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Category Archives: biology

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. 

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 10,000years 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. 

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.

 
7 Comments

Posted by on October 30, 2012 in Anthropometry, biology, epigenetics, mind

 

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 FS 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
 
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Posted by on September 13, 2012 in biology, health, human evolution

 

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

 

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:

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.

 
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Posted by on July 24, 2012 in bear genetics, biology, evolution, Ice Age

 

Neanderthals as leather-crafters

Fig. 1
A new study finds that some peculiarities of adult Neanderthal skeletons may be the product from repetitive scrapping:

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)
 
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Posted by on July 19, 2012 in biology, Middle Paleolithic, Neanderthal