Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog-wolf hybridization

Studies of mitochondrial DNA (mtDNA) diversity indicate explicitly that dogs were domesticated, probably exclusively, in southern East Asia. However, Southwest Asia (SwAsia) has had poor representation and geographical coverage in these studies. Other studies based on archaeological and genome-wide SNP data have suggested an origin of dogs in SwAsia. Hence, it has been suspected that mtDNA evidence for this scenario may have remained undetected. In the first comprehensive investigation of genetic diversity among SwAsian dogs, we analyzed 582 bp of mtDNA for 345 indigenous dogs from across SwAsia, and compared with 1556 dogs across the Old World. We show that 97.4% of SwAsian dogs carry haplotypes belonging to a universal mtDNA gene pool, but that only a subset of this pool, five of the 10 principal haplogroups, is represented in SwAsia. A high frequency of haplogroup B, potentially signifying a local origin, was not paralleled with the high genetic diversity expected for a center of origin. Meanwhile, 2.6% of the SwAsian dogs carried the rare non-universal haplogroup d2. Thus, mtDNA data give no indication that dogs originated in SwAsia through independent domestication of wolf, but dog-wolf hybridization may have formed the local haplogroup d2 within this region. Southern East Asia remains the only region with virtually full extent of genetic variation, strongly indicating it to be the primary and probably sole center of wolf domestication. An origin of dogs in southern East Asia may have been overlooked by other studies due to a substantial lack of samples from this region.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

Chicken domestication: from archeology to genomics

Current knowledge on chicken domestication is reviewed on the basis of archaeological, historical and molecular data. Several domestication centres have been identified in South and South-East Asia. Gallus?gallus is the major ancestor species, but Gallus?sonneratii has also contributed to the genetic make-up of the domestic chicken. Genetic diversity is now distributed among traditional populations, standardized breeds and highly selected lines. Knowing the genome sequence has accelerated the identification of causal mutations determining major morphological differences between wild Gallus and domestic breeds. Comparative genome resequencing between Gallus and domestic chickens has identified 21 selective sweeps, one involving a non-synonymous mutation in the TSHR gene, which functional consequences remain to be explored. The resequencing approach could also identify candidate genes responsible of quantitative traits loci (QTL) effects in selected lines. Genomics is opening new ways to understand major switches that took place during domestication and subsequent selection.     

Molecular genetic analysis of ancient cattle bones excavated from archaeological sites in Jeju, Korea

Ancient cattle bones were excavated from archaeological sites in Jeju, Korea. We used molecular genetic techniques to identify the species and establish its relationship to extant cattle breeds. Ancient DNA was extracted from four sources: a humerus (Gonae site, A.D. 700-800), two fragments of radius, and a tooth (Kwakji site, A.D. 0-900). The mitochondrial DNA (mtDNA) D-loop regions were cloned, sequenced, and compared with previously reported sequences of various cattle breeds (9 Asian, 8 European, and 3 African). The results revealed that these bones were of the breed, Bos taurus, and a phylogenetic tree indicated that the four cattle bones formed a monophyletic group with Jeju native black cattle. However, the patterns of sequence variation and reports from archaeological sites suggest that a few wild cattle, with a different maternal lineage, may have existed on Jeju Island. Our results will contribute to further studies of the origin of Jeju native cattle and the possible existence of local wild cattle.     

Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World

BACKGROUND: Archaeobotany, the study of plant remains from sites of ancient human activity, provides data for studying the initial evolution of domesticated plants. An important background to this is defining the domestication syndrome, those traits by which domesticated plants differ from wild relatives. These traits include features that have been selected under the conditions of cultivation. From archaeological remains the easiest traits to study are seed size and in cereal crops the loss of natural seed dispersal. SCOPE: The rate at which these features evolved and the ordering in which they evolved can now be documented for a few crops of Asia and Africa. This paper explores this in einkorn wheat (Triticum monococcum) and barley (Hordeum vulgare) from the Near East, rice (Oryza sativa) from China, mung (Vigna radiata) and urd (Vigna mungo) beans from India, and pearl millet (Pennisetum glaucum) from west Africa. Brief reference is made to similar data on lentils (Lens culinaris), peas (Pisum sativum), soybean (Glycine max) and adzuki bean (Vigna angularis). Available quantitative data from archaeological finds are compiled to explore changes with domestication. The disjunction in cereals between seed size increase and dispersal is explored, and rates at which these features evolved are estimated from archaeobotanical data. Contrasts between crops, especially between cereals and pulses, are examined. CONCLUSIONS: These data suggest that in domesticated grasses, changes in grain size and shape evolved prior to non-shattering ears or panicles. Initial grain size increases may have evolved during the first centuries of cultivation, within perhaps 500-1000 years. Non-shattering infructescences were much slower, becoming fixed about 1000-2000 years later. This suggests a need to reconsider the role of sickle harvesting in domestication. Pulses, by contrast, do not show evidence for seed size increase in relation to the earliest cultivation, and seed size increase may be delayed by 2000-4000 years. This implies that conditions that were sufficient to select for larger seed size in Poaceae were not sufficient in Fabaceae. It is proposed that animal-drawn ploughs (or ards) provided the selection pressure for larger seeds in legumes. This implies different thresholds of selective pressure, for example in relation to differing seed ontogenetics and underlying genetic architecture in these families. Pearl millet (Pennisetum glaucum) may show some similarities to the pulses in terms of a lag-time before truly larger-grained forms evolved.     

Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication

The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies unable to narrow down where domestication occurred within a broad region of tropical Asia. The most commonly hypothesized region is India, however China has an equally old written record of eggplant use dating ca. 2000 years before present. Both regions have a high diversity of landraces and populations of putatively wild eggplant: Solanum incanum L. in India and Solanum undatum Lam. in SE Asia. An additional complication is that there is taxonomic confusion regarding the two candidate progenitors. Here, we synthesize historic, morphologic, and molecular data (nrITS sequence and AFLP) to interpret the phylogeographic relationships among candidate progenitors and Asian eggplant landraces in order to test theories of domestication. A minimum of two domestication events is supported: one in India and one in southern China/SE Asia. Results also support separate domestication of S. melongena subsp. ovigerum, a group of morphologically distinct eggplants found in SE Asia, and suggest Asian S. incanum and S. undatum may not be genetically distinct. Routes of the spread of eggplant cultivation throughout Asia are proposed, and evolutionary relationships among allied species are discussed.     

The origin of the domestic pig: independent domestication and subsequent introgression

The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before domestication approximately 9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.     

Modern taurine cattle descended from small number of near-eastern founders

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.     

Potential of combining morphometry and ancient DNA information to investigate grapevine domestication

The goal of this work was to explore the possibility (1) of carrying out both morphogeometric and archaeological DNA analyses on the same grape pips and (2) of comparing different molecular markers to reveal DNA variation, namely Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs). We focused on waterlogged seeds originating from three Roman and one medieval archaeological sites in France. Our first results indicate that taking photographs of pips is not detrimental to the preservation of DNA, provided a specific protocol is respected. Regarding the genetic markers, obtaining reliable information in sufficient quantity proved very difficult using SSRs. SNPs have a much more interesting potential, providing greater success rates and reliability. Here in four archaeological pips we studied 842 SNPs, derived from known polymorphisms in several genes, including one gene related to sex. Phylogenies built using these genetic markers indicate that three pips from the Roman site of Gasquinoy are close to modern wild grapevines and/or the female group, while the only medieval pip from Colletière is hermaphrodite and close to the modern cultivated group. Morphogeometrical results are in agreement with these findings. We conclude that the combined use of SNP markers and morphogeometry is promising for deciphering the intricate history of grapevine domestication.     

Chicken domestication: an updated perspective based on mitochondrial genomes

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A–I and W–Z. Common haplogroups A–G were shared by domestic chickens and red junglefowl. Rare haplogroups H–I and W–Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.     

Evolution and domestication of the Bovini species

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.     

Mining the pig genome to investigate the domestication process

Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.     

On the origin and domestication history of Barley (Hordeum vulgare)

Remains of barley (Hordeum vulgare) grains found at archaeological sites in the Fertile Crescent indicate that about 10,000 years ago the crop was domesticated there from its wild relative Hordeum spontaneum. The domestication history of barley is revisited based on the assumptions that DNA markers effectively measure genetic distances and that wild populations are genetically different and they have not undergone significant change since domestication. The monophyletic nature of barley domestication is demonstrated based on allelic frequencies at 400 AFLP polymorphic loci studied in 317 wild and 57 cultivated lines. The wild populations from Israel-Jordan are molecularly more similar than are any others to the cultivated gene pool. The results provided support for the hypothesis that the Israel-Jordan area is the region in which barley was brought into culture. Moreover, the diagnostic allele I of the homeobox gene BKn-3, rarely but almost exclusively found in Israel H. spontaneum, is pervasive in western landraces and modern cultivated varieties. In landraces from the Himalayas and India, the BKn-3 allele IIIa prevails, indicating that an allelic substitution has taken place during the migration of barley from the Near East to South Asia. Thus, the Himalayas can be considered a region of domesticated barley diversification.     

Documenting domestication: the intersection of genetics and archaeology

Domestication, a process of increasing mutual dependence between human societies and the plant and animal populations they target, has long been an area of interest in genetics and archaeology. Geneticists seek out markers of domestication in the genomes of domesticated species, both past and present day. Archaeologists examine the archaeological record for complementary markers--evidence of the human behavior patterns that cause the genetic changes associated with domestication, and the morphological changes in target species that result from them. In this article, we summarize the recent advances in genetics and archaeology in documenting plant and animal domestication, and highlight several promising areas where the complementary perspectives of both disciplines provide reciprocal illumination.     

Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe

Domesticated cattle were one of the cornerstones of European Neolithisation and are thought to have been introduced to Europe from areas of aurochs domestication in the Near East. This is consistent with mitochondrial DNA (mtDNA) data, where a clear separation exists between modern European cattle and ancient specimens of British aurochsen. However, we show that Y chromosome haplotypes of north European cattle breeds are more similar to haplotypes from ancient specimens of European aurochsen, than to contemporary cattle breeds from southern Europe and the Near East. There is a sharp north-south gradient across Europe among modern cattle breeds in the frequencies of two distinct Y chromosome haplotypes; the northern haplotype is found in 20 out of 21 European aurochsen or early domestic cattle dated 9500-1000 BC. This indicates that local hybridization with male aurochsen has left a paternal imprint on the genetic composition of modern central and north European breeds. Surreptitious mating between aurochs bulls and domestic cows may have been hard to avoid, or may have occurred intentionally to improve the breeding stock. Rather than originating from a few geographical areas only, as indicated by mtDNA, our data suggest that the origin of domestic cattle may be far more complex than previously thought.     

Cultivation as slow evolutionary entanglement: comparative data on rate and sequence of domestication

Recent studies have suggested that domestication was a slower evolutionary process than was previously thought. We address this issue by quantifying rates of phenotypic change in crops undergoing domestication, including five crops from the Near East (Triticum monococcum, T. dicoccum, Hordeum vulgare, Pisum sativum, Lens culinaris) and six crops from other regions (Oryza sativa, Pennisetum glaucum, Vigna radiata, Cucumis melo, Helianthus annus, Iva annua). We calculate rates using the metrics of darwin units and haldane units, which have been used in evolutionary biology, and apply this to data on non-shattering cereal spikelets and seed size. Rates are calculated by considering data over a 4,000-year period from archaeological sites in the region of origin, although we discuss the likelihood that a shorter period of domestication (1,000–2,000) years may be more appropriate for some crops, such as pulses. We report broadly comparable rates of change across all the crops and traits considered, and find that these are close to the averages and median values reported in various evolutionary biological studies. Nevertheless, there is still variation in rates between domesticates, such as melon seeds increasing at twice the rate of cereals, and between traits, such as non-shattering evolving faster than grain size. Such comparisons underline the utility of a quantitative approach to domestication rates, and the need to develop larger datasets for comparisons between crops and across regions.     

Cattle demographic history modelled from autosomal sequence variation

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.     

Toward understanding dog evolutionary and domestication history

Dog domestication was probably started very early during the Upper paleolithic period (~35,000 BP), thus well before any other animal or plant domestication. This early process, probably unconscious, is called proto-domestication to distinguish it from the real domestication process that has been dated around 14,000 BC. Genomic DNA analyses have shown recently that domestication started in the Middle East and rapidly expanded into all human populations. Nowadays, the dog population is fragmented in several hundreds of breeds well characterized by their phenotypes that offer a unique spectrum of polymorphism. More recent studies detect genetic signatures that will be useful to highlight breed history as well as the impact of domestication at the DNA level.     

Wheat domestication: lessons for the future

Wheat was one of the first crops to be domesticated more than 10,000 years ago in the Middle East. Molecular genetics and archaeological data have allowed the reconstruction of plausible domestication scenarios leading to modern cultivars. For diploid einkorn and tetraploid durum wheat, a single domestication event has likely occurred in the Karacadag Mountains, Turkey. Following a cross between tetraploid durum and diploid T.?tauschii, the resultant hexaploid bread wheat was domesticated and disseminated around the Caucasian region. These polyploidisation events facilitated wheat domestication and created genetic bottlenecks, which excluded potentially adaptive alleles. With the urgent need to accelerate genetic progress to confront the challenges of climate change and sustainable agriculture, wild ancestors and old landraces represent a reservoir of underexploited genetic diversity that may be utilized through modern breeding methods. Understanding domestication processes may thus help identifying new strategies.     

Are the early holocene cattle in the eastern sahara domestic or wild?

Questions relating to the antiquity of domestic cattle in the Sahara are among the most controversial in North African prehistory. It is generally believed that cattle were first domesticated in southwest Asia, particularly Anatolia, or in southeast Europe, where their remains have been found in several sites dated between 9,000 and 8,000 years ago.1 The discovery, in several small sites in the Western Desert of Egypt, of large bovid bones identified as domestic cattle and having radiocarbon dates ranging between 9,500 and 8,000 B.P. has raised the possibility that there was a separate, independent center for cattle domestication in northeast Africa (Fig. 1).^2–4 However, it has not been universally accepted that these bones are from cattle or, if so, that the cattle were domestic.