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903 results for “Domestication”
Data from: Reduced drought tolerance during domestication and the evolution of weediness results from tolerance-growth trade-offs
The increased reproductive potential, size, shoot allocation, and growth rate of weedy plants may result from reduced resource allocation to other aspects of plant growth and defense. To investigate whether changes in resource allocation occurred during domestication or the evolution of weediness, we compared the mycorrhizal responsiveness, growth, and drought tolerance of nine native ruderal, nine agriculturally weedy (four US weedy and five Australian weedy), and fourteen domesticated populations (eight ancient landraces and six improved cultivars) of the common sunflower (Helianthus annuus). Domesticated sunflower cultivars were less drought tolerant, but had higher plant growth and fecundity and coarser roots than wild populations. There were no changes in level of drought tolerance between improved cultivars and ancient landraces plants, but there was an increase in allocation to flowers with recent selection. Weedy populations were intermediate between domesticated cultivars and native ruderal populations for plant growth rate, root architecture and drought tolerance. Weedy populations benefited most from mycorrhizal inoculation by having fewer wilted leaves and wetter soil. Overall, we found that trade-offs between drought tolerance and several aspects of plant growth, including growth rate, allocation to flowering and root architecture, govern evolution during sunflower domestication and the invasion of disturbed habitat.
Data from: Domestication and geographic origin of Oryza sativa in China: insights from multilocus analyses of nucleotide variation of O. sativa and O. rufipogon
Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC-ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.
Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL
The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic effects, our study found the region on chromosome five fractionates into multiple QTL regions, none with singularly large effects. The smallest 1.5 LOD support interval for a QTL contained 54 genes, one of which was a MADS MIKCC transcription factor, a family of proteins implicated in many developmental programs. We also used simulated trait datasets to investigate the power of our mapping population to identify QTL for which there is a single underlying causal gene. This analysis showed that while QTL for traits controlled by single genes can be accurately mapped, our population design can detect no more than ~4.5 QTL per trait even when there are 100 causal genes. Thus when a trait is controlled by 5 or more genes in the simulated data, the number of detected QTL can represent a simplification of the underlying causative factors. Our results show how a QTL region with effects on several domestication traits may be due to multiple linked QTL of small effect as opposed to a single gene with large and pleiotropic effects.
Data from: Morphological integration in the appendicular skeleton of two domestic taxa: the horse and donkey
Organisms are organized into suites of anatomical structures that typically covary when developmentally or functionally related, and this morphological integration plays a determinant role in evolutionary processes. Artificial selection on domestic species causes strong morphological changes over short time spans, frequently resulting in a wide and exaggerated phenotypic diversity. This raises the question of whether integration constrains the morphological diversification of domestic species and how natural and artificial selection may impact integration patterns. Here, we study the morphological integration in the appendicular skeleton of domestic horses and donkeys, using three-dimensional geometric morphometrics on 75 skeletons. Our results indicate that a strong integration is inherited from developmental mechanisms which interact with functional factors. This strong integration reveals a specialization in the locomotion of domestic equids, partly for running abilities. We show that the integration is stronger in horses than in donkeys, probably because of a greater degree of specialization and predictability of their locomotion. Thus, the constraints imposed by integration are weak enough to allow important morphological changes and the phenotypic diversification of domestic species.
Data from: Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host
Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate changes in life history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems were assessed on the domesticated apple, its central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulences in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity.
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point towards a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
Data from: Genetic structure in village dogs reveals a Central Asian domestication origin
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.
Data from: The evolution of ontogenetic allometric trajectories in mammalian domestication
Morphological divergence of domesticated as compared to wild forms must result from changes in the ontogenetic process. Species-specific tests for heterochrony have rejected a single explanation of domestic forms representing juveniles of their wild relatives. Ontogenetic allometric trajectories for 12 pairs of wild and domestic mammals were examined using skull growth data for 1070 specimens, including representatives from all lineages in which domestication has occurred. A suite of tests were performed to quantify allometric disparity in wild and domestic forms and assess the extent and patterning of modification to allometric trajectories. Domestication has modified postnatal ontogenetic allometric trajectories in mammals, and has generated disparity, achieved through lengthening of trajectory slopes and alteration to slope angles. Allometric disparity was similar for domestic forms compared to their wild relatives, whereas the magnitude of dispersion along allometric vectors differed between precocial mammals and altricial mammals, underscoring the importance of life history and shared evolutionary history in patterns of ontogenetic variation. The results verify the importance of scaling in the morphological changes associated with domestication. The response to domestication for all measured trajectory parameters was variable across species, suggesting multiple pathways of change.
