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Monthly Archives: July 2011

Many interesting short news

Partly because of the arrival of the Archaeo News bulletin but also because of mere randomness, it seems to me, a lot of more or less interesting news items are accumulating. In most cases I lack the information to deal with them in any greater depth but are still interesting to read about:

Genetics

Study suggests that the populations leading to modern Africans and Non-Africans did keep mixing for some 40,000 years before a Non-Africans suffered a severe bottleneck and became truly separated. This period of early divergence with interaction could have begun c. 120,000 or 100,000 years ago and would have ended c. 80-60 Ka ago. It could add support to the idea that Toba explosion caused a bottleneck. I’d like to write more about this but I have no access to the paper. -> Science Daily, -> Nature (PPV).

Inheritable epigenetics confirmed: may explain how living beings of all sorts adapt to changing conditions without need to alter their genetic backbone (DNA). -> Science Daily.

Human evolution

Chimpanzee brains do not shrink with age. Unlike humans, chimpanzee do not suffer the array of symptoms we loosely call senility, this may be therefore a hidden cost of having such large brains and living for so long. -> Science News.

Archaeology

Heacham burial

Magdalenian Age erotic art found in Bavaria (Germany). The unusual rock art was found near Bamberg and are believed to be c. 12,000 years old. It seems that the natural shapes in thecave may have inspired the ancient artists. -> news.com.au (no images provided).
Epipaleolithic open air cemetery found in Somerset (England). It is dated to c. 10,000 years ago. -> BBC.
England: Sheffield 6000 BCE: people lived continuously at nearby Whirlow Hall Farm since the Epipaleolithic and into the Iron Age. -> The Star
5000 years-old skeleton unearthed in Aosta Valley (Italy). The woman has been nicknamed Lady of Introd and was more or less contemporary of Ötzi the iceman, found frozen in Tyrol years ago. -> Archaeo News.

Tall el-Hammam pottery
And more England findings: burial of two women with amber beads found in Yorkshire, near Heacham, and dated to c. 2500 BCE (late Neolithic by British chronology, Chalcolithic by pan-European standards). -> EDP24.
Egyptian Old Kingdom may have succumbed to drought, suggests geological survey at Lake Tana (Ethiopia) at the source of the Blue Nile (the main contributor to the Nile in volume and the responsible of seasonal floods). -> PhysOrg.
Bronze and Iron Age city unearthed in Jordan, NE of the Dead Sea (near modern Kafrein, just across the Jordan river from Jerico). -> Tall el-Hammam (dig site), -> Popular Archaeology.
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South Wales cave could host Britain’s oldest cave art

Update: it’s been known that the site is Gower Cave.

A cave in South Wales, whose exact location is being kept secret by the moment, may host Britain’s oldest rock art. 

The discovery of faint engravings depicting reindeer by professor George Nash was accidental, as he took a relax moment after showing the cave to students. The unnamed cave is known for Late Magdalenian artifacts, dated c. 12-14 Ka ago. 
Full story at BBC

 
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Posted by on July 26, 2011 in Magdalenian, rock art, UK, Upper Paleolithic, Wales

 

Drawing the ancestors

Skhul (Palestine 120 Ka ago)
Just found at NeanderFollia[cat] these wonderful artist’s recreations. Hartmut Zänder’s MySpace page[de] is full of fascinating portraits, just that many of them are from people who are not anymore among us but have been gone for many many thousand years.
Zänder’s art is specially dedicated to mtDNA haplogroup K and of course that implies drawing Ötzi, who has ended up being quite more handsome than in other reconstructions I have seen. Now, thanks to Zänder, we can recognize the iceman as a typical North Italian.
But what really caught my attention are the portraits of early H. sapiens, which are quite in the line of what I could imagine. A nice detail is that Zänder draws them with thin lines within a rectangle; I can’t be sure if he does that for the reason I imagine but as soon as I saw these images, they reminded me stylistically of the engraved Magdalenian portraits of La Marche.

