New Genes Originated via Multiple Recombinational Pathways in the β-Globin Gene Family of Rodents

Species differences in the size or membership composition of multigene families can be attributed to lineage-specific additions of new genes via duplication, losses of genes via deletion or inactivation, and the creation of chimeric genes via domain shuffling or gene fusion. In principle, it should be possible to infer the recombinational pathways responsible for each of these different types of genomic change by conducting detailed comparative analyses of genomic sequence data. Here, we report an attempt to unravel the complex evolutionary history of the β-globin gene family in a taxonomically diverse set of rodent species. The main objectives were: 1) to characterize the genomic structure of the β-globin gene cluster of rodents; 2) to assign orthologous and paralogous relationships among duplicate copies of β-like globin genes; and 3) to infer the specific recombinational pathways responsible for gene duplications, gene deletions, and the creation of chimeric fusion genes. Results of our comparative genomic analyses revealed that variation in gene family size among rodent species is mainly attributable to the differential gain and loss of later expressed β-globin genes via unequal crossing-over. However, two distinct recombinational mechanisms were implicated in the creation of chimeric fusion genes. In muroid rodents, a chimeric γ/ε fusion gene was created by unequal crossing-over between the embryonic ε- and γ-globin genes. Interestingly, this γ/ε fusion gene was generated in the same fashion as the “anti-Lepore” 5’-δ-(β/δ)-β-3’ duplication mutant in humans (the reciprocal exchange product of the pathological hemoglobin Lepore deletion mutant). By contrast, in the house mouse, Mus musculus, a chimeric β/δ fusion pseudogene was created by a β-globin → δ-globin gene conversion event. Although the γ/ε and β/δ fusion genes share a similar chimeric gene structure, they originated via completely different recombinational pathways

Molecular evolution of cytochrome \u3ci\u3eb\u3c/i\u3e in high- and low-altitude deer mice (genus \u3ci\u3ePeromyscus\u3c/i\u3e)

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates to test for evidence of divergent selection between high- and low-altitude haplogroups of the deer mouse, Peromyscus maniculatus. We also tested for evidence of divergent selection among different species of Peromyscus that inhabit different thermal environments. In contrast to the purported evidence for positive selection on mitochondrial proteins in humans and other nonhuman mammals, results of our tests suggest that the evolution of cytochrome b in Peromyscus is chiefly governed by purifying selection

Molecular evolution of cytochrome \u3ci\u3eb\u3c/i\u3e in high- and low-altitude deer mice (genus \u3ci\u3ePeromyscus\u3c/i\u3e)

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates to test for evidence of divergent selection between high- and low-altitude haplogroups of the deer mouse, Peromyscus maniculatus. We also tested for evidence of divergent selection among different species of Peromyscus that inhabit different thermal environments. In contrast to the purported evidence for positive selection on mitochondrial proteins in humans and other nonhuman mammals, results of our tests suggest that the evolution of cytochrome b in Peromyscus is chiefly governed by purifying selection

Birnbaum-Saunders spatial modelling and diagnostics applied to agricultural engineering data

Applications of statistical models to describe spatial dependence in geo-referenced data are widespread across many disciplines including the environmental sciences. Most of these application assume that the data follow a Gaussian distributions. However, in many of them the normality assumption, and even a more general assumption of symmetry, are not appropriate. In non-spatial applications, where the data are uni-modal and positively skewed, the Birnbaum-Saunders distribution has excelled. This paper proposes a spatial log-linear model based in the Birnbaum-Saunders distribution. Model parameters are estimated using the maximum likelihood method. Local influence diagnostics are derived to assess the sensitivity of the estimators to perturbations in the response variable. As illustration, the proposed model and its diagnostics are used to analyse a real-world agricultural data-set, where the spatial variability of phosphorus concentration in the soil is considered- which is extremely important for agricultural management

Global value chain breadth and firm productivity:the enhancing effect of Industry 4.0

Purpose: Global value chains (GVC) incorporate internationally fragmented sources of knowledge so as to increase global competitiveness and performance. This paper sheds light on the role of Industry 4.0 technological capabilities in facilitating knowledge access from international linkages and improving firm productivity. Design/methodology/approach: Drawing on organizational learning research, the present study argues that the relationship between GVC breadth, analyzed in respect to the geographical fragmentation of production facilities and productivity follows an inverted U-shaped pattern that can be explained by the interplay between external knowledge access and the coordination costs associated with GVC breadth. We test our predictions using a purpose-built survey that was carried out among a sample of 426 Spanish manufacturing firms. Findings: Our results indicate that organizations adhering to a traditional manufacturing system are able to benefit from fewer transnational relationships (concretely 11 foreign facilities) in the search for productivity improvements. This can be largely attributed to the marginal value of the knowledge accessed and the costs of coordinating international counterparts' production and knowledge transfer. However, our study reveals that the adoption of Industry 4.0 technologies has the potential to broaden optimal GVC breadth, in terms of the number of linkages to interrelate with (concretely 131 foreign facilities) so as to obtain productivity gains while mitigating the complexities associated with coordination. Originality/value: The study unveils that Industry 4.0 technologies enable management of broader GVC breadth, facilitating knowledge access and counteracting coordination costs from international counterparts. \textcopyright 2021, Emerald Publishing Limited

Gas Exchange Relations of Ungrafted Grapevines (cv. Carménère) Growing Under Irrigated Field Conditions

A study was carried out to evaluate the leaf gas exchange relations and water-use efficiency (WUE) of ungrafted Carménère (Vitis vinifera L.) grapevines growing under field conditions and different levels of water stress. Stomatal conductance (gs), transpiration (E), net CO2 assimilation (AN) and stem water potential (Ψs) were measured at midday in a drip-irrigated commercial vineyard located in the Maule Valley (Chile) during three growing seasons (2005 to 2009). In addition, the instantaneous (AN/E) and intrinsic (AN/gs) water-use efficiencies and stomatal sensitivity factor (k) were estimated for the own-rooted grapevines. In this study a significant non-linear relationship was observed between AN and gs (r2 = 0.82), with values of AN decreasing from 14.9 to 3.5 μmol/m2/sec as gs diminished from 0.5 to 0.05 mol/m2/sec. This resulted in a progressive increase in WUEi (intrinsic water use efficiency). A significant linear relationship was observed between Ψs and gs (r2 = 0.39) for measurements taken before and after véraison, with an increasing scattering from -1.6 to -0.4 MPa. Finally, k decreased as water stress increased, with values of 234 and 120 for no and severe water stress respectively, while k ranged from 264 to 480 and 255 to 297 for the measurements taken before and after véraison respectively. Based on the results obtained in the present study, the cultivar Carménère could be classified as drought tolerant at low water potentials, with a large range of physiological parameters changing in response to water stress

Gene Turnover and Diversification of the α- and β- Globin Gene Families in Sauropsid Vertebrates

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here,we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster,which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globingenes that diversified independently in each lineage.These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids