Domestication Process Research Articles

Domestication provides durum wheat with protection from locust herbivory.

Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.

Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence.

Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000-4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.

Identification of selection signatures in Capra hircus and Capra aegagrus in Iran.

Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.

The Domestication Process of Tea and the Formation of Tea Varieties

The Domestication Process of Tea and the Formation of Tea Varieties

Breaking into the Middle of the Story: Reading Lydia Syson’s Mr Peacock’s Possessions as a Neo-Victorian Robinsonade

ABSTRACT This article analyses Lydia Syson’s Mr Peacock’s Possessions as a neo-Victorian Robinsonade. In order to assess the contemporary pertinence of the format, I organize my discussion around the notion of un/settlement, a concept which applies to both the frustrated process of colonial domestication of the island depicted in the novel and to the author’s project of writing back to the narrative and ideological codes of the Victorian Robinsonade. The term “un/settlement” is also useful to explore the novel’s engagement with the violent colonial history of the region, which resurfaces in the present forcing the characters (and the author) to recover and narrate those stories and thus settle their debt with that past. The article starts by contextualizing Syson’s novel in relation to a long tradition of castaway narratives, and then moves on to discuss the novel in the light of neo-Victorian and postcolonial preoccupations with the possibilities and limitations of historical revision and reparation.

Effects of domestication on responses of chickens and red junglefowl to conspecific calls: A pilot study.

Beyond physical and zootechnical characteristics, the process of animal domestication has also altered how domesticated individuals, compared to their wild counterparts, perceive, process, and interact with their environment. Little is known, however, on whether and how domestication altered the perception of conspecific calls on both domesticated and wild breeds. In the present work, we compared the vigilance behavior of domestic and captive-born wild fowl following the playback of chicken alarm calls and contentment calls (control). The playback tests were performed on four different breeds/lines. We first compared the behavioral reaction of domesticated White Leghorn (WL, a breed selected for egg production) and Red Junglefowl (RJF) hens (ancestor of domestic chickens). We also compared the behavior of Red Junglefowl hens selected for high or low fear of humans (RJF HF and RJF LF, respectively), a proxy to investigate early effects of domestication. Contrary to our expectations, no breed/line reacted accordingly to the calls, as the increase in vigilance behavior after the playback calls was similar for both alarm and contentment calls. Although no call discrimination differences were found, breeds did differ on how they reacted/habituated to the calls. Overall, WL were more vigilant than RJF, and birds from the RJF LF line decreased their vigilance over testing days, while this was not the case for the RJF HF line. These results suggest that birds under commercial-like conditions are unable to discriminate between alarm and contentment calls. Interestingly, domestication and selection for low fear of humans may have altered how birds react to vocal stimuli. It is important to consider that farmed animals may interpret and be affected by the vocalizations of their conspecifics in unexpected ways, which warrants further investigation.

REPRODUCTIVE PERFORMANCE OF INTRASPECIFIC HYBRIDS OF BLUE SWIMMING CRAB (Portunus pelagicus)

High exploitation of the blue swimming crab (Portunus pelagicus) has significantly reduced its wild populations. The domestication process of this species has been started; however, its breeding program has not yet been successful. Therefore, this study aimed to examine the reproduction performance of intraspecific hybrids of blue swimming crab from Sorong (Papua) and Barru (South Sulawesi), Indonesia. P. pelagicus from Sorong has a bigger size, while the crab from Barru has a better reproduction performance, including fecundity and egg diameter. Hybridization was conducted between crabs from Sorong and Barru with different combinations of broodstock, namely: Barru female ><Barru male, (BF><BM); Barru female ><Sorong male (BF><SM); and Sorong female ><Barru male (SF><BM). The results showed no significant difference in the fecundity and egg diameter between the three hybridization trials. The number of successfully spawned broodstock from BF><BM, BF><SM, and SF><BM were 3, 3, and 2 broodstock, respectively. Meanwhile, the mean values of egg fecundity from BF><BM, BF><SM, and SF><BM were 117, 109, and 151 eggs/g BW, respectively. Furthermore, the mean values of broodstock fecundity per crab were 7,797 eggs, 10,103 eggs, and 10,605 eggs, while the mean values of egg diameter were 0.58 mm, 0.57 mm, and 0.62 mm, respectively. In conclusion, the intraspecific hybridization was successfully carried out between the Barru and Sorong crab populations showing no differences in the fecundity values and egg diameter between the three crosses. The successful spawning between female crabs from Sorong and male crabs from Barru was higher than that of female crabs from Barru and male crabs from Sorong.

