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

The Inexorable Spread of a Newly Arisen Neo-Y Chromosome

A newly arisen Y-chromosome can become established in one part of a species range by genetic drift or through the effects of selection on sexually antagonistic alleles. However, it is difficult to explain why it should then spread throughout the species range after this initial episode. As it spreads into new populations, it will actually enter females. It would then be expected to perform poorly since it will have been shaped by the selective regime of the male-only environment from which it came. We address this problem using computer models of hybrid zone dynamics where a neo-XY chromosomal race meets the ancestral karyotype. Our models consider that the neo-Y was established by the fusion of an autosome with the ancestral X-chromosome (thereby creating the Y and the ‘fused X’). Our principal finding is that sexually antagonistic effects of the Y induce indirect selection in favour of the fused X-chromosomes, causing their spread. The Y-chromosome can then spread, protected behind the advancing shield of the fused X distribution. This mode of spread provides a robust explanation of how newly arisen Y-chromosomes can spread. A Y-chromosome would be expected to accumulate mutations that would cause it to be selected against when it is a rare newly arrived migrant. The Y can spread, nevertheless, because of the indirect selection induced by gene flow (which can only be observed in models comprising multiple populations). These results suggest a fundamental re-evaluation of sex-chromosome hybrid zones. The well-understood evolutionary events that initiate the Y-chromosome's degeneration will actually fuel its range expansion

Unraveling Genetic Diversity Amongst European Hazelnut (Corylus avellana L.) Varieties in Turkey

European hazelnut (Corylus avellana) is a diploid (2n = 22), monecious and wind-pollinated species, extensively cultivated for its nuts. Turkey is the world-leading producer of hazelnut, supplying 70–80% of the world’s export capacity. Hazelnut is mostly grown in the Black Sea Region, and maintained largely through clonal propagation. Understanding the genetic variation between hazelnut varieties, and defining variety-specific and disease resistance-associated alleles, would facilitate hazelnut breeding in Turkey. Widely grown varieties ‘Karafındık’ (2), ‘Sarıfındık’ (5), and ‘Yomra’ (2) were collected from Akçakoca in the west, while ‘Tombul’ (8), ‘Çakıldak’ (3), ‘Mincane’ (2), ‘Allahverdi’ (2), ‘Sivri’ (4), and ‘Palaz’ (5) were collected from Ordu and Giresun provinces in the east (numbers in parentheses indicate sample sizes for each variety). Powdery mildew resistant and susceptible hazelnut genotypes were collected from the field gene bank and heavily infected orchards in Giresun. Every individual was subjected to double digest restriction enzyme-associated DNA sequencing (ddRAD-seq) and a RADtag library was created. RADtags were aligned to the ‘Tombul’ reference genome, and Stacks software used to identify polymorphisms. 101 private and six common alleles from nine hazelnut varieties, four private from resistants and only one from susceptible were identified for diagnosis of either a certain hazelnut variety or powdery mildew resistance. Phylogenetic analysis and population structure calculations indicated that ‘Mincane’, ‘Sarıfındık’, ‘Tombul’, ‘Çakıldak’, and ‘Palaz’ were genetically close to each other; however, individuals within every varietal group were found in different sub-populations. Our findings indicated that years of clonal propagation of some preferred varieties across the Black Sea Region has resulted in admixed sub-populations and great genetic diversity within each variety. This impedes the development of a true breeding variety. For example, ‘Tombul’ is the most favored Turkish variety because of its high quality nuts, but an elite ‘Tombul’ line does not yet exist. This situation continues due to the lack of a breed protection program for commercially valuable hazelnut varieties. This study provides molecular markers suitable for establishing such a program

Repeated long-distance dispersal and convergent evolution in hazel

Closely related species with a worldwide distribution provide an opportunity to understand evolutionary and biogeographic processes at a global scale. Hazel (Corylus) is an economically important genus of tree and shrub species found in temperate regions of Asia, North America and Europe. Here we use multiple nuclear and chloroplast loci to estimate a time-calibrated phylogenetic tree of the genus Corylus. We model the biogeographic history of this group and the evolutionary history of tree and shrub form. We estimate that multiple Corylus lineages dispersed long distances between Europe and Asia and colonised North America from Asia in multiple independent events. The geographic distribution of tree versus shrub form of species appears to be the result of 4–5 instances of convergent evolution in the past 25 million years. We find extensive discordance between our nuclear and chloroplast trees and potential evidence for chloroplast capture in species with overlapping ranges, suggestive of past introgression. The important crop species C. avellana is estimated to be closely related to C. maxima, C. heterophylla var. thunbergii and the Colurnae subsection. Our study provides a new phylogenetic hypothesis or Corylus and reveals how long-distance dispersal can shape the distribution of biodiversity in temperate plants

Data from: Molecular footprints of the Holocene retreat of dwarf birch in Britain

Past reproductive interactions among incompletely isolated species may leave behind a trail of introgressed alleles, shedding light on historical range movements. Betula pubescens is a widespread native tetraploid tree species in Britain, occupying habitats intermediate to those of its native diploid relatives, B. pendula and B. nana. Genotyping 1134 trees from the three species at 12 microsatellite loci we found evidence of introgression from both diploid species into B. pubescens, despite the ploidy difference. Surprisingly, introgression from B. nana, a dwarf species whose present range is highly restricted in northern, high-altitude peat bogs, was greater than introgression from B. pendula, which is morphologically similar to B. pubescens and has a substantially overlapping range. A cline of introgression from B. nana was found extending into B. pubescens populations far to the south of the current B. nana range. We suggest that this genetic pattern is a footprint of a historical decline and/or northwards shift in the range of B. nana populations due to climate warming in the Holocene. This is consistent with pollen records that show a broader, more southerly distribution of B. nana in the past. Ecological niche modelling predicts that B. nana is adapted to a larger range than it currently occupies, suggesting additional factors such as grazing and hybridisation may have exacerbated its decline. We found very little introgression between B. nana and B. pendula, despite both being diploid, perhaps because their distributions in the past have rarely overlapped. Future conservation of B. nana may partly depend on minimisation of hybridisation with B. pubescens, and avoidance of planting B. pendula near B. nana populations