Category Archives: Genetics

Adaptionism (humor)

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

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Posted by on August 24, 2012 in biology, evolution, Genetics, humor


Increased complexity in certain regions sets apart human and chimp brains

Frontal lobe (CC-BY-SA-2.1-jp)
This paper looks like a very important research piece for the understanding of the human mind, of what makes our brains specifically human and ultimately of what makes ourselves what we are.
Genevieve Konopka et al., Human-Specific Transcriptional Networks in the Brain. Neuron 2012. (Freely accessible apparently) ··> LINK [doi:10.1016/j.neuron.2012.05.034]


Understanding human-specific patterns of brain gene expression and
regulation can provide key insights into human brain evolution and
speciation. Here, we use next-generation sequencing, and Illumina and
Affymetrix microarray platforms, to compare the transcriptome of human,
chimpanzee, and macaque telencephalon. Our analysis reveals a
predominance of genes differentially expressed within human frontal lobe
and a striking increase in transcriptional complexity specific to the
human lineage in the frontal lobe. In contrast, caudate nucleus gene
expression is highly conserved. We also identify gene coexpression
signatures related to either neuronal processes or neuropsychiatric
diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes coexpressed with FOXP2,
a gene important for language evolution. These data demonstrate that
transcriptional networks have undergone evolutionary remodeling even
within a given brain region, providing a window through which to view
the foundation of uniquely human cognitive capacities.

Hippocampus (CC-BY-SA-2.1-jp)
For what I could understand, mostly from the press release, the authors unveiled increased complexity of the gene expression modulating three regions of our brains: the frontal cortex, the hippocampus and the striatum.
It is not a mere matter of size but specially one of much increased complexity in the wiring of these three regions what seems to make our brains unique. 
The research also reinforces the apparent importance of the much debated genes CLOCK (affecting circadian rhythms, mood, pregnancy and metabolism), FOXP1 and FOXP2 (related specially with speech), whose connectivity is much increased in humans in comparison with our ape cousins.

Denisovan and Neanderthal proviral DNA

A provirus is a strand of autosomal DNA that was inserted by a virus once upon a time and got lost in our genome as junk DNA, not being anymore active (would it remain active it’d be a retrovirus). Such insertions are thought to be unique phylogenetic events. 
New research has identified a provirus* (HERV-K-Ne1 = HERV-K-De6, inserted in Chromosome 5) shared by Neanderthals and Denisovans but not Homo sapiens. This is consistent with the previous data that placed their autosomal DNA closer to each other than to Homo sapiens.
Lorenzo Agoni et al., Neandertal and Denisovan retroviruses. Current Biology, 2012. Freely accessible (letter with supplementary material) at the time of writing this.
It must be noted however the mitochondrial DNA, inherited by pure matrilineage, is much closer among our species and Neanderthals than either one with Denisovans, what to me suggest that Denisovans are no new species but a hybrid of Neanderthal and Homo erectus. A theory not yet fully testable for lack of DNA from Asian Homo erectus.
Interestingly Denisovans have also several proviruses not found in Neanderthals, what could well support my theory of hybridization. The detected provirus could hence have migrated from Neanderthals to Denisovans in the hybridization episode (along with lots of other autosomal DNA), while the rest could have been retained from the H. erectus ancestors by the maternal line. 
However as the article is both very technical and succinct, I can’t be sure right now of how strongly or weakly can this info support the hybridization model (founded opinions welcome). 
In total the researchers detected three Neanderthal proviruses and 12 Denisovan ones, one of which is shared between both nominal species. It is convenient to remind that while the Denisovan genome was very well preserved and sequenced almost completely, the Neanderthal genome is only known in fragmentary form, amounting to about 60% of the actual genome.

Bonobo genome sequenced

Ulundi (source)
The last great ape* to be sequenced has been the bonobo, it complements the Homo sapiens, Neanderthal, Denisovan (probably a hybrid), chimpanzee, gorilla and orangutan genomes:
The reference genome was sequenced from a female bonobo captive at Leizpig Zoo, known as Ulundi.
The genome will, hopefully, help understand better the genetic basis of our being as humans and, maybe also get some inferences on our prehistory. 