Maternal Behavior in Beef Cattle: The Physiology, Assessment and Future Directions-A Review.

Bovine maternal behavior is known to be influenced by a variety of factors including hormonal mediation, breed, age, parity, host genetics and general management practices. Following centuries of varying levels of domestication processes, the behavior of the bovine cow has altered from that of her original wild ungulate ancestors, although many maternal instincts have remained unchanged. The influence of maternal behavior on calf health and performance is of interest to cow-calf beef production operations, as in most instances, the cow is solely responsible for rearing the calf until weaning. However, investigating the magnitude of this influence is challenging, in part because objective measurement of behavioral traits is difficult, particularly in extensive settings. In recent years, while a number of remote monitoring devices have been developed that afford opportunities for objective measurement of behavioral traits in livestock, characterization of physiological mechanisms that underlie superior maternal behavior, including identification of potential biomarkers remains elusive in cattle. Hormonal profiles during the periparturient period have been shown to influence behavioral patterns in both current and future generations in other mammalian species and may provide insights into the physiology of bovine maternal behavior. Therefore, the aim of this review is to describe general characteristics of bovine maternal behavior and the factors known to influence it, including hormonal drivers, through which cross-reference to other species is made. Current methods of measuring and assessing behavior that may also be applicable to most production settings have also been reviewed. At present, there is no known hormonal assay that can be used to measure and/or reliably predict bovine maternal behavior post-calving or across generations. Being able to objectively assess superior maternal behavior, whether that be through remote monitoring, hormonal profiling or indirectly through measuring calf performance will be beneficial to livestock industries in the future.

Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).

Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families' turnover rate (λ). Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (λ = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.

Utopian methodology: Researching educational interventions to promote equity over multiple timescales

ABSTRACT Background This article explores the methodological foundations for a utopian methodology as a form of Design-Based Intervention Research (DBR) that can guide the process of envisioning, implementing, sustaining, and critically evaluating the more radical forms of educational activity systems that prefigure the utopian goal of an equitable and humane education system. Methods We examine, guided by a utopian methodology lens, the examples from three national traditions for designing and implementing equitable educational activities. Each illuminates critical phases in the process of conducting DBR, combining social theory and cultural-historical activity theory. Findings We propose methodological principles for a utopian methodology as a form of DBR: a) Some conditions for sustaining and re-generating the utopian goal should be explicitly considered; b) Examine the recurring challenges to viability and achievability of the utopian design in its learning ecology that emerge for observation over multiple times scales; c) Self-critique and collaborative re-design for a new iteration. Contribution Taken as an ensemble, the cases analyzed here illustrate the broad usefulness of the utopian methodology that we propose in order to maintain the light of the utopian goal and challenge domestication process embedded in any process of change and transformation of the status quo.

Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat.

Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.

