Andrew C. Clarke

• PhD
• Fellow at University of Cambridge

Significance Squashes, pumpkins, and gourds belonging to the genus Cucurbita were domesticated on several occasions throughout the Americas, beginning around 10,000 years ago. The wild forms of these species are unpalatably bitter to humans and other extant mammals, but their seeds are present in mastodon dung deposits, demonstrating that they may...

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant–human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing...

Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better apprecia...

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent st...

Tokelau is a remote archipelago of atolls in western Polynesia, located approximately 500 km north of Samoa. It is thought to have been settled as part of the Austronesian expansion(s). However, its exact role in this population dispersal is not completely understood. Here we describe the results of complete mitochondrial genome sequencing for both...

Background and Aims Paper mulberry or Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion...

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian gen...

Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors’ arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Abo...

Phylogenies reconstruct species’ evolutionary relationships and phylogenetic methods provide a comparative framework when traits correlate with evolutionary relationships. This study reviews the applications of these methods in ethnobiological research, particularly ethnobotany and ethnopharmacology. We discuss the advantages of phylogenetic method...

Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plantcommunity restoration projects. Along with established ecological restoration practices, knowledge of genetic variation in existing and restored forest fragments is important for ensuring the maintenance of natural levels of genetic variation and connecti...

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant–human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing...

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of...

Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better apprecia...

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with hu-mans have contributed to understanding prehistoric migration, trade, exchange...

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The amplified fragment length polymorphism (AFLP) technique is a widely used multi-purpose DNA fingerprinting tool. The ability to size-separate fluorescently labelled AFLP fragments on a capillary electrophoresis instrument has provided a means for high-throughput genome screening, an approach particularly useful in studying the molecular ecology...

With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own spe...

Paper mulberry ( Broussonetia papyrifera (L.) Vent.) was one of the most widely distributed crop species in prehistoric Oceania, occurring from continental East Asia to the Polynesian islands. Its broad distribution is largely due to human-mediated dispersal during colonization of the islands of Near and Remote Oceania. We explore the potential for...

Commensal models, which can be used to infer prehistoric human mobility, have been designed and applied to understand migration and interaction in the Pacific (Matisoo-Smith 1994, 1996). This chapter describes the elements of successful commensal models and examines how these models may pertain to finding evidence for prehistoric contact between Po...

We suggest that the most parsimonious explanation for the material, linguistic, biological, mythological, nautical, chronological, and physical anthropological evidence summarized in chapters 1–13 is that Polynesians made pre-Columbian landfalls in the New World. Further, based on this evidence, we identify three likely locations of contact: southe...

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucl...

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA fragment mobility and amplitude, and current AFLP software allows greater control of data scoring an...

Many postglacial lakes contain fish species with distinct ecomorphs. Similar evolutionary scenarios might be acting on evolutionarily young fish communities in lakes of remote islands. One process that drives diversification in island freshwater fish species is the colonization of depauperate freshwater environments by diadromous (migratory) taxa,...

The common bully (Gobiomorphus cotidianus), a small-bodied New Zealand native fish species, was used to monitor population impacts of multiple effluents in the Tarawera River, New Zealand. In an initial survey, the absence of reproductive development at the expected spawning time for common bullywas observed in a population downstream of effluent d...

The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis o...

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry mat...

New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000–5,000 years ago with the independent domestication of plants and animals in eight world regions. In the Americas, however, understanding the initial domestication of New W...

Genetic analysis of onion has been hampered by a lack of portable co-dominant markers based on the polymerase chain reaction (PCR). The public release of a relatively large set of non-redundant onion expressed sequence tags (ESTs) in 2003 has provided the opportunity to develop such markers for use in Allium research and industry. We have mined thi...