Qasr Ibrim, as photographed by the Allaby Research Group (Link)
This recent paper from the Allaby Research Group discusses the case for parallel domestication of food crops in diverse regions of the world. Its focus is on agricultural crops, so it is not directly related to the process of cattle domestication. However, the discussion in the paper of an independent domestication of cotton at Qasr Ibrim supports the notion of a localized agripastoral tradition on the Nile. Related to this discussion is the previous post which mentions cotton domestication among Saharo-Sahelian speakers.
The blossoming of plant archaeogenetics
Sarah A. Palmer, Oliver Smith, Robin G. Allaby
Annals of Anatomy, Volume 194, Issue 1, 20 January 2012, Pages 146-156
"For the past two decades scientific drivers concerned with the origin and spread of domesticated crops have dominated the utility of ancient DNA from plants (Fig. 1). It is a current aspiration that genomic studies of plant remains could unlock critical evidence of the origins of domestication and strengthen the bridge between phylogenetic studies of modern plants and the archaeology of plant remains (archaeobotany). This study of plant domestication has itself undergone substantial change in recent years in response to new data leading to a different framework of understanding. The interpretation of phylogenetic data with regard to domestication is often seated on the framework of models of human behaviour in the shift from hunter-gathers to agriculturalists ( [Allaby et al., 2008] and [Allaby et al., 2010]). However, theses based on plant phylogeny, which uses extant allelic diversity to infer past genomic events, and archaeobotany, which examines archaeological plant remains by morphology, have sometimes appeared to contradict one another. Recently, mounting archaeological evidence has spurred a shift in thinking from a rapid transition paradigm for the shift from hunter-gatherers to agriculturalists in which a ‘Neolithic package’ of staple food crops were domesticated over a relatively short time period by a small farming group, to a protracted transition paradigm in which domestication of food crops occurred in parallel, over a long time, in diverse regions worldwide (Fuller et al., 2010). The interpretation of genetic diversity needs to be reviewed in light of the modified genetic expectation of the paradigm of protracted transition (Allaby, 2010)."
Reconstruction of the early history and movement of cultivated plant species:
"The arguments for the origin of crop species and movement of these species to where they can be found today are largely dependent on genetic diversity. With the classical underlying expectation of a rapid transition paradigm (where domestication events are discrete and quick), monophyly or polyphyly has been interpreted as evidence of single or multiple origins, respectively (Allaby et al., 2010). Archaeogenetics has been used in parallel with these studies to mine for past allelic diversity (Navascues et al., 2010). Phylogenetic analysis to determine centre of origin and movement has been undertaken of archaeobotanical remains of many of the crop species important to human societies, including members of the cucurbitaceae ( [Szabo et al., 2008], [Zoltan et al., 2007] and [Erickson et al., 2005]), the poaceae ( [Nasab et al., 2010], [Li et al., 2011], [Tanaka et al., 2010], [Lia et al., 2007], [Gyulai et al., 2006], [Lagler et al., 2005], [Lagler et al., 2006], [Freitas et al., 2003] and [Allaby et al., 1999]), grapes ( [Cappellini et al., 2010] and [Manen et al., 2003]), the Prunus genus (Pollmann et al., 2005) and olives (Elbaum et al., 2006)."
"The most extensively archaeogenetically characterised gene family is that of the high molecular weight glutenin gene (Glu) in wheats. The Glu genes have a conveniently short polymorphic region in the promoter that is ideally suited for the identification of alleles unique to hexaploid bread wheat ( [Allaby et al., 1999] and [Nasab et al., 2010]). Recently, Li et al. (2011) discovered the Glu D genome allele in Bronze Age wheat samples from China indicating hexaploid bread wheat. This is in contrast with archaeobotanical evidence of tetraploid emmer wheat predominating Western Eurasia. This finding echoes previous studies in which the D genome was similarly identified in an assemblage from Bronze Age Greece that was thought to be tetraploid wheat only (Allaby et al., 1999). Furthermore, an entirely extinct expansion of wheats into Europe containing the more unusual G genome was initially detected through ancient DNA (Brown et al., 1998), a finding that was later confirmed by archaeobotany (Jones et al., 2000). A similar pattern of replacement has been observed in recent studies of early Japanese rice agriculture which suggest that tropical rice varieties were grown which were later replaced by temperate varieties (Tanaka et al., 2010)."
"Ancient DNA as a marker of phylogeographic stability has also been used with maize ( [Freitas et al., 2003] and [Lia et al., 2007]). In this case the primitive landraces used by Native Americans in South America were used to establish a modern phylogeographic distribution of alleles of alcohol dehydrogenase and microsatellites the antiquity of which was confirmed with archaeobotanical samples, giving a picture of a distinct east west divide suggestive of two expansions of maize into South America from the meso-American homeland of maize. The establishment of 10,000 year old remains in the New World as bottle gourd (Lagenaria siceraria) sets an important biogeographic precedent in that it establishes that paleoindian populations transferred domesticated plants from the Old World, despite their hunter-gatherer life-style (Erickson et al., 2005). Until then evidence that they had been associated with any plant transportation had been scant."
"More recently, archaeoegenetic studies which have exploited herbarium samples of barley to expand the sample set to include extinct landraces and cultivars sampled where they are no longer grown today, facilitated resolution of genetic structuring on a fine geographical scale in Sweden that would have been unavailable from modern crops (Leino and Hagenblad, 2010). In a similar case to that of the maize, in this latter study the distribution is suggestive of two entries of barley into Sweden suggestive of two cultural influences."
"Archaeological plant remains are also studied for the integral part they play in human society. Often excavated in close proximity to remains of humans or their dwellings, plant remains can be examined in light of what plants were being produced, foraged, eaten, traded, or used in some other way. The marriage of archaeogenetics and ethnobotany is one of the most interdisciplinary of the sciences, and is characterised by the interpretation of archaeobotanical phylogenetics in light of theories formulated from archaeology. Archaeobotanical reconstructions are frequently hindered by ambiguous identification of samples (Schlumbaum et al., 2008). Archaeogenetics has been used as a tool for species identification where the morphology is ambiguous."
"A common use of archaeogenetics on ethnological remains has been to reconstruct diets of past peoples including the vegetal dietary elements ( [Rasmussen et al., 2009], [Rollo et al., 2002] and [Poinar et al., 2001]). Of archaeobotanical remains, the inferences of resolved identification have been used to confirm an indigenous independent domestication of the A genome cotton, Gossypium herbaceum in Africa prior to Asian influence (Palmer et al., unpublished) and several instances of hexaploid bread wheat during the Bronze age in China (Li et al., 2011) and Greece (Allaby et al., 1999), much earlier than previously estimated in the former case. Also, the use of Prunus spinosa and P. avium/cerasus by the Romans in the Northern alpine region has been established (Pollmann et al., 2005)."
"The mode in which archaeological remains were used and the evaluation of the importance of trade versus local agricultural diversity have also been areas of ethnobotany where archaeogenetics has made valuable contributions. In our lab, we have examined Barley and Cotton remains from Qasr Ibrim, a border settlement on the River Nile that was subject to numerous cultural transitions. Samples of barley from all six strata examined, spanning more than 3000 years, displayed the same allele at the vrs1 locus (Palmer et al., 2009). Given the settlement's situation on the trade route of the River Nile, it was considered likely that conquering peoples may have introduced foreign germplasm to the area. However, this local landrace appears to have persisted throughout the occupation of this settlement. The identification of the cotton remains at this site as G. herbaceum, suggests local production, rather than the opposing theory that cotton was generally imported from Asia and processed locally."