Ancestral Wild Population Research Articles

Targeted resequencing reveals genomic signatures of barley domestication.

Summary Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear.To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci.We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts.These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.

The wild type as concept and in experimental practice: A history of its role in classical genetics and evolutionary theory

Wild types in genetics are specialised strains of laboratory experimental organism which principally serve as standards against which variation is measured. As selectively inbred lineages highly isolated from ancestral wild populations, there appears to be little wild or typical about them. I will nonetheless argue that they have historically been successfully used as stand-ins for nature, allowing knowledge produced in the laboratory to be extrapolated to the natural world. In this paper, I will explore the 19th century origins of the wild type concept, the theoretical and experimental innovations which allowed concepts and organisms to move from wild nature to laboratory domestication c. 1900 (resulting in the production of standardised lab strains), and the conflict among early geneticists between interactionist and atomist accounts of wild type, which would eventually lead to the conceptual disintegration of wild types and the triumph of genocentrism and population genetics. I conclude by discussing how the strategy of using wild type strains to represent nature in the lab has nonetheless survived the downfall of the wild type concept and continues to provide, significant limitations acknowledged, an epistemically productive means of investigating heredity and evolutionary variation.

Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits.

Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1.

Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today.

Evaluating demographic models for goat domestication using mtDNA sequences

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

From nature to the laboratory: the impact of founder effects on adaptation

Most founding events entail a reduction in population size, which in turn leads to genetic drift effects that can deplete alleles. Besides reducing neutral genetic variability, founder effects can in principle shift additive genetic variance for phenotypes that underlie fitness. This could then lead to different rates of adaptation among populations that have undergone a population size bottleneck as well as an environmental change, even when these populations have a common evolutionary history. Thus, theory suggests that there should be an association between observable genetic variability for both neutral markers and phenotypes related to fitness. Here, we test this scenario by monitoring the early evolutionary dynamics of six laboratory foundations derived from founders taken from the same source natural population of Drosophila subobscura. Each foundation was in turn three-fold replicated. During their first few generations, these six foundations showed an abrupt increase in their genetic differentiation, within and between foundations. The eighteen populations that were monitored also differed in their patterns of phenotypic adaptation according to their immediately ancestral founding sample. Differences in early genetic variability and in effective population size were found to predict differences in the rate of adaptation during the first 21 generations of laboratory evolution. We show that evolution in a novel environment is strongly contingent not only on the initial composition of a newly founded population but also on the stochastic changes that occur during the first generations of colonization. Such effects make laboratory populations poor guides to the evolutionary genetic properties of their ancestral wild populations.

RELATIONSHIPS BETWEEN WEEDY AND CULTIVATED FORMS IN SOME SPECIES OF CHILI PEPPERS (GENUS CAPSICUM).

A question which often arises in studies on the origin and evolution of cultivated plants is whether a weedy race of a crop plant is ancestral to the crop or whether it is necessary to look further for a wild progenitor. Work on a number of different crop-weed complexes has shown that three types of relationship are possible. The weed may have given rise to the crop, as appears to have happened in rye, oats and hemp (Vavilov, 1926). In other cases, such as radish (Panetsos and Baker, 1967) and rye (Suneson et al., 1969) in California, the weedy races may be derived from the crop, usually by hybridisation with related wild species. Thirdly, both crop and weed may be derived from a common ancestral wild population by disruptive selection, as has been suggested by Harlan (1965). The genus Capsicum contains about 20 species, all of which originated in the New World. Some of these are wild species which occur as natural components of undisturbed vegetation, although their fruits may be collected and used by man. Four species (C. annuum, C. baccatum, C. clhinense and C. pubescens) are widely cultivated in Latin America. Each is characteristic of a different area, though their ranges now overlap. C. annuum is widespread in Mexico and Central America but cultivated forms of this species seem to have reached South America rather late, possibly after the Spanish Conquest (Smith and Heiser, 1957). C. baccatum is the common cultivated chili pepper of Peru and Bolivia. It extends northwards to Ecuador and southern Colombia and eastwards to south-eastern Brazil. In the West Indies, northern South America and the Amazon basin the pepper most commonly cultivated is C. chinense. This species is also common in Peru and Bolivia and thus overlaps the range of C. baccatum. C. pubescens is more tolerant of low temperatures than the other cultivated peppers and is found at higher altitudes in the Andes. It extends along the mountains from Bolivia to Colombia and has now reached Mexico. It is sympatric with C. annuumn, C. baccatum and C. chinense in the lower parts of its altitudinal range, but it is morphologically very distinct and is reproductively isolated from the other three species. In both C. annuum and C. baccatum there are, besides the large-fruited cultivated types which have lost their natural mechanisms for seed dispersal, uncultivated forms with small erect deciduous fruits which can be dispersed by birds and other agents. Few observations have been made on the ecology of these uncultivated forms, but they seem usually to occur as weeds of cultivated ground or in other disturbed habitats such as roadsides and margins of rivers. They are recognised taxonomically as distinct varieties, C. annuum var. minimum and C. baccatum var. baccatum, while the cultivated plants are assigned to C. annuum var. annuum and C. baccatum var. pendulum. C. annuum var. minimum has erroneously been called C. baccatum in some of the earlier literature, but Hunziker (1950) has shown this to be a misapplication of the name C. baccatum. The situation with regard to C. chinense is a little more complicated. There are no unequivocal reports of wild or weedy plants belonging to this species. However, there is a closely related species, C. frutescens, most collections of which have small deciduous fruits and occur in weedy situations.