On the 'lost' crops of the neolithic Near East.

The claim that the 'classic' eight 'founder crop' package (einkorn wheat, emmer wheat, barley, lentil, pea, chickpea, bitter vetch, and flax) underlying the emergence of agriculture in the Near East is a relic of a larger number of domesticated species is addressed. The 'lost' crops concept relies on the idea that additional taxa were at certain points in time and in certain locations genuine crops, which were later abandoned. The issue is highly relevant to the debate concerning mono- versus polyphyletic domestication, because if there were numerous 'false starts' that were subsequently lost, this implies that plant domestication occurred over a protracted time period, and across a wide geographic range. Different criteria were used for declaring those taxa as 'lost' crops, including, but not limited to (i) identification in archaeobotanical assemblages of grains from species which are not known as crops at present; (ii) identification of such grains in what is interpreted to have been Neolithic storage facilities; and (iii) recent botanical observations on populations of crop wild relatives in disturbed habitats. The evidence for four presumed 'lost' crops (wild oat, rambling vetch, rye, and wild black lentil) and the broad bean is evaluated, and discussed in light of data on Croatian and Israeli wild pea, and Moroccan wild lentil in disturbed habitats. Based on present knowledge, the broad bean might emerge as a founder crop (without an identified wild progenitor). The same may hold true for rye, which was never lost since its adoption in the Pre-Pottery Neolithic B period in Anatolia. In the remaining three cases, there are alternative, more likely, explanations for the archaeological finds or the recent botanical observations rather than 'lost' domestication episodes.

A critical review of the protracted domestication model for Near-Eastern founder crops: linear regression, long-distance gene flow, archaeological, and archaeobotanical evidence.

The recent review by Fuller et al. (2012a) in this journal is part of a series of papers maintaining that plant domestication in the Near East was a slow process lasting circa 4000 years and occurring independently in different locations across the Fertile Crescent. Their protracted domestication scenario is based entirely on linear regression derived from the percentage of domesticated plant remains at specific archaeological sites and the age of these sites themselves. This paper discusses why estimates like haldanes and darwins cannot be applied to the seven founder crops in the Near East (einkorn and emmer wheat, barley, peas, chickpeas, lentils, and bitter vetch). All of these crops are self-fertilizing plants and for this reason they do not fulfil the requirements for performing calculations of this kind. In addition, the percentage of domesticates at any site may be the result of factors other than those that affect the selection for domesticates growing in the surrounding area. These factors are unlikely to have been similar across prehistoric sites of habitation, societies, and millennia. The conclusion here is that single crop analyses are necessary rather than general reviews drawing on regression analyses based on erroneous assumptions. The fact that all seven of these founder crops are self-fertilizers should be incorporated into a comprehensive domestication scenario for the Near East, as self-fertilization naturally isolates domesticates from their wild progenitors.

A first insight into the genetic diversity of Mycobacterium tuberculosis in Dar es Salaam, Tanzania, assessed by spoligotyping.

BACKGROUND: Tanzania has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis in the country are necessary in order to improve our understanding of the epidemic. Spoligotyping is a potentially powerful genotyping method due to fast generation of genotyping results, high reproducibility and low operation costs. The recently constructed SpolDB4 database and the model-based program 'Spotclust' can be used to assign isolates to families, subfamilies and variants. The results of a study can thus be analyzed in a global context. RESULTS: One hundred forty-seven pulmonary isolates from consecutive tuberculosis patients in Dar es Salaam were spoligotyped. SpolDB4 and 'Spotclust' were used to assign isolates to families, subfamilies and variants. The CAS (37%), LAM (22%) and EAI (17%) families were the most abundant. Despite the dominance of these three families, diversity was high due to variation within M. tuberculosis families. Of the obtained spoligopatterns, 64% were previously unrecorded. CONCLUSION: Spoligotyping is useful to gain an overall understanding of the local TB epidemic. This study demonstrates that the extensive TB epidemic in Dar es Salaam, Tanzania is caused by a few successful M. tuberculosis families, dominated by the CAS family. Import of strains was a minor problem.

Can Triticum urartu (Poaceae) be identified by pollen analysis? Implications for detecting the ancestor of the extinct two-grained einkorn-like wheat.

