Genomics at the origins of agriculture, part one

Tuberculosis origin: The Neolithic scenario

This paper follows the dramatic changes in scientific research during the last 20 years regarding the relationship between the Mycobacterium tuberculosis complex and its hosts - bovids and/or humans. Once the M. tuberculosis and Mycobacterium bovis genomes were sequenced, it became obvious that the old story of M. bovis evolving into the human pathogen should be reversed, as M. tuberculosis is more ancestral than M. bovis. Nevertheless, the timescale and geographical origin remained an enigma. In the current study human and cattle bone samples were examined for evidence of tuberculosis from the site of Atlit-Yam in the Eastern Mediterranean, dating from 9250 to 8160 (calibrated) years ago. Strict precautions were used to prevent contamination in the DNA analysis, and independent centers used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex. These, together with pathological changes detected in some of the bones, confirm the presence of the disease in the Levantine populations during the Pre-pottery Neolithic C period, more than 8000 years ago.

Brain evolution, the determinates of food choice, and the omnivore's dilemma

A coevolutionary paradigm using a biocultural perspective can help to unravel the complex interactions that led to the contemporary pattern of eating. Evolutionary history helps to understand the adaptation of diet and its nutritional implications. Anatomical and behavioral changes linked to changing dietary patterns in the Paleolithic resulted in an adaptive framework that affects modern diet. The evolution of an expanding brain, a shrinking large intestine, and lengthening small intestine necessitated a demand for nutritionally dense foods. The key to these changes is an understanding of the response to the omnivore's dilemma. Omnivores in their search for new items to feed their varied diet (neophilia) have a challenge when they fear (neophobia) novel items that may be poisonous and can cause death. The inborn mechanism initiates palate fatigue (sensory-specific satiety) ensuring a variety of foods will be eaten. Variety will limit the impact of toxins ingested and provide a more balanced diet. The development of cuisine, a momentous event in history, mediated the conflict, and changed the course of human evolution. The cuisine, a biocultural construct, defines which items found in nature are edible, how these products are transformed into food, the flavors used to add a sensory dimension to foods, and rules of eating or etiquette. Etiquette defines how, when, and with whom we eat. Patterns of eating in the modern setting are the end product of the way that Homo sapiens evolved and resolved the omnivore's dilemma. Control of fire and cooking expanded the range of available foods by creating a class of foods that are "predigested." An essential element to the evolution of the human diet was the transition to agriculture as the primary mode of subsistence. The Neolithic revolution dramatically narrowed the dietary niche by decreasing the variety of available foods, with the shift to intensive agriculture creating a dramatic decline in human nutrition. The recent industrialization of the world food system has resulted in a nutritional transition in which developing nations are simultaneously experiencing undernutrition and obesity. In addition, an abundance of inexpensive, high-density foods laden with sugar and fats is available to a population that expends little energy to obtain such large numbers of calories. Furthermore, the abundant variety of ultraprocessed foods overrides the sensory-specific satiety mechanism leading to overconsumption.

The changing disease-scape in the third epidemiological transition

The epidemiological transition model describes the changing relationship between humans and their diseases. The first transition occurred with the shift to agriculture about 10,000 YBP, resulting in a pattern of infectious and nutritional diseases still evident today. In the last two centuries, some populations have undergone a second transition, characterized by a decline in infectious disease and rise in degenerative disease. We are now in the throes of a third epidemiological transition, in which a resurgence of familiar infections is accompanied by an array of novel diseases, all of which have the potential to spread rapidly due to globalization.

Is Cupressus sempervirens native in Italy? An answer from genetic and palaeobotanical data

This study represents the first large-scale analysis using nuclear molecular markers to assess genetic diversity and structure of Cupressus sempervirens L.. Genetic and fossil data were combined to infer the possible role of human activity and evolutionary history in shaping the diversity of cypress populations. We analysed 30 populations with six polymorphic nuclear microsatellite markers. Dramatic reductions in heterozygosity and allelic richness were observed from east to west across the species range. Structure analysis assigned individuals to two main groups separating central Mediterranean and eastern populations. The two main groups could be further divided into five subgroups which showed the following geographical distributions: Turkey with the Greek islands Rhodes and Samos, Greece (Crete), Southern Italy, Northern Italy, Tunisia with Central Italy. This pattern of genetic structure is also supported by SAMOVA and Barrier analyses. Palaeobotanical data indicated that Cupressus was present in Italy in the Pliocene, Pleistocene and Holocene. Furthermore, our molecular survey showed that Italian cypress populations experienced bottlenecks that resulted in reduced genetic diversity and allelic richness and greater genetic differentiation. Recent colonization or introduction may also have influenced levels of diversity detected in the Italian populations, as most individuals found in this range today have multilocus genotypes that are also present in the eastern range of the species. The data reveal a new interpretation of the history of cypress distribution characterized by ancient eastern populations (Turkey and Greek islands) and a mosaic of recently introduced trees and remnants of ancient, depauperate populations in the central Mediterranean range.

Intriguing balancing selection on the intron 5 region of LMBR1 in human population

BACKGROUND

The intron 5 of gene LMBR1 is the cis-acting regulatory module for the sonic hedgehog (SHH) gene. Mutation in this non-coding region is associated with preaxial polydactyly, and may play crucial roles in the evolution of limb and skeletal system.

METHODOLOGY/PRINCIPAL FINDINGS

We sequenced a region of the LMBR1 gene intron 5 in East Asian human population, and found a significant deviation of Tajima's D statistics from neutrality taking human population growth into account. Data from HapMap also demonstrated extended linkage disequilibrium in the region in East Asian and European population, and significantly low degree of genetic differentiation among human populations.

CONCLUSION/SIGNIFICANCE

We proposed that the intron 5 of LMBR1 was presumably subject to balancing selection during the evolution of modern human.

Recent acceleration of human adaptive evolution

Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (i) site heterozygosity at least 10-fold lower than is observed in humans, (ii) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (iii) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (iv) nearly 100 times the observed number of high-frequency linkage disequilibrium blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.

Genome-wide patterns of nucleotide polymorphism in domesticated rice

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms

The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.