Recent increases in archaeobotanical evidence offer insights into the processes of plant domestic... more 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."
Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challen... more Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 alaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA ould be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.
Proceedings of the National Academy of Sciences of the United States of America, Jan 13, 2005
Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize thr... more Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.
The colonization of the human environment by plants, and the consequent evolution of domesticated... more The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plantehuman 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 view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plantehominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plantehominin coevolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.
The Angiosperm seed had a double significance. It not only gave command of dry land to plant life... more The Angiosperm seed had a double significance. It not only gave command of dry land to plant life, but it provided the means by which mankind has been able to obtain an ample and assured food supply. To the Angiosperm seed, perhaps more than to any other structure, the economic evolution of the human race is due.'
Crop domestication has been inferred genetically from neutral markers and increasingly from speci... more Crop domestication has been inferred genetically from neutral markers and increasingly from specific domestication-associated loci. However, some crops are utilized for multiple purposes that may or may not be reflected in a single domesticationassociated locus. One such example is cultivated flax (Linum usitatissimum L.), the earliest oil and fiber crop, for which domestication history remains poorly understood. Oil composition of cultivated flax and pale flax (L. bienne Mill.) indicates that the sad2 locus is a candidate domestication locus associated with increased unsaturated fatty acid production in cultivated flax. A phylogenetic analysis of the sad2 locus in 43 pale and 70 cultivated flax accessions established a complex domestication history for flax that has not been observed previously. The analysis supports an early, independent domestication of a primitive flax lineage, in which the loss of seed dispersal through capsular indehiscence was not established, but increased oil content was likely occurred. A subsequent flax domestication process occurred that probably involved multiple domestications and includes lineages that contain oil, fiber, and winter varieties. In agreement with previous studies, oil rather than fiber varieties occupy basal phylogenetic positions. The data support multiple paths of flax domestication for oil-associated traits before selection of the other domestication-associated traits of seed dispersal loss and fiber production. The sad2 locus is less revealing about the origin of winter tolerance. In this case, a single domestication-associated locus is informative about the history of domesticated forms with the associated trait while partially informative on forms less associated with the trait.
... DOI: 10.1080/00438243.2011.624747 Dorian Q Fuller a , George Willcox b & Robi... more ... DOI: 10.1080/00438243.2011.624747 Dorian Q Fuller a , George Willcox b & Robin G. Allaby c pages 628-652. Available online: 05 Dec 2011. ...
Abstract The origins of agriculture involved pathways of domestication in which human behaviours ... more Abstract The origins of agriculture involved pathways of domestication in which human behaviours and plant genetic adaptations were entangled. These changes resulted in consequences that were unintended at the start of the process. This paper highlights some of the key innovations in human behaviours, such as soil preparation, harvesting and threshing, and how these were coupled with genetic 'innovations' within plant populations. We identify a number of 'traps' for early cultivators, including the needs for extra labour ...
Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that ... more Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that the fixation of key domestication traits such as non-shattering was slower than has often been assumed. This suggests a protracted period of pre-domestication cultivation, and therefore implies that both in time and in space the initial start of cultivation was separated from eventual domestication, when domesticated and wild populations would have become distinct gene pools. Archaeobotanical evidence increasingly suggests more pathways to cultivation than are represented by modern domesticated crop lines, including apparent early experiments with cultivation that did not lead to domestication, and early domesticates, such as two-grained einkorn and striate-emmeroid wheats, which went extinct in prehistory. This diverse range of early crops is hard to accommodate within a single centre of origin for all early Near Eastern cultivars, despite suggestions from genetic datasets that single origins from a single centre ought to be expected. This apparent discrepancy between archaeobotany and genetics highlights the need for modelling the expected genetic signature of different domestication scenarios, including multiple origins.
