Mark Andrew Chapman

• PhD
• Professor at University of Southampton

Although the evolutionary importance of natural hybridization has been debated for decades, it has become increasingly clear that hybridization plays a fundamental role in the evolution of many plant and animal taxa, sometimes resulting in the formation of entirely new species. Although some hybrid species retain the base chromosome number of their...

In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild...

Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome...

Underutilised crops are important for diversifying food systems. The genomics of these crops should not be done in isolation but should align with their breeding and capacity building strategies while leveraging advances made in major crops.

Lychee (Litchi chinensis) fruits have high nutritional and pharmacological value, yet the crop is underutilized on global markets partly due to cultivation problems outside the native area and lack of knowledge/misidentification of cultivars. Using reduced representation sequencing, 78 trees representing 57 cultivars plus 13 trees without varietal...

Individuals across a species exhibit substantial presence-absence variation, to the extent that a reference genome from a single individual only contains a subset of the species’ genome. Cataloguing genome regions absent from a reference genome can therefore reveal novel genome regions, and some of this variation can be adaptive. In this work, exis...

Populations are continually adapting to their environment. Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increasingly challenging environments predicted for the coming century. Landscape genomics, which identifies associations between environm...

Hunger remains a prevalent issue worldwide, and with a changing climate, it is expected to become an even greater problem that our food systems are not adapted to. There is therefore a need to investigate strategies to fortify our foods and food systems. Underutilized crops are farmed regionally, are often adapted to stresses, including droughts, a...

Pollination is an ecosystem process that is crucial to maintain biodiversity and ecosystem function. Bats are important pollinators in the tropics and are an integral part of complex plant–pollinator interaction networks. However, network analysis–based approaches are still scarce at the plant species and bat community levels. We used metabarcoding...

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop, ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and fertilization. We first produced a chromosome-scale de novo genome assembly of feral ram...

Oceanic archipelagos provide striking examples of lineages that have radiated over pronounced ecological gradients. Accompanying this diversification, lineages have evolved adaptations allowing survival in extreme environments. Here, we investigate the genomic basis of ecological adaptation in Canary Island Descurainia (Brassicaceae), an island rel...

Background Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. Results Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find th...

Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a r...

Common buckwheat (Fagopyrum esculentum Moench) is an ancient crop with a world wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will acc...

Oryza rufipogon is the wild progenitor of cultivated rice O. sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress tolerant varieties and genes that could limit future climate-changed induced yield losses. To investigate local adaptation in O. rufipogon, we...

Rhizoctonia solani is a devastating soil-borne pathogen that seriously threatens the cultivation of economically important crops. Multiple strains with a very broad host range have been identified, but only one (AG1-IA, which causes rice sheath blight disease) has been examined in detail. Here, we analyzed AG4-HGI 3 originally isolated from Tartary...

Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomi...

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or sev...

Underutilised crops suffer from under-investigation relative to more mainstream crops, but often possess improved stress tolerance and/or nutrition, making them potentially important for breeding programmes in the context of climate change and an expanding human population. Developing basic genome resources for underutilised crops may therefore cat...

Premise of the study: Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridisation can play an important role in island evolution. Here we use genotyping-by-sequencing (GBS) to u...

Adaptive genetic diversity in crop wild relatives (CWRs) can be exploited to develop improved crops with higher yield and resilience if phylogenetic relationships between crops and their CWRs are resolved. This further allows accurate quantification of genome-wide introgression and determination of regions of the genome under selection. Using broad...

Jaguars and pumas are top-predator species in the Neotropics that are threatened by habitat destruction, illegal poaching of their body parts and their favored prey, and by the human–wildlife conflicts that arise when predators attack livestock. Much of the remaining felid habitat in the Americas is in protected nature reserves that are too small a...

Lablab (Lablab purpureus (L.) Sweet) is a drought-tolerant legume mainly used as human food and livestock forage, and also as medicinal plant. However, it remains underutilised because of negative attributes, including insect pest susceptibility, anti-nutritional compounds in the seeds, a long growth period and daylength sensitivity in landraces. L...

Identification of adaptive genetic variation in plants is important both for improving our understanding of adaptive evolution, as well as tackling the practical challenge of enhancing and developing crops able to tolerate changes in climate, whilst also meeting the demands of a rapidly growing human population. A potentially lucrative source of ad...

