Tim Denham

Current perspectives and the future of domestication studies

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.

Multidisciplinary perspectives on banana (Musa spp.) domestication

Original multidisciplinary research hereby clarifies the complex geodomestication pathways that generated the vast range of banana cultivars (cvs). Genetic analyses identify the wild ancestors of modern-day cvs and elucidate several key stages of domestication for different cv groups. Archaeology and linguistics shed light on the historical roles of people in the movement and cultivation of bananas from New Guinea to West Africa during the Holocene. The historical reconstruction of domestication processes is essential for breeding programs seeking to diversify and improve banana cvs for the future.

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

Significance Agriculture was a transformative development in the history of human societies and natural environments and drove the evolution of new domesticated species. Crop plants are the predominant domesticated species in most agricultural systems and are an essential component in all the food production systems that underpinned the development of urban societies. Archaeological plant remains provide a range of insights into the processes by which plants were domesticated in different parts of the world. The present paper provides a unique synthesis of evidence, including quantitative evidence on the trajectory and rate of domestication in seed crops and patterns in the development of tropical vegetatively propagated crops. Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers.

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.

Farming and Language in Island Southeast Asia Reframing Austronesian History

Current portrayals of Island Southeast Asia (ISEA) over the past 5,000 years are dominated by discussion of the Austronesian “farming/language dispersal,” with associated linguistic replacement, genetic clines, Neolithic “packages,” and social transformations. The alternative framework that we present improves our understanding of the nature of the Austronesian language dispersal from Taiwan and better accords with the population genetics, archaeological evidence, and crop domestication histories for ISEA. Genetic studies do not demonstrate that the dispersal of Austronesian languages through ISEA was associated with large‐scale displacement, replacement, or absorption of preexisting populations. Linguistic phylogenies for Austronesian languages do not support staged movement from Taiwan through the Philippines into Indo‐Malaysia; in addition, the lexical and grammatical structure of many Austronesian languages suggests significant interaction with pre‐Austronesian languages and cultures of the region. Archaeological evidence, including domestication histories for major food plants, indicates that ISEA was a zone of considerable maritime interaction before the appearance of Austronesian languages. Material culture dispersed through ISEA from multiple sources along a mosaic of regional networks. The archaeological evidence helps us to shape a new interpretative framework of the social and historical processes that more parsimoniously accounts for apparent discrepancies between genetic phylogenies and linguistic distributions and allows for more nuanced models of the dispersal of technologies and societies without reference to the farming/language dispersal hypothesis.

Domesticated Landscapes: The Subsistence Ecology of Plant and Animal Domestication

Harvesting different species as foods or raw materials calls for differing skills depending on the species being harvested and the circumstances under which they are being taken. In some situations and for some species, the tactics used are mainly behavioral—that is, people adjust, or adapt, their own actions to fit the behavior and circumstances of the species they are taking. Under other circumstances and for other species, the skills and tactics used may call for greater environmental preparation or manipulation. Therefore, instead of trying to distinguish people today and in the past as either “foragers” or “farmers,” it makes sense to define human subsistence behavior as an interactive matrix of species and harvesting tactics, that is, as a provisions spreadsheet.

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific

Significance Ancient DNA sequences from chickens provide an opportunity to study their human-mediated dispersal across the Pacific due to the significant genetic diversity and range of archaeological material available. We analyze ancient and modern material and reveal that previous studies have been impacted by contamination with modern chicken DNA and, that as a result, there is no evidence for Polynesian dispersal of chickens to pre-Columbian South America. We identify genetic markers of authentic ancient Polynesian chickens and use them to model early chicken dispersals across the Pacific. We find connections between chickens in the Micronesian and Bismarck Islands, but no evidence these were involved in dispersals further east. We also find clues about the origins of Polynesian chickens in the Philippines. The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.

Early Agriculture and Plant Domestication in New Guinea and Island Southeast Asia

A multidimensional conceptual framework is advanced that characterizes early agriculture as a subset of human-environment interactions. Three cross-articulating dimensions of human-environment interaction are considered that accommodate the varied expressions of early agriculture in different parts of the world: spatial scales, transformative mechanisms, and temporalities of associated phenomena. These ideas are applied and exemplified at two different scales of resolution—contextual and comparative—in terms of early agricultural development in the highlands of New Guinea and the dispersal of domesticates from New Guinea into Island Southeast Asia.

Evaluating the roles of directed breeding and gene-flow in animal domestication

For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.

Agricultural emergence and transformation in the Upper Wahgi valley, Papua New Guinea, during the Holocene: theory, method and practice:

A practice-based method is advanced to understand the emergence and transformation of agricultural practices in the Upper Wahgi valley during the Holocene. Conceptually, practices represent the nexus of human—environment interactions, as well as of structure—agency relationships, while methodologically, they are the visible remains — whether encountered directly through archaeology, or inferred through palaeoenvironmental proxy — of people living in the past. Multidisciplinary information from the Upper Wahgi valley is used to reconstruct multilayered practices of plant exploitation across the landscape through time; the intention is to spatialize, temporalize and humanize information often represented chronologically and technically. Practice-oriented interpretations clarify, interrogate and amplify existing multidisciplinary records of the past and shed new light on how the earliest agriculture was originated and transformed in the New Guinea highlands during the Holocene.