Data from: Shifts in plant functional strategies over the course of wheat domestication
1. Human selection, changes in environmental conditions and management practices drove the phenotypic trajectory of crops during domestication. The characterization of the crop domestication syndrome lies mostly on reproductive characters. However, biophysical and ecophysiological constraints during vegetative growth are also at play and can strongly impact crop phenotypes. It has been argued that a broadened examination of crop phenotypes through a functional trait-based lens should improve our understanding of the domestication syndrome. 2. We used a collection of 39 genotypes representative of key steps during tetraploid wheat domestication, and grew them in a common garden experiment. We quantified the vegetative phenotype of each genotype through the measurements of 13 functional traits related to root, leaf and whole-plant dimensions. 3. In modern cultivars, compared to ancestral forms, leaf longevity was shorter while net photosynthetic rate, leaf production rate and nitrogen content were higher. Modern cultivars had a shallower root system and exhibited a larger proportion of fine roots, preferring to invest biomass above rather than below ground. We found ancestral forms to be integrated phenotypes characterized by coordination between above- and below-ground functioning. Conversely, in modern forms, human selection appeared to have broken this coordination and to have generated a new type of network of trait covariations. 4. Synthesis and applications. The examination of leaf, root, and whole-plant traits of wheat accessions indicated a strong shift in plant functional strategies over the course of domestication. Elite genotypes tended to better optimize resource-use acquisition strategies than ancestral ones. The characterization of the crop phenotype based on vegetative traits thus suggests a much more complete domestication syndrome. Our findings highlight the benefits of using a functional trait-based characterization of crop phenotypes to document the extent of domestication syndrome and to further advance the agroecological management of cereals.10-Oct-2017
Data from: Domesticated honeybees facilitate interspecific hybridization between two Taraxacum congeners
1. Interspecific hybridization is common in plants under natural conditions, but the ecological mechanisms underlying when and how it happens have not fully been understood. 2. Taraxacum calanthodium and T. lugubre are two herbaceous annals co-occurring in alpine meadows of the eastern Tibetan Plateau that share the same pollinators including domestic honeybees during their overlapping flowering times. Because honeybees tend to visit flowers less discriminatively when bee densities are high, we hypothesized that intense apiculture would facilitate hybridization between these two congeneric species. 3. We tested this hypothesis by examining the frequencies of the two parent species occurrence and the hybrid (based on morphological and genetic differences) along three transects radiating from well-established apiaries. 4. Experiments show that both Taraxacum calanthodium and T. lugubre produce seeds sexually and asexually, and that they can hybridize via pollen transfer. Bee visitation rates and the frequency of the hybrid were significantly higher in the sites nearest to apiaries compared to distant site along each of the three transects. The hybrids were consistently genetically intermediate between the two species, as indicated by Simple Sequence Repeat- based analyses. 5. Synthesis. These data indicate that domestic honeybees foster interspecific hybridization between the two Taraxacum species and that anthropogenic effects on pollen vectors can significantly influence species hybridization in nature. We suggest that more effort should be made to quantify the effects of environmental change on pollinators and their effects on species evolution.
