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Data from: Identification of quantitative genetic components of fitness variation in farmed, hybrid and native salmon in the wild
Feral animals represent an important problem in many ecosystems due to interbreeding with wild conspecifics. Hybrid offspring from wild and domestic parents are often less adapted to local environment and ultimately, can reduce the fitness of the native population. This problem is an important concern in Norway, where each year, hundreds of thousands of farm Atlantic salmon escape from fish farms. Feral fish outnumber wild populations, leading to a possible loss of local adaptive genetic variation and erosion of genetic structure in wild populations. Studying the genetic factors underlying relative performance between wild and domesticated conspecific can help to better understand how domestication modifies the genetic background of populations, and how it may alter their ability to adapt to the natural environment. Here, based upon a large-scale release of wild, farm and wild x farm salmon crosses into a natural river system, a genome-wide quantitative trait locus (QTL) scan was performed on the offspring of 50 full-sib families, for traits related to fitness (length, weight, condition factor and survival). Six QTLs were detected as significant contributors to the phenotypic variation of the first three traits, explaining collectively between 9.8 and 14.8% of the phenotypic variation. The seventh QTL had a significant contribution to the variation in survival, and is regarded as a key factor to understand the fitness variability observed among salmon in the river. Interestingly, strong allelic correlation within one of the QTL regions in farmed salmon might reflect a recent selective sweep due to artificial selection.
Data from: Organic farming enhances parasitoid diversity at the local and landscape scale
1. The magnitude of the benefits derived from organic farming within contrasting managed landscapes remains unclear and, in particular, the potential scale-dependent response of insect parasitoids is relatively unexplored. Identifying the scale at which parasitoids are affected by organic farming will be an important step to enhance their conservation. 2. We sampled tachinid parasitoids at the centre and margin of arable and grassland fields on paired organic and conventional farms located in landscapes with different proportions of organic land. A total of 192 fields were sampled in two biogeographical regions of the UK. 3. We found that the positive effect of organic farming on tachinid parasitoid diversity can be observed at multiple spatial scales. At the local scale, we found higher abundance and species richness of tachinid parasitoids on organic than on conventional farms and on field margins than on field centres. At the landscape scale, the diversity of tachinids was higher in landscapes with higher proportions of organic land. At both scales, the positive effect of organic farming was clear for arable fields, while it was almost neutral for grasslands. 4. Synthesis and applications. Any attempt to enhance parasitoid diversity in agricultural landscapes needs to consider the local management in relation to the habitat type, location within the field and agricultural management in the surrounding landscape. To restore parasitoid diversity, the promotion of organic agriculture should aim to increase both the total extent of organic farming and the connectivity of individual farms. As the benefits of organic farming to biodiversity clearly spread beyond individual farm boundaries, any assessment of organic farming should consider these positive externalities.
Data from: Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution
Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel SNPs by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to PCR fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice-planting regions. The highest frequency (~57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (~29%) was detected in weedy rice populations from Northeast China where rice farming has a relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.
Data from: Comparisons of reproductive function and fatty acid fillet quality between triploid and diploid farm Atlantic salmon (Salmo salar)
Triploidy could prevent escaped farm salmon breeding in the wild, while also improving nutrient quality within farmed fillets. Despite these potential advantages, triploid Atlantic salmon have not been widely used in aquaculture, and their reproductive function has yet to be fully evaluated. Here, we compare reproductive function and fillet composition between triploid and diploid farm salmon under standard aquaculture rearing conditions. We show that female triploids are sterile and do not develop gonads. In contrast, males produce large numbers of motile spermatozoa capable of fertilising wild salmon eggs. However, compared with diploids, reproductive development and survival rates of eggs fertilised by triploid males were significantly reduced, with less than 1% of eggs sired by triploid males reaching late eyed stages of development. Analyses of fillets showed that total lipid and fatty acid quantities were significantly lower in triploid compared to diploid Atlantic salmon fillets. However, when fatty acids were normalized to total lipid content, triploid fillets had significantly higher relative levels of important omega-3 Long Chain Polyunsaturated Fatty Acids. Our results show that: (1) escaped triploid farm salmon are very unlikely to reproduce in the wild; and (2) if able to match diploid fillet lipid content, triploid farm salmon could achieve better fillet quality in terms of essential fatty acids.
Data from: Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria
Symbiotic associations can allow an organism to acquire novel traits by accessing the genetic repertoire of its partner. In the Dictyostelium discoideum farming symbiosis, certain amoebas (termed "farmers") stably associate with bacterial partners. Farmers can suffer a reproductive cost but also gain beneficial capabilities, such as carriage of bacterial food (proto-farming) and defense against competitors. Farming status previously has been attributed to amoeba genotype, but the role of bacterial partners in its induction has not been examined. Here, we explore the role of bacterial associates in the initiation, maintenance, and phenotypic effects of the farming symbiosis. We demonstrate that two clades of farmer-associated Burkholderia isolates colonize D. discoideum nonfarmers and infectiously endow them with farmer-like characteristics, indicating that Burkholderia symbionts are a major driver of the farming phenomenon. Under food-rich conditions, Burkholderia-colonized amoebas produce fewer spores than uncolonized counterparts, with the severity of this reduction being dependent on the Burkholderia colonizer. However, the induction of food carriage by Burkholderia colonization may be considered a conditionally adaptive trait because it can confer an advantage to the amoeba host when grown in food-limiting conditions. We observed Burkholderia inside and outside colonized D. discoideum spores after fruiting body formation; this observation, together with the ability of Burkholderia to colonize new amoebas, suggests a mixed mode of symbiont transmission. These results change our understanding of the D. discoideum farming symbiosis by establishing that the bacterial partner, Burkholderia, is an important causative agent of the farming phenomenon.
