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Category Archives: pig genetics

Central European farmers, but also Danish "hunter-gatherers" had domestic pigs

It’s often difficult to discern in the archaeological record wild boar remains from those of domestic pigs. Luckily archaeogenetics can solve the problem, sometimes producing striking results.
Ben Krause-Kyora et al., Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe. Nature Communications 2013. Open accessLINK [doi:10.1038/ncomms3348]

Abstract

Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

The most striking result is surely not the demonstration of pigs being in Central Europe a few centuries than previously confirmed but that Ertebølle hunter-gatherers of Denmark had them as well, quite radically casting doubt on their status as hunter-gatherers and placing them fully in the Neolithic context, even still rather marginal and peripheral. 
Figure 1: Map depicting the location of the archaeological Sus samples from which mtDNA haplotypes were obtained.
Samples were recovered from Neolithic LBK, post-LBK and Mesolithic Ertebølle sites dated between 5500 and 4000 cal BC. Each symbol corresponds to a single sample (triangle, square and circle). Domestic (triangle) and wild (square) pigs discussed in the text are labelled; circles represent Sus specimens of unknown domestication status. The red colour indicates the European haplotypes C and A, and yellow the Near Eastern haplotypes Y1 and Y2.
 

Ancient pig genetics

For some a religious taboo but for most a staple food, pigs have been in our farms and kitchens for many millennia now. 
It has been known for long that pigs are just the domestic variety of the Eurasian boar (Sus scrofa) but which populations specifically has been a matter of some debate. Now we know that East Asian pigs were domesticated locally (see appendix) but in the West it was found recently that European pigs have European boar lineages, while West Asian pigs in many cases do not. Previous studies determined that early European pigs were of West Asian ancestry but that by c. 4000 BCE all lineages were local.
This new study explores lineage diversity in ancient West Asian pigs from Anatolia, Kurdistan, Armenia, Georgia and Iran.
Claudio Otoni et al., Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. MBE 2012. Open accessLINK [doi: 10.1093/molbev/mss261]

Abstract

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or appeared so as a result of admixture between introduced pigs and European wild boar. These pigs not only replaced those with Near Eastern signatures in Europe, they subsequently also replaced indigenous domestic pigs in the Near East. The specific details of these processes, however, remainturnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria and Turkey. Our results firstly reveal the genetic signature of early domestic pigs in Eastern Turkey. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, nearly 1,000 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the demographic and societal changes during the Anatolian Bronze and Iron Ages. 

Probably most interesting is figure 1, which synthesizes the new findings:

(click to expand)

Fig. 1. A spatiotemporal depiction of ancient pig haplotypes. Rows represent eight chronological periods and columns pertain to sites organized along a longitudinal axis from west to east. Approximate locations of the archeological sites from which the samples are derived are shown as numbered circles on maps beneath the horizontal axis. Asterisks indicate directly AMS-dated samples. The question mark signifies not enough material was available for AMS dating. Slashed boxes indicate samples on which GMM analyses were performed. Pie charts to the right of each row summarize the haplotype frequencies for each chronological period across all sites. Columns pertain to one or two sites except for two columns that consist of several sites: Armenia (Sevkar-4, Areni-1, Khatunarkh, Shengevit, Lchashen, Tmbatir, Pilorpat, Beniamin, Tsakaektsi) and Iran (Qaleh Rostam, Qare Doyub, Qelīch Qōīneq, Dasht Qal’eh, Doshan Tepe, Malyan, Mehr Ali, Chogha Gavaneh and Gohar Tepe).

All shown West Asian lineages (Y1, Y2, Arm1T and Arm2T) belong to the NE2 clade, a related NE1 clade (common in Southern Iran, Iraq and Egypt, as well as Georgia) was not detected. See fig. 2 for details.

Early European domestic pigs all belonged to the Y1 haplotype, later replaced by the European ones, as mentioned above.

_________________________ . _________________________

Appendix: East Asian pigs were domesticated from local boars

Some references:

 
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Posted by on November 23, 2012 in Neolithic, pig genetics, West Asia, West Eurasia

 

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.