A combination of genetics and archaeology is revealing the complexity of the relationships betwee... more A combination of genetics and archaeology is revealing the complexity of the relationships between crop plants and their wild ancestors. Archaeobotanical studies are showing that acquisition of the full set of traits observed in domesticated cereals was a protracted process, intermediate stages being seen at early farming sites throughout the Fertile Crescent. New genetic data are confirming the multiregional nature of cereal domestication, correcting a previous view that each crop was domesticated by a rapid, unique and geographically localised process. Here we review the evidence that has prompted this reevaluation of the origins of domesticated crops in the Fertile Crescent and highlight the impact that this new multiregional model is having on modern breeding programmes.
A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (s... more A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60-1.71x10(-7) substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.
Computational models of evolutionary processes are increasingly required to incorporate multiple ... more Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (P cd ), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when P cd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors.
The origins of agriculture in the Near East has been associated with a 'core area', located in so... more The origins of agriculture in the Near East has been associated with a 'core area', located in south-eastern Turkey, in which all major crops were brought into domestication within the same local domestication system operated by a single cultural group. Such an origin leads to a scenario of rapid invention of agriculture by a select cultural group and typically monophyletic origins for most crops. Surprisingly, support for a core area has never been directly tested with archaeological evidence. Over the past decade a large amount of new archaeological and genetic evidence has been discovered which brings new light on the origins of agriculture. In this review, this new evidence was brought together in order to evaluate whether a core region of origin is supported. Evidence shows that origins began earlier than previously assumed, and included 'false starts' and dead ends that involved many more species than the typical eight founder crops associated with the core area. The rates at which domestication syndrome traits became fixed were generally slow, rather than rapid, and occurred over a geographically wide range that included the North and South Levant as well as the core area. Finally, a survey of the estimated ages of archaeological sites and the onset of domestication indicates that the domestication process was ongoing in parallel outside of the core area earlier than within it. Overall, evidence suggests a scenario in which crops were domesticated slowly in different locations around the Near East rather than emanating from a core area.
To study the origins of South American maize, without the complicating factors introduced by the ... more To study the origins of South American maize, without the complicating factors introduced by the extensive movement of genotypes during the post-Columbian period, we made a genetic analysis of primitive landraces and preserved maize remains. Fifteen alcohol dehydrogenase 2 (Adh2) allele sequences were obtained from the landraces and 11 from the archaeological specimens. When these and six previously published Adh2 sequences were aligned, three allele groups were seen, distinguished by the structure of a dinucleotide repeat sequence. The three allele groups had distinct distributions within South America, the distributions supporting a model in which the two Central American agricultural systems-highland and lowland-generated separate expansions of maize cultivation into South America. One expansion centred on a highland culture that spread from Central America through the Panama highlands into the Andean regions on the western side of South America, and the second expansion centred on a lowland culture which spread along the lowlands of the northeast coast of South America, entering the continent through the river systems. The Adh2 biogeography was consistent with limited cultural contact across the Andes between northern Chile and Paraguay. From the diversity of the Adh2 allele sequences, we deduced that maize has undergone a rapid rate of evolution since domestication.
A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (s... more A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60–1.71×10−7 substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.
Page 1. Biomolecular archaeology of wheat: past, present and future Terence A. Brown, Robin G. Al... more Page 1. Biomolecular archaeology of wheat: past, present and future Terence A. Brown, Robin G. Allaby, Keri A. Brown and Martin K. Jones Biomolecules and biomolecular archaeology A 'biomolecule' is any type of chemical substance occurring in a living organism. ...
We have used hybridization analysis to detect ancient DNA in wheat seeds collected from three arc... more We have used hybridization analysis to detect ancient DNA in wheat seeds collected from three archaeological sites in Europe and the Middle East. One of these samples, carbonizedT. spelta dated to the first millennium BC, has yielded PCR products after amplification with primers directed at the leader regions of the HMW (high molecular weight) glutenin alleles. Sequences obtained from these products suggest that the DNA present in the Danebury seeds is chemically damaged, as expected for ancient DNA, and also indicate that it should be possible to study the genetic variability of archaeological wheat by ancient DNA analysis. Finally, we describe a PCR-based system that enables tetraploid and hexaploid wheats to be distinguished.
Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joini... more Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joining trees from which monophyletic origins for crops such as einkorn wheat, barley, and emmer wheat have been inferred. We simulated several different multiple domestication scenarios for an imaginary cereal crop and examined the resulting domesticated populations. The simulations showed that the population biology aspects of the domestication process can result in independently domesticated populations merging in such a way that a monophyletic origin is erroneously inferred when the resulting population is examined by AFLP genotyping and neighbor-joining analysis. The results bring into question the use of this method to infer the origins of real crops.
Recent increases in archaeobotanical evidence offer insights into the processes of plant domestic... more 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."
Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challen... more Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 alaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA ould be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.
Proceedings of the National Academy of Sciences of the United States of America, Jan 13, 2005
Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize thr... more Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.
The colonization of the human environment by plants, and the consequent evolution of domesticated... more The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plantehuman 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 view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plantehominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plantehominin coevolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.
The Angiosperm seed had a double significance. It not only gave command of dry land to plant life... more The Angiosperm seed had a double significance. It not only gave command of dry land to plant life, but it provided the means by which mankind has been able to obtain an ample and assured food supply. To the Angiosperm seed, perhaps more than to any other structure, the economic evolution of the human race is due.'
Crop domestication has been inferred genetically from neutral markers and increasingly from speci... more Crop domestication has been inferred genetically from neutral markers and increasingly from specific domestication-associated loci. However, some crops are utilized for multiple purposes that may or may not be reflected in a single domesticationassociated locus. One such example is cultivated flax (Linum usitatissimum L.), the earliest oil and fiber crop, for which domestication history remains poorly understood. Oil composition of cultivated flax and pale flax (L. bienne Mill.) indicates that the sad2 locus is a candidate domestication locus associated with increased unsaturated fatty acid production in cultivated flax. A phylogenetic analysis of the sad2 locus in 43 pale and 70 cultivated flax accessions established a complex domestication history for flax that has not been observed previously. The analysis supports an early, independent domestication of a primitive flax lineage, in which the loss of seed dispersal through capsular indehiscence was not established, but increased oil content was likely occurred. A subsequent flax domestication process occurred that probably involved multiple domestications and includes lineages that contain oil, fiber, and winter varieties. In agreement with previous studies, oil rather than fiber varieties occupy basal phylogenetic positions. The data support multiple paths of flax domestication for oil-associated traits before selection of the other domestication-associated traits of seed dispersal loss and fiber production. The sad2 locus is less revealing about the origin of winter tolerance. In this case, a single domestication-associated locus is informative about the history of domesticated forms with the associated trait while partially informative on forms less associated with the trait.
... DOI: 10.1080/00438243.2011.624747 Dorian Q Fuller a , George Willcox b & Robi... more ... DOI: 10.1080/00438243.2011.624747 Dorian Q Fuller a , George Willcox b & Robin G. Allaby c pages 628-652. Available online: 05 Dec 2011. ...
Abstract The origins of agriculture involved pathways of domestication in which human behaviours ... more Abstract The origins of agriculture involved pathways of domestication in which human behaviours and plant genetic adaptations were entangled. These changes resulted in consequences that were unintended at the start of the process. This paper highlights some of the key innovations in human behaviours, such as soil preparation, harvesting and threshing, and how these were coupled with genetic 'innovations' within plant populations. We identify a number of 'traps' for early cultivators, including the needs for extra labour ...
Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that ... more Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that the fixation of key domestication traits such as non-shattering was slower than has often been assumed. This suggests a protracted period of pre-domestication cultivation, and therefore implies that both in time and in space the initial start of cultivation was separated from eventual domestication, when domesticated and wild populations would have become distinct gene pools. Archaeobotanical evidence increasingly suggests more pathways to cultivation than are represented by modern domesticated crop lines, including apparent early experiments with cultivation that did not lead to domestication, and early domesticates, such as two-grained einkorn and striate-emmeroid wheats, which went extinct in prehistory. This diverse range of early crops is hard to accommodate within a single centre of origin for all early Near Eastern cultivars, despite suggestions from genetic datasets that single origins from a single centre ought to be expected. This apparent discrepancy between archaeobotany and genetics highlights the need for modelling the expected genetic signature of different domestication scenarios, including multiple origins.
