Ecological Genomics for the Conservation of Dwarf Birch

PhDThe persistence of woody plant populations faces numerous environmental challenges, including climate change, hybridisation and population fragmentation. Here I explore the genomic signatures and relative importance of these pressures in Dwarf Birch (Betula nana), which has declined significantly over the last century across the Scottish Highlands. Firstly, I find that future climate is likely to result in a significant range reduction and that relict populations are likely to display reduced fitness. Secondly, I show that combining multiple mutation rate markers yields more accurate estimates of demographic history and the impact of fragmentation. I develop a novel method to derive high mutation rate markers from short sequencing reads, to facilitate more widespread application. Thirdly, I assess the degree of local adaptation, and explore potential for composite provenancing for the restoration of B. nana populations. Surprisingly, the data yields little evidence of adaptive introgression from the related tree B. pubescens, suggesting that this may not be an alternative route to climate tolerance. Finally, I review published literature on the population structure and genetic diversity of genus Betula in Europe and consider options for the conservation and management of B. nana, including assisted gene flow and prioritization of in situ genetic diversity.NERC CASE studentship NE/J017388/

Enset‐based agricultural systems in Ethiopia: A systematic review of production trends, agronomy, processing and the wider food security applications of a neglected banana relative

Enset (Ensete ventricosum (Welw.) Cheesman) is the major starch staple of the Ethiopian Highlands, where its unique attributes enhance the food security of approximately 20 million people and have earned it the title “The Tree Against Hunger”. Yet enset‐based agriculture is virtually unknown outside of its narrow zone of cultivation, despite growing wild across much of East and Southern Africa. Here, we review historical production data to show that the area of land under enset production in Ethiopia has reportedly increased 46% in two decades, whilst yield increased 12‐fold over the same period, making enset the second most produced crop species in Ethiopia—though we critically evaluate potential issues with these data. Furthermore, we address a major challenge in the development and wider cultivation of enset, by reviewing and synthesizing the complex and fragmented agronomic and ethnobotanic knowledge associated with this species; including farming systems, processing methods, products, medicinal uses and cultural importance. Finally, we provide a framework to improve the quality, consistency and comparability of data collected across culturally diverse enset‐based agricultural systems to enhanced sustainable use of this neglected starch staple. In conclusion, we discuss the challenges and opportunities for enset cultivation beyond its restricted distribution, and the regional food security potential it could afford smallholders elsewhere in Southern and East Africa

Measure of indigenous perennial staple crop, Ensete ventricosum, associated with positive food security outcomes in southern Ethiopian highlands

Enset-based food systems are unique to southern Ethiopia where they serve as a staple food for millions of households. Enset, a banana relative of which the entire pseudostem and corm are edible, possesses a highly unusual combination of crop traits including perenniality, highly flexible planting and harvest times, and tolerance of a very wide range of environmental conditions, which together earn it the local name of “the tree against hunger.” Previous studies have identified the strategic food security value of mature enset stands for household food security, but a multisector panel data set makes identifying wider enset food security associations tractable for the first time. We assess whether household data on area of mature enset is associated with four indicators of food security together with demographic, asset, and consumption covariates. We find that area of mature enset significantly improves estimates for three of four food security indicators, thus improving our understanding of the role of understudied indigenous crops. Consistent and reliable food security indicators are needed to improve monitoring, particularly with regard to stability. Variance components of multilevel longitudinal models indicate that exposure to both idiosyncratic and covariate disturbance affects food security stability in a way that is consistent with reports of enset acting as both a food security buffer and an active adaptation strategy in the face of shocks or change. Here we show that living assets comprising culturally relevant indigenous crops such as enset can improve accuracy of food insecurity assessments, which may encourage wider investigation of other agrifood system-specific asset-like natural stores of value associated with food security and resilience

Smallholder farmers expand production area of the perennial crop enset as a climate coping strategy in a drought‐prone indigenous agrisystem

Societal Impact Statement Climate resilient crops will become increasingly important, especially in regions where smallholder farmers are vulnerable to climate extremes. Enset, a multipurpose perennial staple crop consumed by over 20 million people in Ethiopia, purportedly provides food security during periods of drought. Here, we find evidence that frequent severe drought events led to an increase in enset production area. This is consistent with a broader pattern whereby farmers preferentially cultivate perennial and storable crops after long-term drought events, providing an example of adaptation to fluctuations in climate through crop choice in indigenous agrisystems. Summary Smallholder farms in the semiarid and subhumid tropics are particularly vulnerable to increased climate variability. Indigenous agrisystems that have co-evolved with climate variability may have developed resilience strategies. In the Southwest Ethiopian Highlands, agrisystems are dominated by the multipurpose perennial staple enset (Ensete ventricosum), characterised by flexible harvest timing, high yield, long storage, and putative drought tolerance, earning it the name ‘the tree against hunger’. We tested three hypotheses using crop production area and climate data. First, that enset production area is greatest in the most drought-prone locations. Second, that farmers respond to drought events by increasing enset production area. And third, that drought encourages shifts in agrisystem composition more widely towards perennial or storable crops. We found that regions with a higher severe drought frequency are associated with significantly higher proportion of enset production. Similarly, the Standardised Precipitation Evapotranspiration Index of the previous 3 years is significantly negatively correlated with enset production area time series, suggesting that prior drier conditions led farmers to increase the land under enset production. Regarding other crops, storage crops roots and tubers were also preferentially selected after long-term drought over annual crops, indicating their capacity for longer-term resilience. Promoting the production of crops such as perennials, which have more extensive and established root systems, may be a strategy to ensure food security during drought or climate variability. These results indicate the potential of farmer's resilience strategies to improve food security in a changing climate

