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903 results for “Domestication”
Data from: Integrative taxonomy at work: DNA barcoding of taeniids harbored by wild and domestic cats
In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless due to the poor quality of samples. These situations are frequent in parasitology. Here we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free-ranging domestic cats (F. s. catus) and their hybrids populations. Adult taeniids were collected by post-mortem examinations of the hosts, and morphologically identified as Taenia taeniaeformis. We produced the cox1 barcode sequences for all the analyzed specimens and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology-based approaches and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already described taeniid species. Indeed, we detected three well-defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.
Data from: Resource allocation trade-offs and the loss of chemical defences during apple domestication
Background and Aims: Most crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication. Methods: To provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary >26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays. Key Results: The results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths. Conclusions: The negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield–defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant–herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.
Data from: Gene flow from domesticated escapes alters the life history of wild Atlantic salmon
Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals.
Data from: Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple
Understanding the way in which the climatic oscillations of the Quaternary Period have shaped the distribution and genetic structure of extant tree species provides insight into the processes driving species diversification, distribution and survival. Deciphering the genetic consequences of past climatic change is also critical for the conservation and sustainable management of forest and tree genetic resources, a timely endeavour as the Earth heads into a period of fast climate change. We used a combination of genetic data and ecological niche models to investigate the historical patterns of biogeographic range expansion of a wild fruit tree, the European crabapple (Malus sylvestris), a wild contributor to the domesticated apple. Both climatic predictions for the last glacial maximum and analyses of microsatellite variation indicated that M. sylvestris experienced range contraction and fragmentation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one genetic cluster spanning a large area in Western Europe and two other genetic clusters with a more limited distribution range in Eastern Europe, one around the Carpathian Mountains and the other restricted to the Balkan Peninsula. Approximate Bayesian computation appeared to be a powerful technique for inferring the history of these clusters, supporting a scenario of simultaneous differentiation of three separate glacial refugia. Admixture between these three populations was found in their suture zones. A weak isolation by distance pattern was detected within each population, indicating a high extent of historical gene flow for the European crabapple.
Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
Data from: Towards a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)
Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N=274). These SNPs were variable both in wild (HE=0.107) and domestic cats (HE=0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise FCT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average FCT>0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest FCT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.
Data from: New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)
This investigation establishes the first sequence-based phylogenetic hypothesis of species relationships in the Coca family (Erythroxylaceae). We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that Neotropical Erythroxylum are monophyletic within the Paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense but relationships within this "coca" clade remain equivocal, suggesting a more complicated origin than Plowman's single-domestication hypothesis. Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.
Data from: Domesticated tomatoes are more vulnerable to negative plant-soil feedbacks than their wild relatives
Domesticated plants can differ from their wild counterparts in the strength and outcome of species interactions, both above- and belowground. Plant-soil feedbacks influence plant success, and plant-associated soil microbial communities can influence plant interactions with herbivores and their natural enemies, yet, it is unclear if domestication has changed these relationships. To determine the effects of domestication on plant-soil interactions, we characterized soil microbial communities associated with various cultivars of domesticated tomato and some of its wild relatives. We measured the strength and direction of plant-soil feedbacks for domesticated and wild tomatoes, and the effects of soil on plant resistance to specialist herbivory by Manduca sexta, and the attraction of a parasitoid wasp, Cotesia congregata. Domesticated tomatoes and their wild relatives had negative plant-soil feedbacks, as conspecifics cultivated soil that negatively impacted performance of subsequent plants (longer germination time, lower biomass) than if they grew in non-tomato soils. Significant variation existed among domesticated and wild tomato varieties in the strength of these feedbacks, ranging from neutral to strongly negative. For aboveground plant biomass, tomato wild relatives were unaffected by growing in tomato-conditioned soil while domesticated tomatoes grew smaller in tomato soil, indicating effects of plant domestication. Overall, increased microbial biomass within the rhizosphere resulted in progressively less-negative plant-soil feedbacks. Plant cultivars had different levels of resistance to herbivory by M. sexta, but this did not depend on plant domestication or soil type. The parasitoid C. congregata was primarily attracted to herbivore damaged plants, independent of plant domestication status, and for these damaged plants, wasps preferred some cultivars over others, and wild plants grown in tomato soil over wild plants grown in non-tomato soil. Synthesis: These results indicate that crop tomatoes are more likely to show negative plant-soil feedbacks than wild progenitors, which could partially explain their sensitivity to monocultures in agricultural soils. Further, cultivar-specific variation in the ability to generate soil microbial biomass, independent of domestication status, appears to buffer the negative consequences of sharing the same soil. Last, soil legacies were relatively absent for herbivores, but not for parasitoid wasps, suggesting trophic level specificity in soil feedbacks on plant-insect interactions.