A combination of genetics and archaeology is revealing the complexity of the relationships betwee... more A combination of genetics and archaeology is revealing the complexity of the relationships between crop plants and their wild ancestors. Archaeobotanical studies are showing that acquisition of the full set of traits observed in domesticated cereals was a protracted process, intermediate stages being seen at early farming sites throughout the Fertile Crescent. New genetic data are confirming the multiregional nature of cereal domestication, correcting a previous view that each crop was domesticated by a rapid, unique and geographically localised process. Here we review the evidence that has prompted this reevaluation of the origins of domesticated crops in the Fertile Crescent and highlight the impact that this new multiregional model is having on modern breeding programmes.
A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (s... more A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60-1.71x10(-7) substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.
Computational models of evolutionary processes are increasingly required to incorporate multiple ... more Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (P cd ), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when P cd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors.
The origins of agriculture in the Near East has been associated with a 'core area', located in so... more The origins of agriculture in the Near East has been associated with a 'core area', located in south-eastern Turkey, in which all major crops were brought into domestication within the same local domestication system operated by a single cultural group. Such an origin leads to a scenario of rapid invention of agriculture by a select cultural group and typically monophyletic origins for most crops. Surprisingly, support for a core area has never been directly tested with archaeological evidence. Over the past decade a large amount of new archaeological and genetic evidence has been discovered which brings new light on the origins of agriculture. In this review, this new evidence was brought together in order to evaluate whether a core region of origin is supported. Evidence shows that origins began earlier than previously assumed, and included 'false starts' and dead ends that involved many more species than the typical eight founder crops associated with the core area. The rates at which domestication syndrome traits became fixed were generally slow, rather than rapid, and occurred over a geographically wide range that included the North and South Levant as well as the core area. Finally, a survey of the estimated ages of archaeological sites and the onset of domestication indicates that the domestication process was ongoing in parallel outside of the core area earlier than within it. Overall, evidence suggests a scenario in which crops were domesticated slowly in different locations around the Near East rather than emanating from a core area.
To study the origins of South American maize, without the complicating factors introduced by the ... more To study the origins of South American maize, without the complicating factors introduced by the extensive movement of genotypes during the post-Columbian period, we made a genetic analysis of primitive landraces and preserved maize remains. Fifteen alcohol dehydrogenase 2 (Adh2) allele sequences were obtained from the landraces and 11 from the archaeological specimens. When these and six previously published Adh2 sequences were aligned, three allele groups were seen, distinguished by the structure of a dinucleotide repeat sequence. The three allele groups had distinct distributions within South America, the distributions supporting a model in which the two Central American agricultural systems-highland and lowland-generated separate expansions of maize cultivation into South America. One expansion centred on a highland culture that spread from Central America through the Panama highlands into the Andean regions on the western side of South America, and the second expansion centred on a lowland culture which spread along the lowlands of the northeast coast of South America, entering the continent through the river systems. The Adh2 biogeography was consistent with limited cultural contact across the Andes between northern Chile and Paraguay. From the diversity of the Adh2 allele sequences, we deduced that maize has undergone a rapid rate of evolution since domestication.
A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (s... more A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60–1.71×10−7 substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.
Page 1. Biomolecular archaeology of wheat: past, present and future Terence A. Brown, Robin G. Al... more Page 1. Biomolecular archaeology of wheat: past, present and future Terence A. Brown, Robin G. Allaby, Keri A. Brown and Martin K. Jones Biomolecules and biomolecular archaeology A 'biomolecule' is any type of chemical substance occurring in a living organism. ...