Maintenance and expansion of genetic and trait variation following domestication in a clonal crop

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability

Toward unifying global hotspots of wild and domesticated biodiversity

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives.We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species onWikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people

Indigenous crop diversity maintained despite the introduction of major global crops in an African centre of agrobiodiversity

Societal Impact Statement The global success and expansion of a small pool of major crops, including rice, wheat and maize, risks homogenising global agriculture. Focusing on the agriculturally diverse Ethiopian Highlands, this study tested whether farm diversity tends to be lower among farmers who grow more introduced crops. Surprisingly, it was found that farmers have successfully integrated introduced crops, resulting in more diverse and heterogenous farms without negatively impacting indigenous crop diversity. This is encouraging because diverse farms, comprising indigenous agricultural systems supplemented by introduced crops, may help address global challenges such as food insecurity. Summary The global expansion of a handful of major crops risks eroding indigenous crop diversity and homogenising agroecosystems, with significant consequences for sustainable and resilient food systems. Here, we investigate the farm-scale impact of introduced crops on indigenous agroecosystems. We surveyed 1369 subsistence farms stratified across climate gradients in the Ethiopian Highlands, a hotspot of agrobiodiversity, to characterise the richness and cultivated area of the 83 edible crops they contained. We further categorise these crops as being indigenous to Ethiopia, or introduced across three different eras. We apply non-metric multidimensional scaling and mixed effects modelling to characterise agroecosystem composition across farms with different proportions of introduced crops. Crops from different periods do not differ significantly in frequency or abundance across farms. Among geographically matched pairs of farms, those with higher proportions of modern introduced crops had significantly higher overall crop richness. Furthermore, farms with a high proportion of modern introduced crops showed higher heterogeneity in crop composition. An analysis of socio-economic drivers indicated that poverty is negatively associated with the cultivated area of introduced crops. In our Ethiopian case study, global patterns of major crop expansion are not necessarily associated with agrobiodiversity loss at the farm scale or higher homogeneity across indigenous agricultural systems. Importantly, socioeconomic factors may influence farmers' propensity to adopt novel species, suggesting targets for agricultural extension policies. Given the rapid climatic, economic and demographic changes impacting global food systems and the threats to food security these entail, robust indigenous agricultural systems enriched with diverse introduced crops may help maintain resilience

Explanatory pluralism in the medical sciences: theory and practice

Explanatory pluralism is the view that the best form and level of explanation depends on the kind of question one seeks to answer by the explanation, and that in order to answer all questions in the best way possible, we need more than one form and level of explanation. In the first part of this article, we argue that explanatory pluralism holds for the medical sciences, at least in theory. However, in the second part of the article we show that medical research and practice is actually not fully and truly explanatory pluralist yet. Although the literature demonstrates a slowly growing interest in non-reductive explanations in medicine, the dominant approach in medicine is still methodologically reductionist. This implies that non-reductive explanations often do not get the attention they deserve. We argue that the field of medicine could benefit greatly by reconsidering its reductive tendencies and becoming fully and truly explanatory pluralist. Nonetheless, trying to achieve the right balance in the search for and application of reductive and non-reductive explanations will in any case be a difficult exercise

Perceived Discrimination and Health Outcomes Among Asian Indians in the United States

Background: Perceived interpersonal discrimination while seeking healthcare services is associated with poor physical and mental health. Yet, there is a paucity of research among Asian Americans or its subgroups. This study examined the correlates of reported interpersonal discrimination when seeking health care among a large sample of Asian Indians, the 3rd largest Asian American subgroup in the US, and identify predictors of adverse self-rated physical health, a well-accepted measure of overall health status. Methods: Cross-sectional survey. Participants comprised of 1824 Asian Indian adults in six states with higher concentration of Asian Indians. Results: Mean age and years lived in the US was 45.7 ± 12.8 and 16.6 ± 11.1 years respectively. The majority of the respondents was male, immigrants, college graduates, and had access to care. Perceived interpersonal discrimination when seeking health care was reported by a relatively small proportion of the population (7.2 %). However, Asian Indians who reported poor self-rated health were approximately twice as likely to perceived discrimination when seeking care as compared to those in good or excellent health status (OR 1.88; 95 % CI 1.12–3. 14). Poor self-rated health was associated with perceived health care discrimination after controlling for all of the respondent characteristics (OR 1.93; 95 % CI: 1.17–3.19). In addition, Asian Indians who lived for more than 10 years in the U.S. (OR 3.28; 95 % CI: 1.73–6.22) and had chronic illnesses (OR 1.39; 95 % CI: 1.17–1.64) (p \u3c 0.05) were more likely to perceive discrimination when seeking health care. However, older Asian Indians, over the age of 55 years, were less likely to perceive discrimination than those aged 18–34 years Indian American. Conclusion: Results offers initial support for the hypothesis that Asian Indians experience interpersonal discrimination when seeking health care services and that these experiences may be related to poor self-rated health status