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).
Data Used for Article: Speeding up large wind farms layout optimization using gradients, parallelization, and a heuristic algorithm for the initial layout
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IMPROVEMENT ACCOUNTING OF PROCESS REALIZATION IN FARM ENTERPRISES
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Farm Equipment
Created with Polycam Source: Objaverse 1.0 / Sketchfab
Quantifying the contribution of individual inputs used in Zero Budget Natural Farming
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Table 2 in Checklist of bees (Hymenoptera: Apoidea) from small diversified vegetable farms in south-western Montana
<p>Table 2. List of published keys used for species identification. Genus-level identifications were done using Michener et al. (1994).</p><table><tbody><tr><td>Family</td><td>References</td></tr><tr><td>Andrenidae</td><td>Bouseman and LaBerge 1979 Donovan 1977 LaBerge 1967 LaBerge 1969 LaBerge 1973 LaBerge 1977 LaBerge 1980 LaBerge 1985 LaBerge 1986 LaBerge 1989 LaBerge and Bouseman 1970 LaBerge and Ribble 1975 Ribble 1967 Ribble 1974 Thorp 1969 Timberlake 1956 Timberlake 1960 Timberlake 1964 Timberlake 1967</td></tr><tr><td>Apidae</td><td>Brumley 1965 Daly 1973 Hurd and Linsley 1951 Koch et al. 2012 LaBerge 1956b LaBerge 1956a LaBerge 1961 LaBerge 1963 Rightmyer 2008 Sipes 2001 Thorp et al. 1983 Williams et al. 2014</td></tr><tr><td>Colletidae</td><td>Snelling 1966b Snelling 1966a Snelling 1970 Stephen 1954</td></tr><tr><td>Halictidae</td><td>Coelho 2004 Dumesh and Sheffield 2012 Gibbs 2010 McGinley 1986 McGinley 2003 Roberts 1972 Roberts 1973</td></tr><tr><td>Megachilidae</td><td>Baker 1975 De Silva and Packer 2012 Gonzalez and Griswold 2013 Grigarick and Stange 1968 Hurd and Michener 1955 Michener 1938 Michener 1939 Michener 1947 Rightmyer et al. 2010 Sandhouse 1939 Sheffield et al. 2011</td></tr></tbody></table>
THE ROLE OF THE BRONZE AGE SEDENTARY FARMING CULTURE IN THE WORK OF THE UZBEK ARCHAEOLOGIST AKHMADALI ASKAROV
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Evaluation of MEMS NIR spectrometers for on-farm analysis of raw milk composition
<p>Today, measurement of raw milk quality and composition relies on Fourier-transform infrared spectroscopy to monitor and improve dairy production and cow health. However, these laboratory analyzers are bulky, expensive and can only be used by experts. Moreover, the sample logistics and data transfer delay the information on product quality, and the measures taken to optimize the care and feeding of the cattle rendering them less suitable for real-time monitoring. An on-farm spectrometer with compact size and affordable cost could bring a solution for this discrepancy. This paper evaluates the performance of Micro-Electro-Mechanical-System (MEMS) based near-infrared (NIR) spectrometers as on-farm milk analysers. These spectrometers use Fabry-Pérot interferometers for wavelength tuning, giving them the advantage of very compact size and affordable price. This study discusses the ability of MEMS spectrometers to reach the accuracy limits set by ICAR for at-line analyzers of the milk content regarding fat, protein and lactose. According to achieved results, the transmission measurements with the NIRONE2.5 spectrometer perform best, with an acceptable root mean squared error of prediction (RMSEP=0.21% w/w) for the measurement of milk fat and excellent performance (RMSEP≤0.11% w/w) for protein and lactose. In addition, the transmission measurements using the NIRONE2.0 module give similar results for fat and lactose (RMSEP of 0.21 and 0.10% w/w respectively), while the prediction of protein is slightly deteriorated (RMSEP=0.15% w/w). These results show that the MEMS spectrometers can reach sufficient accuracy for at-line and in-line fat, protein and lactose prediction.</p>
Fig. 1 in Weight-length relationship, condition factor and blood parameters of farmed Cichla temensis Humboldt, 1821 (Cichlidae) in central Amazon
Fig. 1. Weight-length relationship in Cichla temensis (n = 40) farmed in central Amazon. Data values as plotted: a. Values of the determination coefficient/R2; b. Linear regression.
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America
<p>Tambaqui or cachama (<i>Colossoma macropomum</i>) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High-throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single-nucleotide polymorphism (SNP) markers obtained with double-digest restriction site-associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global F<sub>ST</sub> analyses of SNP loci (F<sub>ST</sub> = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.</p>
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