We have used hybridization analysis to detect ancient DNA in wheat seeds collected from three arc... more We have used hybridization analysis to detect ancient DNA in wheat seeds collected from three archaeological sites in Europe and the Middle East. One of these samples, carbonizedT. spelta dated to the first millennium BC, has yielded PCR products after amplification with primers directed at the leader regions of the HMW (high molecular weight) glutenin alleles. Sequences obtained from these products suggest that the DNA present in the Danebury seeds is chemically damaged, as expected for ancient DNA, and also indicate that it should be possible to study the genetic variability of archaeological wheat by ancient DNA analysis. Finally, we describe a PCR-based system that enables tetraploid and hexaploid wheats to be distinguished.
Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joini... more Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joining trees from which monophyletic origins for crops such as einkorn wheat, barley, and emmer wheat have been inferred. We simulated several different multiple domestication scenarios for an imaginary cereal crop and examined the resulting domesticated populations. The simulations showed that the population biology aspects of the domestication process can result in independently domesticated populations merging in such a way that a monophyletic origin is erroneously inferred when the resulting population is examined by AFLP genotyping and neighbor-joining analysis. The results bring into question the use of this method to infer the origins of real crops.
Press Release
Strict Embargo until 14:00 EST / 19:00 GMT 26th February 2015
DNA evidence shows su... more Press Release Strict Embargo until 14:00 EST / 19:00 GMT 26th February 2015 DNA evidence shows surprise cultural connections between Britain and Europe 8,000 years ago 25 February 2015 - New evidence shows wheat reached Britain 2,000 years before the arrival of wheat farming - Mesolithic Britons interacted with Neolithic Europeans - Shows Britain not be insular or isolated - early communities had social and trade networks linking them across Europe 8,000 years ago - Published in the journal Science The ancient British were not cut off from Europeans on an isolated island 8,000 years ago as previously thought, new research suggests. Researchers found evidence for a variety of wheat at a submerged archaeological site off the south coast of England, 2,000 years before the introduction of farming in the UK. The team argue that the introduction of farming is usually regarded as a defining historic moment for almost all human communities leading to the development of societies that underpin the modern world. Published in the journal Science, the researchers suggest that the most plausible explanation for the wheat reaching the site is that Mesolithic Britons maintained social and trade networks spreading across Europe. These networks might have been assisted by land bridges that connected the south east coast of Britain to the European mainland, facilitating exchanges between hunters in Britain and farmers in southern Europe. Called Einkorn, the wheat was common in Southern Europe at the time it was present at the site in Southern England – located at Bouldnor Cliff. The einkorn DNA was collected from sediment that had previously formed the land surface, which was later submerged due to melting glaciers. The work was led by Dr Robin Allaby of the University of Warwick, in collaboration with co-leads Professor Vincent Gaffney of the University of Bradford and Professor Mark Pallen of Warwick Medical School, the Maritime Archaeology Trust, the University of Birmingham and the University of St. Andrews. Dr Allaby, Associate Professor at the University of Warwick’s School of Life Sciences, argues that the einkorn discovery indicates that Mesolithic Britain was less insular than previously understood and that inhabitants were interacting with Neolithic southern Europeans: “8,000 years ago the people of mainland Britain were leading a hunter-gatherer existence, whilst at the same time in southern Europeans farming was gradually spreading across Europe. “Common throughout Neolithic Southern Europe, einkorn is not found elsewhere in Britain until 2,000 years after the samples found at Bouldnor Cliff. For the einkorn to have reached this site there needs to have been contact between Mesolithic Britons and Neolithic farmers far across Europe. “The land bridges provide a plausible facilitation of this contact. As such, far from being insular Mesolithic Britain was culturally and possibly physically connected to Europe. “The role of these simple British hunting societies, in many senses, puts them at the beginning of the introduction of farming and, ultimately, the changes in the economy that lead to the modern world”. “The novel ancient DNA approach we used gave us a jump in sensitivity allowing us to find many of the components of this ancient landscape” Commenting on the research’s findings Professor Vincent Gaffney, research co-lead and Chair in Landscape Archaeology at the University of