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903 results for “Domestication”
The tepary bean genome provides insight into evolution and domestication under heat stress
<p>Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Analysis of the tepary genome revealed mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid, hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.</p>
FIGURES 10–12 in Endosymbiotic Ciliated Protozoan Biota of Dromedary Camels and Domestic Cattle in Tunisia
FIGURES 10–12. SEM images of B. krugerensis. ACZ, adoral ciliary zone; SCZ, somatic ciliary zone; CC, caudal cilia; pore of contractile vacuole (arrowhead).
FIGURES 7–9 in Endosymbiotic Ciliated Protozoan Biota of Dromedary Camels and Domestic Cattle in Tunisia
FIGURES 7–9. Photomicrographs of Blepharoconus krugerensis in MFS. ACZ, adoral ciliary zone; C, cytostome; CC, caudal cilia; CP, cytoproct; CTV, concretion vacuole; CV, contractile vacuole; MA, macronucleus; MI, micronucleus; SCZ, somatic ciliary zone.
FIGURES 3–6 in Endosymbiotic Ciliated Protozoan Biota of Dromedary Camels and Domestic Cattle in Tunisia
FIGURES 3–6. SEM images of Caloscolex camelinus. 3–4. C. camelinus m. laevis, 5–6. C. camelinus m. cuspidatus. ACZ, adoral ciliary zone; DCZ, dorsal ciliary zone; S, spine; pore of contractile vacuoles (arrowheads).
FIGURES 1–2 in Endosymbiotic Ciliated Protozoan Biota of Dromedary Camels and Domestic Cattle in Tunisia
FIGURES 1–2. Photomicrographs of Caloscolex camelinus m. laevis. 1. In MFS from the right side, 2. In MFS and Lugol's iodine from the right side. CP, cytoproct; CV, contractile vacuole; MA, macronucleus; MI, micronucleus; SP, skeletal plate.
Data from: Thermal plasticity in farmed, wild and hybrid Atlantic salmon during early development: has domestication caused divergence in low temperature tolerance?
Background: In the past three decades, millions of domesticated Atlantic salmon Salmo salar L. have escaped from farms into the wild. Their offspring display reduced survival in the natural environment, which demonstrates that gene-flow is likely to have a negative effect on wild populations. However, inter-population differences in introgression of farmed salmon have been observed, and the underlying ecological mechanisms remain enigmatic. We hypothesised that domestication-driven divergence in tolerance to low temperatures during early development may contribute to lower survival of farmed salmon offspring in the wild, which in turn, may influence patterns of introgression among populations exposed to different temperature regimes. We reared the offspring of 35 families of wild, farmed and hybrid origin at three temperatures (3.9, 5.6 and 12 °C) from the onset of exogenous feeding and throughout their first summer. Thermal reaction norms for growth and survival were investigated along the gradient. Results: The main results of this study, which is based upon the analysis of juvenile salmon from five wild strains, two farmed strains and two hybrid strains, can be summarised as; (i) salmon of all origins were able to successfully initiate feeding at all temperatures and similar survival reaction norms were detected in all strains across the temperature gradient; (ii) deviating growth reaction norms were detected between strains, although this result was most likely due to an overall lack of growth in the lower temperature treatments. Conclusions: This study revealed no evidence of domesticated-driven divergence in low temperature tolerance in Atlantic salmon during early development. Although the potential interaction between low temperature and other river-specific factors cannot be excluded, our results indicate that the reduced survival of farmed offspring in the wild is not explained by farmed salmon displaying impaired abilities to initiate feeding at low temperatures. We therefore suggest that the observed inter-population patterns of introgression are not low-temperature driven and that other ecological or biological factors may explain why detection of farmed salmon in wild rivers is not synonymous with introgression. In general, our results support the literature indicating that phenotypic plasticity instead of thermal adaption has been selected for in Atlantic salmon.
Data from: Reconstructing the origin and spread of horse domestication in the Eurasian steppe
History of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the Q:7 scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA.