FiG. 7 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 7. — The process of re-domestication of the feral goat at Shillourokambos, adapted from Vigne et al. (in press): A, histograms of distribution of the densities and mixture analyses for two measurements (according to the standards of von den Driesch 1976), one for the humerus and one for the talus, as examples of the protocol which has been used for estimating the sex ratio and the separate mean and standard deviation for males and females; B, evolution of the average size (expressed by the Log Size Index, LSI) of males and females (separated by mixture analyses) over the different phases of occupation of the village of Shillourokambos (Early AB to Mid. B + Late) and at Khirokitia; grey dots correspond to small samples; arrows and (+) indicates the statistically significant differences; significant size decreases due to domestication appear at the end of the sequences, c. 9500-8500 cal BP; C, evolution of the goat sex ratio over three successive phases of the PPN's (Pre-Pottery Neolithic) evolution in Shillourokambos and Khirokitia, according to the mixture analyses of different measurements of the humerus distal part (Bd, BT, H, HTC according to von den Driesch 1976, and Davis pers. obs.) of adult goats; the vertical segments delimitate the standard deviation of the mean; light grey columns indicate no statistically significant differences between the sex ratio estimate and 50%; conversely, dark grey columns indicate significant differences. The sex ratio is well balanced during the early step, but tends to decrease below 50% (i.e. less adult males than females) during the middle phase. It is significantly biased toward adult females during the most recent phase. Together with the size decrease, this unbalanced sex ratio advocates for the local domestication of goats. Abbreviations: Bd,braedth of the distal end; BT, breadth of the trochlea; H, heigth of the medial edge of the trochlea; HTC, minimal height of the trochlea groove; N, number of specimens of animal bones studied.
FiG. 6 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 6.— Processing the traditional morphometric measurements for studying separately the two components of the form,i.e. isometric size and shape (Mosiman's protocole): A, geometric representation of the independency of shape and isometric size; B, example based on the measurement of four variables (V1 to V4) on the talus of the PPNA (Pre-Pottery Neolithic A) and PPNB (Pre-Pottery Neolithic B) Cypriot suids (Sus scrofa ssp.) at the sites of Klimonas and Shillourokambos. Isometric size analyses confirm a size decrease tendency which is probably due to the intensification of the cultural control during the occupation of Shillourokambos. Conversely, the analyses of the Log Shape Ratios (LSR, i.e. shape analyses) evidences no change all along the two millennia sequence, suggesting local domestication of the autochthonous small wild boar. Abbreviations: KL, Klimonas; N, number of specimens of animal bones studied.
FiG. 5 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 5. — Evolution of large mammals on Cyprus during the neolithisation,with particular focus on the data from Shillourokambos (adapted from Vigne et al. 2014). Abbreviations: NISP, number of identified specimens of animal bones; PPNA, Pre-Pottery Neolithic A; PPNB, Pre-pottery Neolithic B.
FiG. 1 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 1. — Schematic representation of the processes of domestication and of the belated consecutive emergence of the domestic populations, lineages or species (after Vigne 2011a, modified according to Zeder 2012, Larson & Burger 2013, and Hulme-Beaman 2014).
FiG. 9. — A in Early domestication and farming: what should we know or do for a better understanding?
FiG. 9. — A, Evolution of meat production through the chronological phases of Shillourokambos (Cyprus; Vigne et al. 2011b) in comparison with the global climatic fluctuations, as evidenced by the rate of 18O in the GISP2 record (Stuiver et al. 1995); B, Demography of the village, estimated by the number of identified specimens of animal bones (NISP, for an excavated surface of 5000 m²; the dotted line indicates low reliability due to much smaller archaeozoological datasets). Bone weight percentages are not exact estimates of meat procurement. Only the relative variations between the different phases can be taken into consideration in this diagram, which is why ordinates are not graduated. Abbreviation: PPNB, Pre-Pottery Neolithic B.
FiG. 10 in Early domestication and farming: what should we know or do for a better understanding?
FiG. 10. — Evolution of the demography before and after the Neolithic transition (dt=0) in the Near East (Guerrero et al. 2007), in Europe (Bocquet-Appel 2002) and in North America (Bocquet-Appel & Naji 2006), estimated by the fertility index. The demographic transition occured at different times during the Holocene, unconnected to any major climate change (referenced by the global temperature fluctuations at the bottom of the graphic), estimated by the ratio of the 18 stable isotope of oxygen in the GISP2 ice core (adapted from Stuiver et al. 1995).