Bradford, said: “This find is the start of a new chapter in British and European history. Not only do we now realise that the introduction of farming was far more complex than previously imagined. It now seems likely that the hunter-gather societies of Britain, far from being isolated were part of extensive social networks that traded or exchanged exotic foodstuffs across much of Europe. “The research also demonstrates that scientists and archaeologists can now analyse genetic material preserved deep within the sediments of the lost prehistoric landscapes stretching between Britain and Europe. This not only tells us more about the introduction of farming into Britain, but also about the societies that lived on the lost coastal plains for hundreds of thousands of years. “The use of ancient DNA from sediments also opens the door to new research on the older landscapes off the British Isles and coastal shelves across the world” Co-lead Professor Mark Pallen, leader of the Pallen Group at the University of Warwick’s Medical School, explains how the researchers employed a metagenomic approach to study the einkorn DNA: “We chose to use a metagenomics approach in this research even though this has not commonly been used for environmental and ancient DNA research. This means we extracted and sequenced the entire DNA in the sample, rather than targeted organism-specific barcode sequences. From this we then homed in on the organisms of interest only when analysing DNA sequences”. The research builds on the work of the Maritime Archaeology Trust, who also collected the sediment samples from the site. The Trust’s Director, Garry Momber, commented: “Of all the projects I have worked on, Bouldnor Cliff has been the most significant. Work in the murky waters of the Solent has opened up an understanding of the UK’s formative years in a way that we never dreamed possible. “The material remains left behind by the people that occupied Britain as it was finally becoming an island 8,000 years ago, show that these were sophisticated people with technologies thousands of years more advanced than previously recognised. The DNA evidence corroborates the archaeological evidence and demonstrates a tangible link with the continent that appears to have become severed when Britain became an island”. The research is published in a Science paper entitled: ‘Sedimentary DNA from a submerged site reveals wheat in the British Isles 8,000 years ago’. ENDS. Notes for Editors: To access a video of Professor Vince Gaffney visit http://bit.ly/1za99UQ The researchers gratefully acknowledge the funding support of the University of Warwick Medical School. The paper is supported by research by the Maritime Archaeology Trust The project team were: Oliver Smith, Garry Momber, Paul Garwood, Richard Bates, Simon Fitch, Mark Pallen, Vincent Gaffney and Robin Allaby. Pictures available upon request Ends. CONTACT Press Office Jenny Watkinson [email protected] 01274 236030 Mark Thompson [email protected] 01274 233064 Other [email protected] 01274 233089 Out of hours 07879 437996 ABOUT THE UNIVERSITY OF BRADFORD Founded in 1966, the University of Bradford is one of the UK’s ‘traditional’ universities. It is a research-intensive institution, ranked in the top 50 in the UK for the quality of its research, with three quarters being classed as either world-leading or internationally excellent in the 2014 Research Excellence Framework (REF). The University was ranked No 1 in Yorkshire for employed graduates obtaining professional & managerial level jobs. Known for its strong emphasis on employability skills and knowledge transfer work with businesses, the University has a truly global make up with over 20 per cent of its student population being international. The University is also a leader in sustainable development and education, and is within the top ten greenest universities in the UK, according to the Green League 2013.
Marine palaeolandscapes and the historic impact of long-term climate change:
Royal Society
Chic... more Marine palaeolandscapes and the historic impact of long-term climate change: Royal Society Chicheley Hall May 15-16 2017
The Royal Society are hosting a Theo Murphy international scientific meeting on the implications of current research on marine palaeolandscapes. “Lost and Future Worlds: Marine palaeolandscapes and the historic impact of long-term climate change” has been organised by Professor Vincent Gaffney, Professor Geoff Bailey, Dr Richard Bates, Dr Philip Murgatroyd, Dr Eugene Ch’ng and Professor Robin G. Allaby the meeting will be held the Royal Society at conference centre at Chicheley Hall, Buckinghamshire (https://goo.gl/jgO5Ri), between Monday 15 May – Tuesday 16 May.
Global warming following the last glacial maximum led to the global submergence of vast, populated landscapes. These largely unexplored lands hold a unique record of habitation linked to climate change. Frequently inaccessible, and unamenable to conventional analysis, this meeting brings together experts across historical and scientific disciplines to identify new analytical methods and the contemporary relevance of these lost lands.
