The natural adaptation and human selection history of African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of ∼54x for 130 samples (Ethiopia, Libya) and ∼10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.

Human Impact on Antler Conformation in Western Red Deer (Cervus elaphus elaphus Linnaeus, 1758)

A stray find of red deer antler from Sweden with the braincase was collected due to an apparently pathological deformation, the strongly retarded right antler. Measurements of the complete left antler inspired the analysis of general antler conformation in order to place this archaeological specimen in a zoological context. This stray find and another prehistoric antler from Sweden as well as three complete prehistoric antlers from Hungary were metrically compared using measurements of over 17,000 trophies of extant red deer from Hungary. The results confirmed that the stray specimen from Sweden and prehistoric antlers from Hungary were similar in that they were stouter (smaller length measurements but greater circumferences) than their 20th century counterparts. Most of their measurements fell within the ±1 standard deviation interval of the means of extant trophies. The pathological lesion on the studied stray specimen directed attention to the role of human selection. Twentieth century record trophies show a significant increase in antler weight and “quality” as defined in the international trophy grading system. While these morphometric observations cannot be taken as a proxy for absolute dating or precise contextual identification for the stray find central to this study, its size and apparent lack of consistent human selection (pathological deformation, “archaic” antler proportions) point to possibly early origins, prior to major human influence.

Evolution under domestication of correlated characters in populations of Stenocereus stellatus (Pfeiff.) Riccob., under different forms of management in central Mexico: genetic diversity, damage, and defense mechanisms

Across the process of domestication, human selection produces changes in target attributes as well as changes that are not necessarily desired by humans due to pleiotropic or linked genes. In this paper we addressed, correlated changes between genetic diversity, damage level, defense mechanisms (resistance and tolerance), and fitness due to the domestication process of Stenocereus pruinosus (Otto ex Pfeiff.) Buxbaum and Stenocereus stellatus (Pfeiff.) Riccobono, an endemic columnar cactus of south-central Mexico. One hundred eighty individuals of S. stellatus from wild, in situ managed, and cultivated populations of Valle de Tehuacán and Mixteca Baja, Puebla, were sampled, and attributes including damage level, defense mechanisms and fitness (number of fruits) were measured. The DNA of 176 individuals was extracted to amplify and analyze five microsatellites in order to estimate genetic diversity and structure. As expected, cultivated populations showed a significantly higher damage level, as well as lower resistance and genetic diversity. Depending on the form of management, correlations between genetic diversity and the rest of the attributes exhibited different patterns. In wild populations, genetic diversity was positively correlated with damage and negatively with resistance; in situ managed populations exhibited the opposite pattern, and in cultivated populations, no correlations were found between these attributes. We propose a hypothetic model of human selection to explain the variation in these correlations. No differences in genetic diversity and tolerance were detected between regions; however, the populations of Valle de Tehuacán exhibited more damage and more resistance. In both regions, populations showed a positive correlation between fitness and resistance and a negative correlation between damage and resistance, suggesting the existence of a defense mechanism to ensure fitness. Also, non-regional differentiation suggests an eventual gene flow due to pollinators, human movement of branches, or a common ancestry before the domestication process.

Consequences of Traditional Management in the Production and Quality of Copal Resin (Bursera bipinnata (Moc. & Sessé ex DC.) Engl.) in Mexico

Copal is a resin of ritual uses in Mexico that is extracted from several species of trees of the genus Bursera. The effect of traditional management on phenotypical traits of copal trees has not been sufficiently studied. This research analyzed the traditional management and human selection on populations of Bursera bipinnata, and it also examined their influence on the quantity and quality of the resin produced by wild and managed trees. The management of copal was documented through semi-structured interviews and workshops. Samples of 60 trees from six wild and managed populations were selected to quantify the production of resin during two consecutive years. Fresh resin was collected to identify organic volatile compounds through gas chromatography and Principal Components Analysis (PCA); individuals were classified according to the amount and type of organic compounds produced. We identified management strategies from simple harvesting to seeds planting. The criteria of local people for selecting managed trees and seeds are based on the quantity and quality of the resin produced per tree, which were significantly higher in managed than in wild trees: 190.17 ± 329.04 g vs. 29.55 ± 25.50 g (p = 0.003), and 175.88 ± 179.29 g vs. 63.05 ± 53.25 g (p = 0.008) for the production seasons of 2017 and 2018, respectively. Twenty organic volatile compounds were identified, and the PCA showed that managed trees produce higher percentages of compounds associated with scent. The traditional management of Bursera bipinnata involves selective pressures, which generate the differentiation of wild and managed trees that may represent incipient domestication through silvicultural management.

Consequences of traditional management in the production and quality of copal resin (Bursera bipinnata (Moc. & Sessé ex DC.) Engl.) in Mexico

Background Copal is a resin of ritual uses in Mexico, extracted from several species of trees of the genus Bursera. The effect of traditional management on phenotypical traits of copal trees has not been sufficiently studied. This research analyzed the traditional management and human selection on populations of Bursera bipinnata, and their influence on the quantity and quality of the resin produced by wild and managed trees.Method Management of copal were documented through semi-structured interviews and workshops. Samples of 60 trees from six wild and managed populations were selected to quantify the production of resin during two consecutive years. Fresh resin was collected to identify organic volatile compounds through gas chromatography and Principal Components Analysis (PCA); individuals were classified according to the amount and type of organic compounds produced.Results We identified management strategies from simple harvesting to seeds planting. The criteria for selecting managed trees and seeds are based on the quantity and quality of the resin produced and on higher quantity of resin yield per tree, which were much higher in managed than in wild trees: 190.17 ± 329.04 g vs 29.55 ± 25.50 g, and 175.88 ± 179.29 g vs 63.05 ± 53.25 g for the production seasons of 2017 and 2018, respectively. Twenty organic volatile compounds were identified and the PCA showed that managed trees produce higher percentages of compounds associated with scent.Conclusion Traditional management of Bursera bipinnata involves selective pressures, which generate differentiation of wild and managed trees that may represent incipient domestication through of silvicultural management.

Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments

Background Plant domestication/adaptation is a good model for evo-devo studies. Mutations that caused morphological and physiological change, followed by human selection, finally led to improvement of phenotypes suitable for different kinds of environments. Originating from the Yangtze Valley, rice is a facultative short-day plant. Rice spread southward thousands of years ago, but one of the new traits beneficial to crop yield would be loss of sensitivity to photoperiod. That is, if rice could be cultivated 2 or 3 seasons each year, the production would at least double. Results We used the sequence information for Heading date 1 (Hd1) gene to reveal the relationship of sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes were reported previously. By data mining the genome sequencing information in the public domain, we discovered another 3 types. Allele haplotypes are present in sub-tropical and tropical regions, which indicates human selection. Two of these alleles, types 7 and 13, must have occurred early in southern Asia and then were introgressed in many local landraces. According to the rice 3K database, more than one-third of the world’s rice accessions contain these 2 loss-of-function haplotypes. We also demonstrate that these haplotypes are present in weedy rice populations, again indicating that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice. Conclusion In the current study, we analyzed how sequence changes in a rice flowering-control gene occurred, were selected and were retained during rice cultivation. Many loss-of-function hd1 alleles have existed in sub-tropical and tropical Asia rice-growing areas for a long time. Some of these haplotypes were present locally, but 2, types 7 and 13, were spread in many regions and are now included in most of the modern varieties in southern Asia.

Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavour and texture in blue cheeses

Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. The Penicillium roqueforti fungus consists of four genetically differentiated populations, two of which have been domesticated for blue cheese-making, the other two thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain and using three strains from each of the four populations. The strain population-of-origin had a minor impact on bacterial diversity and none on the main microorganism abundance. The strains from cheese populations produced cheeses with higher percentages of blue area and larger amounts of desired volatile compounds. In particular, the Roquefort strains produced larger amounts of appealing aromatic compounds, in part due to their greater efficiency of proteolysis and lipolysis. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, and the two cheese populations have acquired specific features. This has important implications for our understanding of adaptation and domestication, and for cheese improvement.

Eugenics as a direction of scientific thought and practice of human selection in the late 19th — early 21st centuries

Introduction. The article raises the problem of eugenics as a direction of scientific thought and practice of improving the human species. The modern advances in reproductive medicine, the development of biology, the emergence of methods for editing the human genome have updated the debate around eugenics. The aim of the work is a comprehensive study of the discourse and practice of eugenics in the period of the 19th — 21st centuries. This aim involves solving a number of tasks: 1) analysis of the historical context and prerequisites for the eugenics emergence; 2) the study of the institutionalization and practical implementation of its ideas in Western countries in the period until the end of World War II; 3) research on the position of eugenics after the war and the transition of discussions to the mainstream of genetics, bioethics, transhumanism; 4) study of the modern discourse of eugenics, ethical issues and the degree of government intervention in population reproduction. Methods. The author uses the historical-retrospective method, which makes it possible to comprehensively consider the context of the emergence and development of eugenics, the comparative method (when comparing the characteristic features of the «old» (authoritarian, forced) and «new» (democratic, based on personal choice) eugenics), the institutional approach ( when identifying the main institutions involved in the development, dissemination, implementation of the ideas of eugenics) and a discursive approach (to study modern discussions about the «new» eugenics and related ethical problems). Scientific novelty of the research. A comprehensive study of eugenics has been carried out, a connection has been established between the «old» and «new» eugenics, and their similarities and differences have been investigated. Results. The need to distinguish eugenics as a theory of human selection and as a practice has been proven, and the latter, depending on the political, cultural and socio-economic situation in the country, can take a variety of forms: from counseling and preventive measures to racial cleansing. It was found that population growth, urbanization, mass migration, instability in society, combined with the ideas of modernism about social order by the forces of science and technology, contributed to the spread of eugenics ideas in the late 19th - early 20th centuries. After the Nuremberg trials, the concept under study temporarily dropped out of scientific discourse. The article examines in detail the socio-economic and other preconditions that contributed to the revival of interest in eugenics in the 60s of XX century and at the present stage. It is shown that today part of the discussion has shifted to the mainstream of genetics, bioethics and transhumanism. Conclusions. It has been established that discussions about eugenics run up against the problem of breeding control, which means that they raise the question of who should perform selection, how, what are its criteria. The ethical aspects of introducing control are complicated by the fact that perceptions of the «norm» and the degree of permitted interference depend on the particular society.