Changes in microbial community structure and co-metabolism during the domestication of ofloxacin-degrading bacteria

BackgroundOfloxacin (OFL) is stable and difficult to degrade. It has been detected in water, soil, and plants throughout the world. This study domesticated OFL-contaminated livestock manure soil with simplified carbon sources to identify flora capable of effectively degrading OFL. The changes in the structural composition and diversity of the microbial community and the functional abundance of the soil flora were analyzed by metagenome sequencing technology. The Biolog-ECO microplate method was used to study the utilization of 31 different carbon sources by selected bacteria and to identify the best co-metabolized carbon source for degradation.ResultsAmino acid carbon sources were more likely to cause significant changes in community structures with increasing OFL concentrations during the acclimation stage. The abundance of Sphingobacterium decreased from 69.23% to 9.84%, while Alcaligenes increased from 0.27% to 62.79%, and Stenotrophomonas increased from 11.63% to 33.33%, becoming the dominant genus. The results suggested that Stenotrophomonas and Alcaligenes were potential candidate bacteria for the degradation of quinolone antibiotics, such as OFL. Compared with the first stage of acclimation, there was an 87% increase (the concentration was 30 mg·L−1) in the OFL degradation rate by functional flora obtained by gradient acclimation, and the functional abundance of the microbial community also increased and stabilized with the depth of the domestication process. The most significant changes in membrane transport were observed in the functional abundance of the microbial community, and it was found that itaconic acid, Tween 80, and L-aspartic acid could increase the biomass of the microbial community under OFL stress.ConclusionSignificant changes in the bacterial composition and functional abundance of the microbial community resulted from the addition of amino acid carbon sources, together with the OFL concentration. Functional flora resulting from domestication were better able to degrade OFL. The addition of a co-metabolic carbon source significantly enhanced the biomass of the functional flora. In this study, co-metabolism was performed by adding specific carbon sources, thus achieving metabolic diversity of functional flora and ultimately efficient biodegradation of OFL. This was an important discovery in the field of microbial remediation of environmental contamination.

One- and Two-Month-Old Dog Puppies Exhibit Behavioural Synchronization with Humans Independently of Familiarity

Behavioural synchronization is a widespread skill in social species as it helps increase group cohesion among individuals. Such a phenomenon is involved in social interactions between conspecifics as well as between individuals from different species. Most importantly, familiarity and affiliation between interacting partners influence the degree of behavioural synchronization they would exhibit with each other. For example, in human-dog dyads, the more a dog is affiliated with its human partner, the more it behaves in a synchronous way with them. However, little is known about the ontogeny of such a behaviour, especially from an interspecific perspective. The aim of the present study was thus to investigate the existence and modalities of activity synchrony, a type of behavioural synchronization, between humans and puppies. To do so, we observed 29 dog puppies interacting with two different humans (familiar and unfamiliar experimenters). Puppy movements and general activity in relation to the human ones were observed. Results evidenced that puppies did exhibit locomotor synchrony with humans, but familiarity did not affect its degree. It is the first time that activity synchrony with human walk is evidenced in puppies, highly suggesting that dogs' ability to behave in synchronization with humans seems to be genetically selected through the process of domestication, while the effect of familiarity on it might develop later during the individual ontogeny.

Comparative metabolic analysis of the adaptive Candida tropicalis to furfural stress response

The novel tolerant strain Candida tropicalis Y31-N (Y31-N) with the high tolerance against furfural was obtained by the continuous domestication processes from the parent strain Candida tropicalis Y-3 (Y-3). The xylitol yield was increased by more than 84.8% with the Y31-N, as well as the furfural consumption at about five-times rate than the Y-3. The Y31-N was able to control the cells membrane fluidity by regulating the composition of the fatty acids in cells, thus maintaining the integrity of cells membrane function to resist furfural stress, and could produce more ATP and NAD(P)H rapidly through the metabolic rearrangement to alleviate the furfural stress, compared to the Y-3. Moreover, several genes related to trehalose synthesis, GABA metabolism and NADPH production were verified to be essential for resistance to furfural by single-gene knockout. It provided a broader understanding of the mechanisms of furfural tolerance and prospective evidence for the further metabolic engineering.

Halloween and Valentine’s Day in Slovakia: new holidays or new opportunities for celebration?