Update: An older site by the same author with dozens of reconstructed or rather imagined haplogroup matriarchs by Zänder. Quite impressive.

Update (Mar 17 2012): Zaender has a blog: Regional Ancestry Bands, you may want to visit.

 
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Posted by on July 25, 2011 in Anthropometry, art, human evolution, reconstruction

 

Three genetic papers

Follow titles, links and abstracts of three open access genetic papers that I feel are interesting enough to mention but are too technical and distant from my main focus to be discussed meaningfully here:
What is a species? The example of lemurs
Matthias Markoff et al., On species delimitation: Yet another lemur species or just genetic variation? BMC Evolutionary Biology 2011. [LINK]
Abstract (provisional)
Background
Although most taxonomists agree that species are independently evolving metapopulation lineages that should be delimited with several kinds of data, the taxonomic practice in Malagasy primates (Lemuriformes) looks quite different. Several recently described lemurs are based solely on evidence of genetic distance and diagnostic characters of mitochondrial DNA sequences sampled from a few individuals per location. Here we explore the validity of this procedure for species delimitation in lemurs using published sequence data.
Results
We show that genetic distance estimates and Population Aggregation Analysis (PAA) are inappropriate for species delimitation in this group of primates. Intra- and interspecific genetic distances overlapped in 14 of 17 cases independent of the genetic marker used. A simulation of a fictive taxonomic study indicated that for the mitochondrial D-loop the minimum required number of individuals sampled per location is 10 in order to avoid false positives via PAA.
Conclusions
Genetic distances estimates and PAA alone should not be used for species delimitation in lemurs. Instead, several nuclear and sex-specific loci should be considered and combined with other data sets from morphology, ecology or behavior. Independent of the data source, sampling should be done in a way to ensure a quantitative comparison of intra- and interspecific variation of the taxa in question. The results of our study also indicate that several of the recently described lemur species should be reevaluated with additional data and that the number of good species among the currently known taxa is probably lower than currently assumed.
Horizontally acquired genes: breaching the gate is not getting the treasure automatically, you may also end in the dungeons
H. Deborah Chen et al., Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits. PLoS Genetics 2011. [LINK]
Abstract
Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P), protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.
Author Summary
The traits that distinguish closely related bacterial species are often ascribed to differences in gene content, which arise primarily through horizontal gene transfer. In some instances, the genes mediating a new trait act as independent entities that function in a variety of organisms. However, the ability of a horizontally acquired gene product(s) to operate on an ancestral pathway might be constrained by subtle differences between orthologous ancestral proteins. Here, we examine why the horizontally acquired pmrD gene product post-translationally activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related species Escherichia coli. This allows Salmonella, but not E. coli, to transcribe PmrA-activated genes including those conferring antibiotic resistance when grown in low Mg2+, which is a condition that promotes PmrD expression. We now demonstrate that, paradoxically, the E. coli PmrD protein activates the PmrA/PmrB system in Salmonella even though it fails to do so in E. coli. We establish that quantitative differences in the biochemical activities of the PmrB proteins from Salmonella and E. coli dictate the functionality of PmrD, which protects phosphorylated PmrA from PmrB’s phosphatase activity. Our findings demonstrate that ancestral genes can control the ability of horizontally acquired genes to confer species-specific traits upon different organisms.
Day and night cycle in our cells, the clock inside us and its epigenetic synchronization

