Evidence for Hitchhiking of Deleterious Mutations within the Human Genome

Deleterious mutations present a significant obstacle to adaptive evolution. Deleterious mutations can inhibit the spread of linked adaptive mutations through a population; conversely, adaptive substitutions can increase the frequency of linked deleterious mutations and even result in their fixation. To assess the impact of adaptive mutations on linked deleterious mutations, we examined the distribution of deleterious and neutral amino acid polymorphism in the human genome. Within genomic regions that show evidence of recent hitchhiking, we find fewer neutral but a similar number of deleterious SNPs compared to other genomic regions. The higher ratio of deleterious to neutral SNPs is consistent with simulated hitchhiking events and implies that positive selection eliminates some deleterious alleles and increases the frequency of others. The distribution of disease-associated alleles is also altered in hitchhiking regions. Disease alleles within hitchhiking regions have been associated with auto-immune disorders, metabolic diseases, cancers, and mental disorders. Our results suggest that positive selection has had a significant impact on deleterious polymorphism and may be partly responsible for the high frequency of certain human disease alleles

Migration, environmental change and agrarian transition in upland regions: learning from Ethiopia, Kenya and Nepal

This paper analyses the relationship between cyclical labour migration and agrarian transition in the uplands of Nepal, Ethiopia and Kenya. It shows that while migration decision-making is linked to expanding capitalist markets, it is mediated by local cultural, political and ecological changes. In turn, cyclical migration goes on to shape the trajectory of change within agriculture. The dual dependence on both migrant income and agriculture within these upland communities often translates into an intensifying work burden on the land, and rising profits for capitalism. However, on some occasions this income can support increased productivity and accumulation within agriculture – although this depends on both the agro-ecological context and the local agrarian structure

Development of a Soil Organic Carbon Baseline for Otjozondjupa, Namibia

Land Degradation Neutrality (LDN) has been piloted in 14 countries and will be scaled up to over 120 countries. As a LDN pilot country, Namibia developed sub-national LDN baselines in Otjozondjupa Region. In addition to the three LDN indicators (soil organic carbon, land productivity and land cover change), Namibia also regards bush encroachment as an important form of land degradation. We collected 219 soil profiles and used Random Forest modelling to develop the soil organic carbon stock baseline. Values range between 0.53 and 4.27 kg/m2 in the sandy Otjozondjupa soils. LDN baselines were integrated into other national planning processes to add value to LDN products. Analyses of the relationship between soil carbon and land cover change, especially from grassland to bushland, increased the usefulness of soil carbon maps for the Integrated Regional Land Use Planning process. Local ownership of LDN baseline development, from data collection to digital soil mapping, was crucial for local stakeholders

Exploring the concept of agroecological food systems in a city-region context

Based on urgent needs for food security compounded by a changing climate which impacts and is impacted by agricultural land-use and food distribution practices, we explore the processes of action in implementing agroecological food systems. We identified the following characteristics for an agroecological food system: 1. Minimizing use of external inputs, 2. Extent of internal resource recycling, 3. Resilience, 4. Multifunctionality, 5. Building on complexity and incorporating greater systems integration, 6. Contextuality, 7. Equity and, 8. Nourishment. We focus on the city-region food systems context, concluding with practical drivers for realizing more agroecological food systems in city-region contexts. Agroecological food systems are widely diverse, shaped by context, and achieved through multi-actor planning in rural, peri-urban and urban areas. Application of agroecological food systems in rural–urban contexts emphasize the necessity of diversification, zoning rural–urban landscapes, planning for seasonality in a food systems context, and producing at scale. Rural–urban food systems are a relevant and challenging entry point that provides opportunities for learning how food systems can be shaped for significant positive change. Social organization, community building, common learning, and knowledge creation are crucial for agroecological contextualized food systems, as are the supports from appropriate governing and institutional structures

Assessing the Impact of 10 years of FTA Research: a synthesis of the 5 integrated impact studies

In 2021, the CGIAR Research Program on Forests, Trees and Agroforestry (FTA) completed a set of studies, under the guidance and oversight of its Independent Steering Committee (ISC), to document its progress in addressing five key global challenges. These studies had the following purposes: (i) to design a workable approach and operational method to assess impacts at scale at the level of the FTA program, since 2011; (ii) to deploy the method effectively on a set of five identified development challenges addressed by FTA; (iii) to learn lessons from the exercise for FTA post 2021. This document provides a synthesis of the five studies and draws lessons and recommendations for research for development programs

A parthenogenesis allele from apomictic dandelion can induce egg cell division without fertilization in lettuce

Apomixis, the clonal formation of seeds, is a rare yet widely distributed trait in flowering plants. We have isolated the parthenogenesis (PAR) gene from apomictic dandelion that triggers embryo development in unfertilized egg cells. PAR encodes a K2-2 zinc finger, EAR-domain protein. Unlike the recessive sexual alleles, the dominant PAR allele is expressed in egg cells and has a miniature inverted-repeat transposable element (MITE) transposon insertion in the promoter. The MITE-containing promoter can invoke a homologous gene from sexual lettuce to complement dandelion LOSS OF parthenogenesis mutants. A similar MITE is also present in the promoter of the PAR gene in apomictic forms of hawkweed, suggesting a case of parallel evolution. Heterologous expression of dandelion PAR in lettuce egg cells induced haploid embryo-like structures in the absence of fertilization. Sexual PAR alleles are expressed in pollen, suggesting that the gene product releases a block on embryogenesis after fertilization in sexual species while in apomictic species PAR expression triggers embryogenesis in the absence of fertilization

Characterisation of four novel fibrillin-1 (FBN1) mutations in Marfan syndrome.

Forty-four percent of the fibrillin-1 gene (FBN1) from 19 unrelated families with Marfan syndrome was screened for putative mutations by single strand conformational polymorphism (SSCP) analysis. Four novel mutations were identified and characterised in five people, three with classical Marfan syndrome (two from one family, and one from an unrelated family), one with a more severe phenotype, and one with neonatal Marfan syndrome. The base substitutions G2113A, G2132A, T3163G, and G3458A result in amino acid substitutions A705T, C711Y, C1055G, and C1152Y, respectively. C711Y, C1055G, and C1152Y lead to replacement of a cysteine by another amino acid; the latter two occur within epidermal growth factor-like motifs in exon 25 and 27, respectively. The A705T mutation occurs at exon 16 adjacent to the GT splice site. The A705T and C711Y mutations, at exon 16 and 17, respectively, are the first documented in the second transforming growth factor-beta 1 binding protein-like motif of FBN1