Data from: Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes
Background: Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis (MLVA). Phylogenetic relationships among MST genotypes show how these Hungarian samples are related to others collected around the world. Results: Three MST genotypes were identified: sequence type (ST) 20 has also been identified in ruminants from other European countries and the USA, ST28 was previously identified in Kazakhstan, and the proposed ST37 is novel. All MST genotypes yielded different MLVA genotypes and three different MLVA genotypes were identified within ST20 samples alone. Two novel MLVA types 0-9-5-5-6-2 (AG) and 0-8-4-5-6-2 (AF) (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34) were defined in the ovine materials correlated with ST28 and ST37. Samples from different parts of the phylogenetic tree were associated with different hosts, suggesting host-specific adaptations. Conclusions: Even with the limited number of samples analysed, this study revealed high genetic diversity among C. burnetii in Hungary. Understanding the background genetic diversity will be essential in identifying and controlling outbreaks.
FIGURES 1–5 in A new species of the genus Amyrsidea (Phthiraptera: Amblycera: Menoponidae) parasitizing domestic chickens in Saudi Arabia
FIGURES 1–5. Amyrsidea (Argimenopon) saudiensis n. sp.: 1, female habitus. 2, male habitus. 3, female head and prothorax. 4, male genitalia. 5, hypopharyngeal sclerites.
FiG. 3 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 3. — Comparison of the different components of the Neolithic transition in Southwest Asia and North China and their chronological succession, and the schematic representation of the origins of domestic pigs, sheep, goats, cattle and horse in the two regions, according to Vila (1998), Huot (2004), Helmer et al. (2005), Peters et al. (2005), Flad et al. (2007), Elisseeff (2008) Boaretto et al. (2009),Outram et al. 2009, Bar-Yosef (2011), Cohen (2011), Cucchi et al. (2011), Zhao (2011), and Willcox & Stordeur (2012).
FiG. 2 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 2. — Location and dates of the earliest ungulate domestication in Asia (animal outlines),of the Neolithic routes of transportation (arrows), of the early domesticates and of the different steps of the early spread of husbandry starting from the nucleus zones (concentric degraded green patches); according to Meadow (1981), Helmer et al. (2005), Larson et al. (2005, 2007), Peters et al. (2005), Flad et al. (2007), Cucchi et al. (2008, 2011), Yang et al. (2008), Hongo et al. (2009), Dobney & Jacques (2010), Linseele (2013), and Vigne & Debue (in press).
FiG. 4 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 4. — The Cypriot Aetokremnos shelter, where evidence of 'predomestic' control of wild boars has been discovered: A, location (Map: MODIS/MODLAND/ Decloîtres); B, view of the excavations (courtesy Allan Simmons); C, schematic interpretation of the fillings of the shelter;D, abaxial (left) and axial third phalanges of small sized wild boar found in the upper layer. Scale bar: 5 cm.
FiG. 8 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 8. — Medial view of a right upper third molar of a Late Neolithic sheep of Orkneys (Skara Brae; first half of the 3rd millennium cal BC). The enamel of the anterior lobe has been sequentially sampled by drilling, in order to analyze the variations of the oxygen and carbon stable isotopes ratios during the period of mineralisation of the tooth. Scale bar: 1 cm (Photo by M. Balasse).
FIGURES 13–16 in Rumen Ciliate Fauna of Domestic Sheep (Ovis aries) in İzmir, Turkey and Scanning Electron Microscopic Observations
FIGURES 13–16. SEM images of (13) Enoploplastron triloricatum, (14)–(16) Dasytricha ruminantium. AL: Adoral Lip, CR: Ciliary Rows, DL: Dorsal Lip, O: Operculum, P: Pore of contractile vacuole. Small numerous holes (arrowheads).
FIGURES 1–4 in Rumen Ciliate Fauna of Domestic Sheep (Ovis aries) in İzmir, Turkey and Scanning Electron Microscopic Observations
FIGURES 1–4. SEM images of (1) Entodinium longinucleatum, (2) E. bursa, (3) E. rectangulatum m. rectangulatum, (4) E. semahatae. AL: Adoral Lip, CL: Caudal Lobe, CS: Caudal Spine, P: Pore of contractile vacuole.
FIGURES 17–20 in Rumen Ciliate Fauna of Domestic Sheep (Ovis aries) in İzmir, Turkey and Scanning Electron Microscopic Observations
FIGURES 17–20. SEM images of (17)–(18) Ophryoscolex caudatus m. tricoronatus, (19) Epidinium ecaudatum m. parvicaudatum, (20) Polyplastron multivesiculatum. ACZ: Adoral Ciliary Zone, CP: Cytoproct, CS: Caudal Spine, DCZ: Dorsal Ciliary Zone, O: Operculum, P: Pore of contractile vacuole.
FIGURES 5–8 in Rumen Ciliate Fauna of Domestic Sheep (Ovis aries) in İzmir, Turkey and Scanning Electron Microscopic Observations
FIGURES 5–8. SEM images of (5) Entodinium exiguum, (6) E. minimum, (7) E. simulans m. caudatum, (8) E. dilobum. ACZ: Adoral Ciliary Zone, AL: Adoral Lip, CL: Caudal Lobe, CP: Cytoproct, CS: Caudal Spine, P: Pore of contractile vacuole.
"Out of South Asia": distinctive genomic profile of wild boar and domestic pig populations in South Asia
<p> content:</p> <p>hic matrix for p1, p2, p3</p>
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