William J. Belden et al., CHD1 Remodels Chromatin and Influences Transient DNA Methylation at the Clock Gene frequency. PLoS Genetics 2011. [LINK]
Abstract
Circadian-regulated gene expression is predominantly controlled by a transcriptional negative feedback loop, and it is evident that chromatin modifications and chromatin remodeling are integral to this process in eukaryotes. We previously determined that multiple ATP–dependent chromatin-remodeling enzymes function at frequency (frq). In this report, we demonstrate that the Neurospora homologue of chd1 is required for normal remodeling of chromatin at frq and is required for normal frq expression and sustained rhythmicity. Surprisingly, our studies of CHD1 also revealed that DNA sequences within the frq promoter are methylated, and deletion of chd1 results in expansion of this methylated domain. DNA methylation of the frq locus is altered in strains bearing mutations in a variety of circadian clock genes, including frq, frh, wc-1, and the gene encoding the frq antisense transcript (qrf). Furthermore, frq methylation depends on the DNA methyltransferase, DIM-2. Phenotypic characterization of Δdim-2 strains revealed an approximate WT period length and a phase advance of approximately 2 hours, indicating that methylation plays only an ancillary role in clock-regulated gene expression. This suggests that DNA methylation, like the antisense transcript, is necessary to establish proper clock phasing but does not control overt rhythmicity. These data demonstrate that the epigenetic state of clock genes is dependent on normal regulation of clock components.
Author Summary
Circadian rhythms facilitate daily changes in gene expression via a transcriptional negative feedback loop. In eukaryotes, chromatin remodeling is an integral part of transcriptional regulation and is proving to be one of the major determinants for the proper timing and amplitude of clock-gene expression. We describe here the action of chromodomain helicase DNA–binding (CHD1), one of two ATP–dependent chromatin-remodeling enzymes required for normal circadian regulated gene expression of the central clock gene frequency (frq). Molecular analysis of strains lacking chd1 indicates that CHD1 is required for remodeling chromatin structure at the frq locus as a part of the daily clock cycle. Moreover, we discovered DNA methylation in the promoter of frq that diminishes over time in the absence of light/dark cycles and determined that normal DNA methylation appears to require a functional clock. The DNA methyltransferase DIM-2 is responsible for this DNA methylation, and the DNA methylation is required for proper phasing of clock gene expression. Collectively, these data demonstrate a close connection among chromatin remodeling, DNA methylation, and clock gene expression.
 
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Posted by on July 23, 2011 in biology, epigenetics, Genetics

 

Otxandio, ‘the first Gernika’

While the bombing of Gernika on April 1937 became known worldwide, it was not the only civilian massacre perpetrated by the fascist winged criminals in those years. A less known episode is achieving recognition as of late thanks to the effort of historian Zigor Olabarria, concerned by the loss of memory as the survivors from that terrible era die from old age: the massacre of Otxandio.
On July 22 1936, just four days after the fascist coup, in the mountain village of Otxandio, Biscay, nobody was still really concerned or truly aware of what was going on. The fact that it was the local holidays, Santa Marina, had the people quite distracted in any case: it was still time to dance and party… or so they thought. 
There were anyhow some militiamen in the center of the village cooking breakfast. 
Early in the morning two small airplanes flew over the town, they greeted and were answered in kind. When they dropped something everybody thought they would be leaflets. But they were bombs.
61 people were killed, mostly women and children. One of the bombers was born in the nearby city of Orduña, his name was Ángel Salas Larrazabal, the other pilot was José Muñoz Jiménez. Salas was congratulated by the rebel General Mola for his feat, he was later appointed Senator by King Juan Carlos I and even made Captain General (the highest ranking in the Spanish Army) in 1991. He died in bed in 1994. 
Sources and further information (in Spanish): Otxandio Town Hall, Deia newspaper, Sare Antifaxista. Watch also for the publication (in Basque) of the booklet Gerra Zibila Otxandion (The Civil War in Otxandio), which is being presented today in that village.
 