A starting point to understanding more about underutilised and orphan crops is to investigate their genetic diversity and origins. Whilst whole genome analyses will give a wealth of information in this regard, this is often impractical in terms of cost and an overkill in terms of these initial goals. Therefore, molecular markers are used to establi...

H1s, or linker histones, are ubiquitous proteins in eukaryotic cells, consisting of a globular GH1 domain flanked by two unstructured tails. Whilst it is known that numerous non-allelic variants exist within the same species, the degree of interspecific and intraspecific variation and divergence of linker histones remain unknown. The conserved basi...

Microglia, the brain’s resident macrophages, shape neural development and are key neuroimmune hubs in the pathological signatures of neurodevelopmental disorders. Despite the importance of microglia, their development has not been carefully examined in the human brain, and most of our knowledge derives from rodents. We aimed to address this gap in...

Golden buckwheat (Fagopyrum dibotrys or Fagopyrum cymosum) and Tartary buckwheat (Fagopyrum tataricum) belong to the Polygonaceae and the Fagopyrum genus is rich in flavonoids. Golden buckwheat is a wild relative of Tartary buckwheat, yet golden buckwheat is a traditional Chinese herbal medicine and Tartary buckwheat is a food crop. The genetic bas...

This article comments on: Williams O, Vander Schoor JK, Butler JB, Ridge S, Sussmilch FC, Hecht VFG, Weller JL. 2022. The genetic architecture of flowering time changes in pea from wild to crop. Journal of Experimental Botany 73,3978–3990.

Chemical or drug treatments are successfully used to treat parasitic nematode infections that impact human, animal and plant health. Many of these exert their effects through modifying neural function underpinning behaviours essential for parasite viability. Selectivity against the parasite may be achieved through distinct pharmacological propertie...

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-re...

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-re...

Underutilized crops are, by definition, under‐researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress‐tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by...

Unravelling the history of range shifts is key for understanding past, current and future species distributions. Anthropogenic transport of species alters natural dispersal patterns and directly affects population connectivity. Studies have suggested that high levels of anthropogenic transport homogenize patterns of genetic differentiation and blur...

Microglia, the brain's resident macrophages, shape neural development and wiring, and are key neuroimmune hubs in the pathological signature of neurodevelopmental disorders. In the human brain, microglial development has not been carefully examined yet, and most of our knowledge derives from rodents. We established an unprecedented collection of 97...

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A ‘bottom up’ population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication....

Phylogenetic analysis has revealed that Argyranthemum broussonetii is polyphyletic, with subsp. broussonetii (Tenerife) and subsp. gomerensis (La Gomera) resolved in separate clades within the Macaronesian endemic genus Argyranthemum. We show that A. broussonetii subsp. broussonetii and subsp. gomerensis are similar in leaf traits, likely a consequ...

Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genet...

The sub-alpine zones of oceanic islands are unique and dynamic ecosystems with high levels of endemism, making them particularly suitable model systems in which to investigate evolutionary and biogeographic processes. The sub-alpine flora of the Canary Islands is restricted to the islands of Tenerife and La Palma. Its origins are poorly understood....

The high usage of castor oil in industrial applications and bio-diesel production has led to an increase in castor bean (Ricinus communis L.) cultivation in many countries. Wild species present a source of genetic variation for germplasm improvement, often important because of their adaptation to a wide range of habitats and stresses. Chloroplast g...

Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation. We employed...

Societal awareness of healthy eating is increasing alongside the market for processed bagged salads, which remain as one of the strongest growing food sectors internationally, including most recently from indoor growing systems. Lettuce represents a significant proportion of this ready-to-eat salad market. However, such products typically have a sh...

Unravelling plant responses to rising atmospheric CO2 concentration ([CO2 ]) has largely focussed on plastic functional attributes to single generation [CO2 ] exposure. Quantifying the consequences of long-term, decadal multigenerational exposure to elevated [CO2 ] and the genetic changes that may underpin evolutionary mechanisms with [CO2 ] as a d...

Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular g...

The Asian eggplant, Solanum melongena (also known as aubergine or brinjal), is a widely grown and economically important crop, especially in South and Southeast Asia and the Mediterranean. A large amount of morphological diversity is present in eggplant, suggesting that genetic variation is high; however, limited work has been carried out on traits...