Learning to Grasp Unknown Objects in Domestic Environments with GP-net+
<p>This record includes data for the paper "Learning to Grasp Unknown Objects in Domestic Environments", currently under review.<br><br><strong>Simulation environment with pre-trained GP-net+ model</strong><br><br>The paper presents a simulation environment for grasping objects in domestic environments. The presented objects and furniture units, as well as a pre-trained GP-net+ model can be found in the "gpnetplus_simulation_data.zip" file. After this zip file is downloaded, it can be unpacked it into the <a href="https://github.com/AuCoRoboticsMU/GP-netplus" target="_blank" rel="noopener">GP-net+ directory</a>. It includes all necessary data to use the simulation environment, for example, for testing GP-net+ or other grasping models in simulated domestic environments.</p> <p> </p> <p><strong>ROS model</strong></p> <p>The paper additionally presents an <a href="https://github.com/AuCoRoboticsMU/GP-netplus-ros" target="_blank" rel="noopener">ROS package</a> that can be deployed for grasping unknown objects in domestic environments with simulated or real robots. We make a ROS-compatbile model of GP-net+ available in the "ros_gpnet_plus.zip" file, which can be used with the ROS package.</p> <p> </p> <p><strong>Training dataset</strong></p> <p>We used the simulation environment in our paper to generate a training dataset and train GP-net+. This training dataset is included in this record and can be used to replicate our results or train modifications of GP-net+.</p> <p>To improve handling of the training dataset (total size 25GB+), we split the dataset into several .zip files, named val.zip (validation data) and train_[0-6].zip (training data). Download all files individually and extract them into a single folder. Combine all files train_[0-6].zip directory into a single directory called 'train', for example, by using the 'move_train_data.sh' script provided.<br><br>The final structure for the dataset should look similar to this:<br><br>gpnet_data</p> <p>|-- val</p> <p> |-- depth_image_0000000.npz</p> <p> |-- depth_image_0000001.npz</p> <p> ...</p> <p> |--segmask_image_0052346.npz</p> <p>|-- train</p> <p> |-- depth_image_0000000.npz</p> <p> |-- depth_image_0000001.npz</p> <p> ...</p> <p> |-- segmask_image_0602506.npz</p> <p> |-- segmask_image_0602507.npz</p> <p><br><br><br>For generation of the training and simulation data, the following mesh databases have been used:<br><br>B. Calli, A. Walsman, A. Singh, S. Srinivasa, P. Abbeel, and A. M. Dollar,"Benchmarking in Manipulation Research: Using the Yale-CMU-Berkeley Object and Model Set," IEEE Robotics and Automation Magazine, vol. 22, no. 3, pp. 36–52, 2015<br><br>A. Singh, J. Sha, K. S. Narayan, T. Achim, and P. Abbeel, "BigBIRD: A large-scale 3D database of object instances," 2014 IEEE International Conference on Robotics and Automation (ICRA), pp. 509–516, 2014.<br><br>A. X. Chang, T. Funkhouser, L. Guibas, P. Hanrahan, Q. Huang, Z. Li, S. Savarese, M. Savva, S. Song, H. Su, J. Xiao, L. Yi, and F. Yu, "ShapeNet: An Information-Rich 3D Model Repository," Tech. Rep. arXiv:1512.03012 [cs.GR], Stanford University — Princeton University — Toyota Technological Institute at Chicago, 2015.</p> <p>D. Morrison, P. Corke, and J. Leitner, "EGAD! An Evolved Grasping Analysis Dataset for Diversity and Reproducibility in Robotic Manipulation," IEEE Robotics and Automation Letters, vol. 5, no. 3, pp. 4368–4375, 2020</p>
Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files</p>
A graph-based goat pangenome reveals structural variations involved in domestication and adaptation
<p>Data are organized as a folder and compressed with tar.gz.</p> <p> </p>
Relationship between mineral extraction, oil extraction, and agribusiness with employability, municipal gross domestic product, and voting data in Brazil
<p>This dataset looks at the number of Brazilian municipalities where mining is a key economic activity and those where mining is a key job provider. We also listed municipalities that have mining as both a main economic activity and the main employer in a given town. We have also generated maps to visualize the impact of mining in Brazil as a key economic activity and/or job provider. Similarly, we have listed the same information for all the municipalities that received oil royalties in 2019, and the top 100 municipalities whose wealth was mainly generated by agribusiness in 2022. By detailing the economic and employment situation in Brazilian extractive municipalities (mining, oil, and crops), we demonstrate that company towns in Brazil (locations that are highly dependent on one key economic activity for employment generation) are few. Extractive industries may no longer be labour intensive, although economic dependency may follow indirectly, such as because of tax generation. We also offer data on national elections to demonstrate that there is not a clear correlation between economic activity and voting patterns, which may be explained by low employability. The main objective of this dataset is to generate a discussion on the need to redefine company towns in Brazil.</p>
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