Data from: Evolutionary history of almond tree domestication in the Mediterranean basin
Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean Basin, using a combination of nuclear and chloroplast microsatellites (i.e. SSRs) to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the late Holocene, a result that is compatible with human-mediated dispersal of almonds out of its center of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild pre-glacial populations (in North Africa) or from wild counterparts (in the Near-East) could account for a fraction of the diversity observed.
Data from: Genetic control of seed shattering during African rice domestication
Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from a core heartland and introgression from local wild rice. The cloning of ObSH3 not only provides new insights into a critical crop domestication process but also adds to the body of knowledge on the molecular mechanism of seed dispersal.
Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region
The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in South China and North Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China-Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China-Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3,900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.
Data from: Skull morphology diverges between urban and rural populations of red foxes mirroring patterns of domestication and macroevolution
<p class="western"><span><span><span>Human activity is drastically altering the habitat use of natural populations. This has been documented as a driver of phenotypic divergence in a number of wild animal populations. Here we show that urban and rural populations of red foxes (<i>Vulpes vulpes</i>) from London and surrounding boroughs are divergent in skull traits. These changes are primarily found to be involved with snout length, with urban individuals tending to have shorter and wider muzzles relative to rural individuals, smaller braincases, and reduced sexual dimorphism. Changes were widespread and related to muscle attachment sites and thus are likely driven by differing biomechanical demands of feeding or cognition between habitats. Through extensive sampling of the genus <i>Vulpes</i>, we found no support for phylogenetic effects on skull morphology, but patterns of divergence found between urban and rural habitats in <i>V. vulpes</i> quantitatively aligned with macroevolutionary divergence between species. The patterns of skull divergence between urban and rural habitats matched the description of morphological changes that can occur during domestication. Specifically, urban populations of foxes show variation consistent with 'domestication syndrome'. Therefore, we suggest that occurrences of phenotypic divergence in relation to human activity, while interesting themselves, also have the potential to inform us of the conditions and mechanisms that could initiate domestication. Finally, this also suggests that patterns of domestication may be developmentally biased toward larger patterns of interspecific divergence. </span></span></span></p>
Data from: Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.
Data from: Prediction and attenuation of seasonal spillover of parasites between wild and domestic ungulates in an arid mixed-use system
1.Transmission of parasites between host species affects host population dynamics, interspecific competition, and ecosystem structure and function. In areas where wild and domestic herbivores share grazing land, management of parasites in livestock may affect or be affected by sympatric wildlife due to cross-species transmission. 2.We develop a novel method for simulating transmission potential based on both biotic and abiotic factors in a semi-arid system in Botswana. Optimal timing of antiparasitic treatment in livestock is then compared under a variety of alternative host scenarios, including seasonally migrating wild hosts. 3.In this region, rainfall is the primary driver of seasonality of transmission, but wildlife migration leads to spatial differences in the effectiveness of treatment in domestic animals. Additionally, competent migratory wildlife hosts move parasites across the landscape. 4.Simulated transmission potential matches observed patterns of clinical disease in the study area. Increased wildlife contact is correlated with a decrease in disease, suggesting that noncompetent wild hosts may attenuate transmission by removing infective parasite larvae from livestock pasture. 5.Optimising the timing of treatment according to within-year rainfall patterns was considerably more effective than treating at a standard time of year. By targeting treatment in this way, efficient control can be achieved, mitigating parasite spillover from wildlife where it does occur. 6.Synthesis and applications: This model of parasite transmission potential enables evidence-based management of parasite spillover between wild and domestic species in a spatio-temporally dynamic system. It can be applied in other mixed-use systems to mitigate parasite transmission under altered climate scenarios or changes in host ranges.
Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations
Current conservation practices exclude human-generated hybridized populations from protection, as the genetic effects of hybridization in the wild have been observed to be long-lasting based on neutral genetic markers and are considered potentially irreversible. Theory, however, predicts otherwise for genes under selection. We transplanted combinations of wild, domesticated and hybridized populations of a fish species to new environments. We then compared survival, phenotypic variation and plasticity to determine whether hybridization affects adaptive potential after multiple generations of selection in the wild. Although the fitness of our hybridized populations at the onset of hybridization cannot be assessed, our results suggest that within five to eleven generations, selection can remove introduced foreign genes from wild populations that have hybridized with domesticated conspecifics. The end result is hybridized populations that, in terms of survival, phenotypic plasticity, mean trait expression and overall general responses to environmental change, closely resemble neighbouring wild populations. These results have important implications for considering the potential conservation value of hybridized populations and illustrate the effectiveness of selection in a local environment.
Data from: Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism
<p>Domestication of animals imposes strong targeted selection for desired traits but can also result in unintended selection due to new domestic environments. Atlantic salmon was domesticated in the 1970s and has subsequently been selected for faster growth in systematic breeding programmes. More recently, salmon aquaculture has replaced fish oils (FO) with vegetable oils (VO) in feed, radically changing the levels of essential long-chain polyunsaturated fatty acids (LC-PUFA). Our aim was to study the impact of domestication on metabolism and explore the hypothesis that the shift to VO-diets has unintentionally selected for a domestication-specific lipid metabolism. We conducted a 96-day feeding trial of domesticated and wild salmon fed diets based on FO, VO or phospholipids (PL), and compared transcriptomes and fatty acids in tissues involved in lipid absorption (pyloric caeca) and lipid turnover and synthesis (liver). Domesticated salmon had faster growth and higher gene expression in glucose and lipid metabolism compared to wild fish, possibly linked to differences in regulation of circadian rhythm pathways. Only the domesticated salmon increased expression of LC-PUFA synthesis genes when given VO. This transcriptome response difference was mirrored at the physiological level, with domesticated salmon having higher LC-PUFA but lower 18:3n-3 and 18:2n-6 levels. In line with this, the VO diet decreased growth rate in wild but not domesticated salmon. Our study revealed a clear impact of domestication on transcriptomic regulation linked to metabolism and suggests that unintentional selection in the domestic-environment has resulted in evolution of stronger compensatory mechanisms to a diet low in LC-PUFA. </p>
Data from: On the origin of a domesticated species: identifying the parent population of Russian silver foxes (Vulpes vulpes)
The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In the present study, we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mitochondrial DNA, cytochrome b and d-loop, from 24 Novosibirsk foxes (eight foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b–d-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern Canada. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. ΦST analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for approximately 50 years with unconscious selection for behaviour; the second corresponds to > 50 years of additional intensive selection for tame behaviour.
Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.
Data from: Reduction of the pectoral spine and girdle in domesticated Channel Catfish is likely caused by changes in selection pressure
Locked pectoral spines of the Channel Catfish Ictalurus punctatus more than double the fish's width and complicate ingestion by gape-limited predators. The spine mates with the pectoral girdle, a robust structure that anchors the spine. This study demonstrates that both spine and girdle exhibit negative allometric growth and that pectoral spines and girdles are lighter in domesticated than in wild Channel Catfish. This finding could be explained by changes in selection pressure for spine growth during domestication or by an epigenetic effect in which exposure to predators in wild fish stimulates pectoral growth. We tested the epigenetic hypothesis by exposing domesticated Channel Catfish fingerlings to Largemouth Bass Micropterus salmoides predators for 13 weeks. Spines and girdles grow isometrically in the fingerlings, and regression analysis indicates no difference in proportional pectoral growth between control and predator-exposed fish. Therefore a change in selection pressure likely accounts for smaller pectoral growth in domesticated Channel Catfish. Decreasing spine growth in older fish suggests anti-predator functions are most important in smaller fish. Additionally, growth of the appendicular and axial skeleton is controlled differentially, and mechanical properties of the spine and not just its length are an important component of this defensive adaptation.
Data from: Supplementary stocking selects for domesticated genotypes
Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.
Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.
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