Neolithic versus actual archaeological data)

The Mesolithic–Neolithic transition in southern Iberia 10.1016/j.yqres.2011.12.003 : Quaternary Research (ppv - proposes some Neolithic colonization/influence in Iberia via North Africa), also: Una tercera ruta de expansión del Neolítico explicaría los rasgos de identidad en el sur de la Península Ibérica[es] (a bit skeptic I am of some of the claims)

Rare monument find leaves wind farm in doubt

Seeing Beneath Stonehenge | Exploring the Stonehenge Riverside project with Google Earth

Ancient popcorn discovered in Peru

Debating early African bananas  

Denuncian la destrucción de una tumba del Neolítico en un monte de Redondela (Neolithic tomb destroyed at Redondela, Galicia).

Metal Ages and History

 

Malta inscription

Rare Cuneiform Script Found on Island of Malta

«Tartessos no era un pueblo de catetos. Eran sensibles y técnicamente capacitados»[es] (Tartessos was not a redneck people: they were sensible and technically capable - there's been some Tartessos conference these days in Andalusia, with nothing new).

Aparecen en Liédena los restos de un poblado de la transición entre la Edad de Bronce y la de Hierro[es] (settlement from the Bronze-Iron ages' transition discovered in Liedena, Navarre)

'Available for rent: The Acropolis of Athens'

Excavation of Bosnian Sun Pyramid given green light (remember the Bosnian "pyramid"? - it is back!)

Human genetics and evolution

PLoS ONE: Y Chromosome Lineages in Men of West African Descent (open access)

Fig. 2 - PCA (BAM stands for Bamileke)

New Genetic Research Suggests Link Between Earliest Native Americans and Southern Siberia. The relevant paper: AJHG - Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians (ppv for 6 months)

Following genetic footprints out of Africa: First modern humans settled in Arabia and the relevant paper: AJHG - The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa (ppv for 6 months)

Master controller of memory identified (this is kind of scary: they wiped out memories in mice!)

Study Reveals Possible New Key to Human Evolution (synapsis making in early childhood allows for extreme learning)

Low IQ & Conservative Beliefs Linked to Prejudice and Social conservatives have a lower I.Q.? (probably) and the relevant paper: Bright Minds and Dark Attitudes: Lower Cognitive... [Psychol Sci. 2012] - PubMed - NCBI (ppv) and a related accessible 2011 paper: political-orientations-intelligence-and-education.pdf

Bonobos' unusual success story (like humans bonobo males are more successful at mating with relatively low testosterone levels).

Chimp 'X factor': Extensive adaptive evolution specifically targeting the X chromosome of chimpanzees, also: Extensive X-linked adaptive evolution in central chimpanzees

Other

Biologists replicate key evolutionary step

Mouse to elephant? Just wait 24 million generations

Isolated Amazonian tribe makes uncomfortable contact