This study deals with Halloween and Valentine’s Day in Slovakia from the perspective of the eventisation theory elaborated on by Winfried Gebhardt (2000), which reflects on internal as well as external changes in the field of holidays in modern societies and seeks to elucidate the cultural dimension of the processes of individualisation and pluralisation during the late-modernity period. The authors explore these two holidays as global phenomena with a focus on their holiday practice, i.e. on the ways of celebrating and spending holidays. At the same time, they analyse the historical and social processes related to the transformations of Europe’s and Slovakia’s holiday culture since the end of the 20th century. On this basis, they present research materials that clarify these processes of domestication as well as the ways of celebrating Halloween and Valentine’s Day in Slovakia. The empirical data form the basis for formulating findings on the ways of spending these two “new” holidays and their relationship to the process of eventisation of the holiday culture.

Variations in genetic diversity in cultivated Pistacia chinensis.

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

IDENTIFIKASI FITOPLANKTON PADA PERUT IKAN SELINCAH (Belontia hasselti) DARI RAWA MENTUKUL DI KABUPATEN BANGKA SELATAN

The Selincah fish (Belontia hasselti) is a local Indonesian fish that is widely consumed and has the potential to become ornamental fish. This fish must be domesticated to suppress its exploitation from natural catches. The domestication process requires biological information including eating habits. For this reason, in this study, the identification of phytoplankton contained in the stomach contents of the agile fish was carried out. Fish samples were obtained from Rawa Metukul, South Bangka Regency. The types of phytoplankton in the stomach and intestines of lively fish are the classes Bacillariophyceae, Chlorophyceae, Cyanophyceae, Chlorophyceae, Chrysophyceae, Chrysophyceae. The most dominant species were found in the Chlorophyceae class with an Index of preponderance value of 42.42%, while the Chrystophyceae class was found at least 2.99%.

Comparing Pears to Apples: Unlike Dogs, Cats Need Habituation before Lab Tests.

Research on the socio-cognitive skills of different species often benefit from comparative experiments, however, the ecology of the species and development of the individuals may differently determine how they react to the same test situation. In this study, our aims were twofold: to observe and compare the spontaneous behaviour of companion cats and dogs in the same novel environment, and to habituate them (if needed) to the novel environment in the presence of their owners and an unfamiliar experimenter. The behaviour of 62 family cats, 31 experienced (which had the opportunity to meet strangers and explore unfamiliar places) and 31 inexperienced cats, and 27 family dogs was compared in an unfamiliar room. The subjects' behaviour was coded during the first five minutes in the presence of two passive persons, their owners, and an unfamiliar experimenter. Then, based on a set of rules, first the owner, and then the experimenter tried to initiate interactions with the subjects and the subjects' willingness to interact was evaluated. To pass the habituation test, subjects were expected to play with the experimenter or accept food from them. All dogs passed the test on the first occasion, while almost 60% of the cats failed. The cats' experience did not play a significant role, in fact, younger cats passed more easily. We found marked differences between dogs and cats in all behavioural variables; compared to dogs, cats spent more time crouching and close to their box, while less time exploring or close to the owner. We did not find a difference in the cats' behaviour based on their experience. Our results support the hypothesis that unlike dogs, cats need extensive habituation in a novel environment. This could partially be explained by the difference in the ecology and/or domestication process of the species, although developmental effects cannot be excluded. Our findings have fundamental consequences not only for the considerations of the testability of cats and on the interpretation of their data collected in the laboratory, but in a more general sense on developing comparative experiments.

Breeding toward improved ecological plant-microbiome interactions.

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Genetic introgression between different groups reveals the differential process of Asian cultivated rice

The Asian cultivated rice consists of two major subspecies: indica and japonica. There are already many reports about the existence of genetic introgression between the two subspecies. They propose some possible introgression-related genes from the comparison of population parameters. This study uses the genome-wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica populations. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions, they generally get consistent results. Some previously known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays a vital role in the determination of both the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and the domestication process.