Catering and accommodation are available to purchase during registration
Poster session There will be a poster session at 17:00 on Monday 15 May 2017. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team no later than Monday 3 April 2017.
Please note that places are limited and are selected at the scientific organisers discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.
Uploads
Papers by Robin Allaby
mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 alaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA ould be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.
mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 alaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA ould be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.
Strict Embargo until 14:00 EST / 19:00 GMT 26th February 2015
DNA evidence shows surprise cultural connections between Britain and Europe 8,000 years ago
25 February 2015
- New evidence shows wheat reached Britain 2,000 years before the arrival of wheat farming
- Mesolithic Britons interacted with Neolithic Europeans
- Shows Britain not be insular or isolated - early communities had social and trade networks linking them across Europe 8,000 years ago
- Published in the journal Science
The ancient British were not cut off from Europeans on an isolated island 8,000 years ago as previously thought, new research suggests.
Researchers found evidence for a variety of wheat at a submerged archaeological site off the south coast of England, 2,000 years before the introduction of farming in the UK.
The team argue that the introduction of farming is usually regarded as a defining historic moment for almost all human communities leading to the development of societies that underpin the modern world.
Published in the journal Science, the researchers suggest that the most plausible explanation for the wheat reaching the site is that Mesolithic Britons maintained social and trade networks spreading across Europe.
These networks might have been assisted by land bridges that connected the south east coast of Britain to the European mainland, facilitating exchanges between hunters in Britain and farmers in southern Europe.
Called Einkorn, the wheat was common in Southern Europe at the time it was present at the site in Southern England – located at Bouldnor Cliff.
The einkorn DNA was collected from sediment that had previously formed the land surface, which was later submerged due to melting glaciers.
The work was led by Dr Robin Allaby of the University of Warwick, in collaboration with co-leads Professor Vincent Gaffney of the University of Bradford and Professor Mark Pallen of Warwick Medical School, the Maritime Archaeology Trust, the University of Birmingham and the University of St. Andrews.
Dr Allaby, Associate Professor at the University of Warwick’s School of Life Sciences, argues that the einkorn discovery indicates that Mesolithic Britain was less insular than previously understood and that inhabitants were interacting with Neolithic southern Europeans:
“8,000 years ago the people of mainland Britain were leading a hunter-gatherer existence, whilst at the same time in southern Europeans farming was gradually spreading across Europe.
“Common throughout Neolithic Southern Europe, einkorn is not found elsewhere in Britain until 2,000 years after the samples found at Bouldnor Cliff. For the einkorn to have reached this site there needs to have been contact between Mesolithic Britons and Neolithic farmers far across Europe.
“The land bridges provide a plausible facilitation of this contact. As such, far from being insular Mesolithic Britain was culturally and possibly physically connected to Europe.
“The role of these simple British hunting societies, in many senses, puts them at the beginning of the introduction of farming and, ultimately, the changes in the economy that lead to the modern world”.
“The novel ancient DNA approach we used gave us a jump in sensitivity allowing us to find many of the components of this ancient landscape”
Commenting on the research’s findings Professor Vincent Gaffney, research co-lead and Chair in Landscape Archaeology at the University of Bradford, said:
“This find is the start of a new chapter in British and European history. Not only do we now realise that the introduction of farming was far more complex than previously imagined. It now seems likely that the hunter-gather societies of Britain, far from being isolated were part of extensive social networks that traded or exchanged exotic foodstuffs across much of Europe.
“The research also demonstrates that scientists and archaeologists can now analyse genetic material preserved deep within the sediments of the lost prehistoric landscapes stretching between Britain and Europe. This not only tells us more about the introduction of farming into Britain, but also about the societies that lived on the lost coastal plains for hundreds of thousands of years.