The utilization of most legumes for human consumption in the present day is low relative to cereal crops. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is a valuable legume due to the presence of soybean-equivalent nutrients. Early work identified that winged bean has favorable agronomic features suitable for cultivation in the tropics with hi...

Bats pollinate many plants of high socio‐economic value, including the majority of columnar cacti (Cactaceae) in Mexico, which have been used by humans for food and materials for thousands of years. However, the importance of bats as pollinators has been overlooked, with a consequent lack of knowledge of the reliance of crops on bats for harvest yi...

PREMISE: Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discov...

Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication...

In this summary, I bring together the work detailed in this volume, highlight the research directions currently being traversed and combine this with examples from other Solanaceous crops to suggest where the future of eggplant research could take us. The sequencing of the eggplant genome, which is likely to be published publicly in the next few mo...

Linkage and quantitative trait locus (QTL) mapping allow regions of the genome conferring adaptive traits to be identified; this is often an early step in identifying the genetic basis of said trait. In addition, comparative mapping, i.e. using orthologous genetic markers to create linkage and QTL maps, allows genome structure (translocations, inve...

In this chapter, I highlight how the eggplant, whilst being globally dwarfed by other members of the Solanaceae, notably potato and tomato, offers a number of important ecological, evolutionary and agronomic features making it unique and interesting, warranting further study. It also highlights the parallels and differences between Solanaceous crop...

Agriculture, and in particular systematic and repeated cultivation of plants, is one of the main characteristics of post-Neolithic sedentary human societies. Deciphering the domestication pathways that have allowed for extensive cultivation of crops is of great scientific importance: first, because it can reveal the patterns and processes of human-...

Aim The relationship of population genetics with the ecology and biogeography of species may be explored by comparing phenotypically similar but ecologically different congeners with overlapping ranges. We compared genetic differentiation between two congeneric rocky intertidal gastropods across a major portion of their sympatric range. We hypothes...

Rising atmospheric CO2 concentration is a key driver of enhanced global greening, thought to account for up to 70% of increased global vegetation in recent decades. CO2 fertilization effects have further profound implications for ecosystems, food security and biosphere‐atmosphere feedbacks. However, it is also possible that current trends will not...

The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume‐based farming is particularly important in Africa, where small‐scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to...

Well‐characterised examples of homoploid hybrid speciation (HHS) are rare in nature yet they offer the potential to study a number of evolutionary processes. In this study we investigate putative homoploid hybrid species in the genus Argyranthemum (Asteraceae), a group of plants endemic to the Macaronesian archipelagos of the North Atlantic Ocean....

Premise of the Study For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobu...

Studying molecular genetic relationships can substantially contribute to the understanding of the pathways of domestication of a species. Although an increasing number of molecular genetic studies have been performed on Lablab purpureus (hyacinth bean), many covered germplasm of restricted geographic origin or limited intra-specific systematic posi...

Microglia play key roles in brain development, homeostasis, and function, and it is widely assumed that the adult population is long lived and maintained by self-renewal. However, the precise temporal and spatial dynamics of the microglial population are unknown. We show in mice and humans that the turnover of microglia is remarkably fast, allowing...

Population genetic studies are effective ways of researching the origin of, and genetic variation within, crop species, with a view to breeding for increased tolerances or novel traits. This is particularly important now that we are facing climate change and an increasing global population. Lablab purpureus (L.) Sweet (hyacinth bean) is an under-ut...

Atmospheric carbon dioxide (CO2) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambi...

Premise of the study: Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asterac...

Recently evolved island lineages that exhibit a broad range of ecologies are particularly suitable model systems for addressing such issues. The 29 species of Echium endemic to Macaronesia display a diverse range of growth forms and occupy almost every ecological zone on the islands. The morphological and ecological diversity of this plant radiatio...

The contribution of gene expression modulation to phenotypic evolution is of major importance to an understanding of the origin of divergent or convergent phenotypes during and following polyploid speciation. Here we analysed genome-wide gene expression in two subspecies of the allotetraploid species, Senecio mohavensis A. Gray, and its diploid par...

Consuming watercress is thought to provide health benefits as a consequence of its phytonutrient composition. However, for watercress there are currently limited genetic resources underpinning breeding efforts for either yield or phytonutritional traits. In this paper, we use RNASeq data from twelve watercress accessions to characterize the transcr...

The role of hybridisation between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via int...

A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore unde...