Stubbornly under-estimating divergence times by almost 100%

In this sense I want to emphasize that the paper insists in producing Pan-Homo and internal Pan divergence times that are irrationally low. The cause of this systematic error that persists through some literature seems to be rooted on the Homo-Pongo divergence estimate, which I do not know the details about but seems from context to be an extreme under-estimate. 
The matter was already debated in 2008 by Jenniffer L. Caswell, who explained that the Bonobo-Chimpanzee split cannot be more recent than 1.5 to 2.0 million years because it was then when the Congo River was formed separating the two populations radically (allopatric speciation). This is quite apparent in the distribution of bonobos and chimpanzees:
fig. 1a
So unless the geology is wrong, bonobos and chimpanzees diverged 1.5 to 2 million years ago, and not a mere million years ago, as this paper claims.
This has important implications for the Homo-Pan divergence age, as I have discussed again and again. Assuming that the 4.5:1 ration estimated in this paper is correct, then the actual Homo-Pan divergence age ranges between 6.8 to 9.0 million years ago (and not a mere 4.5 Ma), with a median of 7.9 Ma, quite similar to the 8 Ma estimate I have been defending since the Caswell paper was published in 2008.

See also


* Note: I know someone will say that Homo sp. are not “apes” but I say Homo are a subset of the great apes clade (Hominidae) phylogenetically and therefore great apes ourselves – something to be irrationally proud of, of course.


Concern for the use of genetic tests for Nazi purposes

As Van Ardsdale explains purity is not a genetic reality, first of all because each time a new person is conceived (by the enjoyable but quite impure act of sex) admixture takes place (and if mum and dad are genetically too similar, then inbreeding happens what is generally bad). So whoever would wish to imagine themselves as pure should not look into genetics but into Platonic solids or something.
But the right tools in the wrong hands typically has the wrong results. And the tool of genetic analysis in the hands of Hitler* or the like could be used to entice racist discrimination. 
Nature reports that a Hungarian genetic testing company, Nagy Gén, has issued a certificate by which a person, a Hungarian Nazi member of the criminal Jobbik party, was said to have no Jewish nor Roma ancestry. 

Nagy Gén scanned 18 positions in the MP’s genome for variants that it says are characteristic of Roma and Jewish ethnic groups; its report concludes that Roma and Jewish ancestry can be ruled out.

It’s difficult to imagine how the company could certify that because there are no absolute lines defining such ethnic categories, not in the genetic aspect either, just clinal trends.
I understand from the context (18 positions) that the test is one of those biometric AIM-based tests that police uses sometimes to attempt to guess (without any certainty) the ancestry of suspects.
The scandalous certificate was first posted at a Nazi site, which praised the intent but (correctly) dismissed the scientific quality of the test. It was later republished at a Magyar-language news blog
The affair underlines the dangers of all kind of biometrics, be them genetic or anthropometric, when used for reasons that are not pure science. That’s a reason why I do not generally favor private, commercial genetic testing but rather academic studies of populations with prehistory reconstruction intent. 
Personally I have never got myself tested nor I really care much because what matter for me is not “my” private ancestry but, if anything, the ancestry of the diverse peoples and communities, what can tell us something about their history and prehistory.
* Incidentally, I suspect that Hitler would have got serious problems promoting his racist ideas if he would have got access to genetic analysis because his paternal lineage was quite Mediterranean and ultimately rooted in Africa (it could even be Jewish, although hard to tell ultimately). He would have had to lie even to himself, abandon his racism or maybe kill himself (mostly good results).
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Posted by on June 12, 2012 in Europe, genetic testing, Genetics, Hungary, race


Gorilla genome sequenced

Kamilah the gorilla
The full genome of Kamilah, a female gorilla from San Diego zoo, has been sequenced. With this one all extant great apes, excepted the bonobo, have been fully sequenced.
The authors propose a divergence of Gorilla from the Pan-Homo branch c. 10 million years ago. But this is based on a most unlikely assumption of Pan-Homo divergence happening only 6 million years ago, when it’s surely of at least 8 million years (and maybe as many as 10 million). A corrected estimate for the Gorilla branch could then be between 13 to 18 million years in fact. 
See on this regard:

Posted by on March 8, 2012 in Genetics, gorilla, human evolution


Intelligence genes more elusive than Higgins’ boson

Havard University has issued a press release where Christopher F. Chabris, author of a yet unpublished paper on the matter, ponders the elusiveness of genes that could define intelligence. 
Twin studies have suggested that there is at least some truth to an association of intelligence (measured by IQ) with inherited genes, however now it seems clear that no individual gene is likely responsible of any notable influence on expressed intelligence. 
Chabris ponders that the genetic influence is probably the work of many genes acting collectively and not any single one of them, and also of the interactions of genes and environment.

What our results show is that the way researchers have been looking for genes that may be related to intelligence — the candidate gene method — is fairly likely to result in false positives, so other methods should be used.


Posted by on February 26, 2012 in Genetics, intelligence, mind