“The use of ancient DNA from sediments also opens the door to new research on the older landscapes off the British Isles and coastal shelves across the world”
Co-lead Professor Mark Pallen, leader of the Pallen Group at the University of Warwick’s Medical School, explains how the researchers employed a metagenomic approach to study the einkorn DNA:
“We chose to use a metagenomics approach in this research even though this has not commonly been used for environmental and ancient DNA research. This means we extracted and sequenced the entire DNA in the sample, rather than targeted organism-specific barcode sequences. From this we then homed in on the organisms of interest only when analysing DNA sequences”.
The research builds on the work of the Maritime Archaeology Trust, who also collected the sediment samples from the site. The Trust’s Director, Garry Momber, commented:
“Of all the projects I have worked on, Bouldnor Cliff has been the most significant. Work in the murky waters of the Solent has opened up an understanding of the UK’s formative years in a way that we never dreamed possible.
“The material remains left behind by the people that occupied Britain as it was finally becoming an island 8,000 years ago, show that these were sophisticated people with technologies thousands of years more advanced than previously recognised. The DNA evidence corroborates the archaeological evidence and demonstrates a tangible link with the continent that appears to have become severed when Britain became an island”.
The research is published in a Science paper entitled: ‘Sedimentary DNA from a submerged site reveals wheat in the British Isles 8,000 years ago’. ENDS.
Notes for Editors:
To access a video of Professor Vince Gaffney visit http://bit.ly/1za99UQ
The researchers gratefully acknowledge the funding support of the University of Warwick Medical School.
The paper is supported by research by the Maritime Archaeology Trust
The project team were: Oliver Smith, Garry Momber, Paul Garwood, Richard Bates, Simon Fitch, Mark Pallen, Vincent Gaffney and Robin Allaby.
Pictures available upon request
Ends.
CONTACT
Press Office
Jenny Watkinson
[email protected]
01274 236030
Mark Thompson
[email protected]
01274 233064
Other
[email protected]
01274 233089
Out of hours
07879 437996
ABOUT THE UNIVERSITY OF BRADFORD
Founded in 1966, the University of Bradford is one of the UK’s ‘traditional’ universities. It is a research-intensive institution, ranked in the top 50 in the UK for the quality of its research, with three quarters being classed as either world-leading or internationally excellent in the 2014 Research Excellence Framework (REF). The University was ranked No 1 in Yorkshire for employed graduates obtaining professional & managerial level jobs.
Known for its strong emphasis on employability skills and knowledge transfer work with businesses, the University has a truly global make up with over 20 per cent of its student population being international. The University is also a leader in sustainable development and education, and is within the top ten greenest universities in the UK, according to the Green League 2013.
Royal Society
Chicheley Hall
May 15-16 2017
The Royal Society are hosting a Theo Murphy international scientific meeting on the implications of current research on marine palaeolandscapes. “Lost and Future Worlds: Marine palaeolandscapes and the historic impact of long-term climate change” has been organised by Professor Vincent Gaffney, Professor Geoff Bailey, Dr Richard Bates, Dr Philip Murgatroyd, Dr Eugene Ch’ng and Professor Robin G. Allaby the meeting will be held the Royal Society at conference centre at Chicheley Hall, Buckinghamshire (https://goo.gl/jgO5Ri), between
Monday 15 May – Tuesday 16 May.
Global warming following the last glacial maximum led to the global submergence of vast, populated landscapes. These largely unexplored lands hold a unique record of habitation linked to climate change. Frequently inaccessible, and unamenable to conventional analysis, this meeting brings together experts across historical and scientific disciplines to identify new analytical methods and the contemporary relevance of these lost lands.
Information on the meeting is held at https://goo.gl/nXtwS7
A t programme (PDF) is available to download at ...
https://royalsociety.org/~/media/events/2017/05/climate-change/Programme%20draft%206.pdf?la=en-GB
This residential conference is free to attend!
Advanced registration is essential (please request an invitation from https://goo.gl/nDjGbR
Catering and accommodation are available to purchase during registration
Poster session
There will be a poster session at 17:00 on Monday 15 May 2017. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team no later than Monday 3 April 2017.
Please note that places are limited and are selected at the scientific organisers discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.
see also https://lostfrontiers.teamapp.com/