Nasty gut bacterian genetics in Asia

A new paper that researches human-hosted bacterium Helicobacter pylori may be of some interest for understanding humankind.
H. pylori may be present in more than half of humankind but only a fraction of infected people display symptoms, which can be vague or quite nasty: stomach pain, heartburn, regurgitation, vomiting, belching, flatulence, nausea. If untreated it may degenerate into serious illnesses like gastroesophageal reflux disease, peptic ulcers or even cancer. 
I don’t really appreciate the pretense of the authors of using this parasite’s genome as substitute of genuine human markers nor I agree with some of their conclusions, however the data is interesting. 
There are three major clades of H. pylori, these are named hpEastAsia, hpAsia2 and hpEurope. They are found as follows:
1. Population East Asia (hpEastAsia)

hpEAsia – Fig. 2NJ tree C (supopulation hspEAsia) is a subset of B

This macro-clade would seem, I understand, the ancestral one to the region and reflects well the expectations, including the ordered divergence of hpSahul, hspAmerind, hspMaori (Austronesian-specific) and the large hspEAsia, which also shows the expected south-to-north fanning structure, found in so many other markers.

Some north-to-south colonization pattern (interspersed with south-to-north bouts) is also apparent in the tree C but it is hard to understand because it is not clear how it relates with hspEAsian in tree B. It may be related to Han Chinese expansion or to Neolithic flows or a combination of the two.

2. Population Asia 2 (hp Asia2)

hpAsia2 – Fig. 3

This is a bit more difficult to interpret but it could be original from South Asia however notice how Bengali and Malaysia Indian clades seem derived (and not ancestral) in an otherwise fully SE Asian subtree. The Ladakh clade does not help much because it is a region of largely East Asian genetics and we have already seen hpEastAsia over there (most closely related to Yunnan, surely via Tibet). 
This clade seems to demand better, wider sampling if we are to understand its evolutionary dynamics. 
3. Population Europe (hpEurope)

hpEurope – Fig.1

This macro-clade shows two subpopulations: ‘Europe’ (including in fact West Asians) and ‘Asia’, which seems centered in India. The migration of this clade to SE Asia should be related to the Hindu (and Buddhist) influences of some 2200 years ago (otherwise it cannot be explained its presence in Thailand and Cambodia).

A curiosity is the presence of a Basque strain in Philippines, which is clearly a product of Spanish colonization (in which Basques were quite active as mariners, priests and businessmen specially). It clearly shows that, under the right circumstances, no particularly important demographic flow is needed to cause an impact with this nasty bug.
I suspect that the lack of the hpEastAsia clade in Philippines is due to some oddity, be it founder effect or some dietary reason. It suggests that Filipinos (at least in the sampled areas) lacked the bug until the arrival of European colonialism or maybe Muslim influences (do they explain the hpAsia2 clade?)

Update (Jul 22): 

It is interesting for background and a wider picture to take a look at this older paper, which is freely available as author’s manuscript at PubMed Central:

Bodo Linz et al., An African origin for the intimate association between humans and Helicobacter pylori. Nature, 2007.

Most interesting is surely this image (fig. 1):

click here for original and legend

While this paper does not yet mention the Asia 2 clade, it does indicate the other relevant clades as well as their African relatives, some of which are closer, while others are more distant (b).

The first split in this human parasite seems to be between Africa 2  (Southern Africa) and the rest, in agreement with what human genetics tells about our early history in Africa.

Then the lineage seems to divide among a branch remaining in Africa (Africa 1 and Europe 2, aka AE2, centered in West and East Africa respectively) and another one migrating to Asia (Europe 1, centered in India, and East Asia). It seems that Helicobacter pylori also experienced an Out of Africa migration… in our stomachs.

Beurec 2011 (the main paper mentioned above) says:

Strains of the hpEurope population were shown to be hybrids of two ancestral populations, AE1 from central Asia and AE2 from northeast Africa while modern hpEastAsia strains are almost pure descendants of ancestral EastAsia. 

This explanation (hat tip to Gioello) was what lead me to find this other paper by Linz et al.

 

Laetoli footprints prove human-like walk 3.7 million years ago.

Careful research by Liverpool scientists appears to confirm that Australopitecus afarensis (or whichever australopithecine species that left the footprints at Laetoli, Tanzania) walked like us or almost so, rather than in the crouched position that has been long attributed to them.
Discussed at Science Daily.
 
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Posted by on July 21, 2011 in Africa, human evolution