The domestication of the one-grained einkorn (Triticum monococcum) in the Near East is relatively well known. However, an independent two-grained einkorn-like domestication has been archaeobotanically detected and scarce information is available. Triticum urartu, a wild wheat, was not fully described until the 1970s because the phenology does not allow it to be distinguished easily from wild einkorn (Triticum boeoticum subsp. thaoudar), although a genetic separation exists. Both species are mostly two grained and could potentially be the relatives of the extinct two-grained form. Pollen grains of several genetically well-identified wheat species, including T. urartu and T. boeoticum subsp. thaoudar, were studied by measuring the grain diameter and examining the exine sculpturing with phase-contrast microscopy and scanning electron microscopy to gain an insight into differences enabling taxonomic identification. This work showed that, although T. urartu pollen is smaller on average, grain diameter is not sufficient because of the size overlap between the species, but T. urartu presents a different exine sculpturing (scabrate) from other Triticum spp. (aerolate). This outcome is useful for taxonomists and archaeobotanists. First, it will allow a simple re-classification of herbarium materials. Second, further research could establish whether T. urartu was cultivated.

Reassessing domestication events in the Near East: Einkorn and Triticum urartu.

To reassess domestication events in the Near East, accessions of Triticum urartu from a well-described sampling were combined with a representative sample covering the Karacadag Einkorn wheat domestication. The observed DNA separation between the two wheat species accounts for the main differentiation, but geographic variation within T. urartu is evident and so is the domestication scenario among wild, feral, and domesticated Einkorn. In contrast to the clear DNA differences, it is difficult to separate living T. urartu from wild Einkorn based on morphology. With archaeobotanical material a distinction of carbonized remains of these two wheats is considered to be impossible. We reviewed the differences concerning morphology and maturity and combined these observations with information about archaeological sites in the Near East. In conclusion, the excavation sites in the middle Euphrates may contain T. urartu rather than Einkorn wheat and T. urartu may underlie the reported occurrence of the extinct 2-grained domesticated "Einkorn" wheat. The first Einkorn wheat domestication sensu stricto seems to have happened around the Karacadag, as reported earlier. The human dimension shown by the excavation of Göbekli Tepe can explain why domesticated phenotypes might have spread quickly.

AFLP-based differentiation of tropical African Festuca species compared to the European Festuca complex.

For the first time amplified fragment length polymorphism (AFLP) fingerprinting is applied to classify tropical African Festuca species. Five afro-alpine narrow- and two afro-montane broad-leaved species from Uganda and Ethiopia are compared to ten European grass species. A principal coordinate analysis (PCoA) accounts for 62.5% with its first three coordinates. The PCoA and the neighbor-joining (NJ) distinguish the five narrow-leaved African Festuca species from all other species. The broad-leaved African Festuca africana and Festuca simensis are linked to the broad-leaved European species through Festuca altissima and Festuca gigantea, respectively. The narrow- and broad-leaved European species are separated as expected in the NJ. One narrow-leaved African alpine species recently described appears merged (i.e. Festuca richardii with Festuca abyssinica). We provide chromosome numbers for all seven Ugandan species and compare taxonomy and AFLP classification. Our most striking result is that the narrow-leaved African Festuca species are unique and not clustering with the narrow-leaved European species.

Genetic diversity and geographic pattern in early South American cotton domestication.

Amplified fragment length polymorphism fingerprinting was applied to survey the genetic diversity of primitive South American Gossypium barbadense cotton for establishing a possible link to its pre-Columbian expansion. New germplasm was collected along coastal Peru and over an Andean transect in areas where most of the archaeological evidence relating to cotton domestication has been recorded. Gene bank material of three diploid (G. raimondii, G. arboreum, and G. herbaceum) and four allotetraploid cotton species (G. hirsutum, G. mustelinum, G. tomentosum and additional G. barbadense) was added for inter- and intra-specific comparison. Eight primer combinations yielded 340 polymorphic bands among the 131 accessions. The obtained neighbor joining and unweighted pair-group method with arithmetic means are in full agreement with the known cytogenetics of the tetraploid cottons and their diploid genome donors. The four tetraploid species are clearly distinct based on taxonomic classification. The genetic diversity within G. barbadense reveals geographic patterns. The locally maintained cottons from coastal Peru display a distinct genetic diversity that mirrors their primitive agro-morphological traits. Accessions from the northernmost coast of Peru and from southwestern (SW) Ecuador cluster basal to the east-of-Andes accessions. The remaining accessions from Bolivia, Brazil, Columbia, Venezuela, and the Caribbean and Pacific islands cluster with the east-of-Andes accessions. Northwestern Peru/SW Ecuador (the area flanking the Guayaquil gulf) appears to be the center of the primitive domesticated G. barbadense cotton from where it spread over the Andes and expanded into its pre-Columbian range.