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Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
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Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
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2
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Leonardi M, Boschin F, Boscato P, Manica A. Following the niche: the differential impact of the last glacial maximum on four European ungulates. Commun Biol 2022; 5:1038. [PMID: 36175492 PMCID: PMC9523052 DOI: 10.1038/s42003-022-03993-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future. European megafaunal ungulates living in open habitats over the last 50,000 years showed evidence for niche change, possibly driven by climatic change and extinction of competitors and predators
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Affiliation(s)
- Michela Leonardi
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Francesco Boschin
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy.
| | - Paolo Boscato
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Aurochs roamed along the SW coast of Andalusia (Spain) during Late Pleistocene. Sci Rep 2022; 12:9911. [PMID: 35701579 PMCID: PMC9198092 DOI: 10.1038/s41598-022-14137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
In the Iberian Peninsula the fossil record of artiodactyls spans over 53 million years. During the Pleistocene, wild cattle species such as Bison and especially Bos became common. In Late Pleistocene, the aurochs (Bos primigenius) was widespread and the only bovine living along the large river valleys of southern Iberia. Although commonly found in fossil sites and especially in cave bone assemblages, the trace fossil record of aurochs was known worldwide only from the Holocene. Large bovine and roe deer/caprine tracks were found in at least five horizons of the early Late Pleistocene (MIS 5) beach and eolian deposits of Cape Trafalgar (Cadiz Province, South of Spain). The large bovine tracks are formally described as Bovinichnus uripeda igen. et isp. nov. and compared with the record of aurochs tracks, large red deer tracks and steppe bison biogeographical distribution in Iberia. Aurochs were the most likely producers of the newly described Trafalgar Trampled Surface (TTS) and some of the large artiodactyl tracks in the Matalascañas Trampled Surface, representing the oldest aurochs track record known. This new evidence, together with comparisons with the record of possible aurochs tracks in the Mid-Late Pleistocene coastal deposits from the Asperillo cliff section in Matalascañas (Huelva Province, SW Spain) and bone assemblages known in Gibraltar, point to a recurrent use of the coastal habitat by these large artiodactyls in SW Iberia.
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Torre S, Sebastiani F, Burbui G, Pecori F, Pepori AL, Passeri I, Ghelardini L, Selvaggi A, Santini A. Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis. FRONTIERS IN PLANT SCIENCE 2022; 13:826158. [PMID: 35242155 PMCID: PMC8886209 DOI: 10.3389/fpls.2022.826158] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 05/27/2023]
Abstract
Riparian ecosystems, in long-time developed regions, are among the most heavily impacted by human activities; therefore, the distribution of tree riparian species, such as Ulmus laevis, is highly affected. This phenomenon is particularly relevant at the margins of the natural habitat of the species, where populations are small and rare. In these cases, it is difficult to distinguish between relics or introductions, but it is relevant for the restoration of natural habitats and conservation strategies. The aim of this study was to study the phylogeography of the southern distribution of the species. We sequenced the entire chloroplast (cp) genomes of 54 individuals from five sampled populations across different European regions to highlight polymorphisms and analyze their distribution. Thirty-two haplotypes were identified. All the sampled populations showed private haplotypes that can be considered an indicator of long-term residency, given the low mutation rate of organellar DNA. The network of all haplotypes showed a star-like topology, and Serbian haplotypes were present in all branches. The Balkan population showed the highest level of nucleotide and genetic diversity. Low genetic differentiation between populations was observed but we found a significant differentiation among Serbia vs. other provenances. Our estimates of divergent time of U. laevis samples highlight the early split of above all Serbian individuals from other populations, emphasizing the reservoir role of white elm genetic diversity of Serbian population.
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Affiliation(s)
- Sara Torre
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Federico Sebastiani
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Guia Burbui
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Francesco Pecori
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Alessia L. Pepori
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Iacopo Passeri
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
| | - Luisa Ghelardini
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali (DAGRI), Università di Firenze, Florence, Italy
| | - Alberto Selvaggi
- Istituto per le Piante da Legno e l’Ambiente - I.P.L.A. S.p.A., Turin, Italy
| | - Alberto Santini
- Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Florence, Italy
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Mannen H, Yonezawa T, Murata K, Noda A, Kawaguchi F, Sasazaki S, Olivieri A, Achilli A, Torroni A. Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci Rep 2020; 10:20842. [PMID: 33257722 PMCID: PMC7704668 DOI: 10.1038/s41598-020-78040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.
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Affiliation(s)
- Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Kako Murata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Aoi Noda
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Asadollahpour Nanaei H, Dehghani Qanatqestani M, Esmailizadeh A. Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle. Genomics 2020; 112:880-885. [DOI: 10.1016/j.ygeno.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/02/2019] [Accepted: 06/01/2019] [Indexed: 12/23/2022]
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da Fonseca RR, Ureña I, Afonso S, Pires AE, Jørsboe E, Chikhi L, Ginja C. Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle. BMC Genomics 2019; 20:334. [PMID: 31053061 PMCID: PMC6500009 DOI: 10.1186/s12864-019-5685-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. RESULTS We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. CONCLUSIONS Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irene Ureña
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ana Elisabete Pires
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- LARC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisbon, Portugal
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lounès Chikhi
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande n°6, P-2780-156 Oeiras, Portugal
| | - Catarina Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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Wutke S, Sandoval-Castellanos E, Benecke N, Döhle HJ, Friederich S, Gonzalez J, Hofreiter M, Lõugas L, Magnell O, Malaspinas AS, Morales-Muñiz A, Orlando L, Reissmann M, Trinks A, Ludwig A. Decline of genetic diversity in ancient domestic stallions in Europe. SCIENCE ADVANCES 2018; 4:eaap9691. [PMID: 29675468 PMCID: PMC5906072 DOI: 10.1126/sciadv.aap9691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/01/2018] [Indexed: 05/12/2023]
Abstract
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
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Affiliation(s)
- Saskia Wutke
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | | | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
- Université de Toulouse, Université Paul Sabatier, Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Toulouse, France
| | - Monika Reissmann
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Alexandra Trinks
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Corresponding author.
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Hofman-Kamińska E, Bocherens H, Borowik T, Drucker DG, Kowalczyk R. Stable isotope signatures of large herbivore foraging habitats across Europe. PLoS One 2018; 13:e0190723. [PMID: 29293647 PMCID: PMC5749876 DOI: 10.1371/journal.pone.0190723] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
We investigated how do environmental and climatic factors, but also management, affect the carbon (δ13C) and nitrogen (δ15N) stable isotope composition in bone collagen of the two largest contemporary herbivores: European bison (Bison bonasus) and moose (Alces alces) across Europe. We also analysed how different scenarios of population recovery- reintroduction in bison and natural recovery in moose influenced feeding habitats and diet of these two species and compared isotopic signatures of modern populations of bison and moose (living in human-altered landscapes) with those occurring in early Holocene. We found that δ13C of modern bison and moose decreased with increasing forest cover. Decreasing forest cover, increasing mean annual temperature and feeding on farm crops caused an increase in δ15N in bison, while no factor significantly affected δ15N in moose. We showed significant differences in δ13C and δ15N among modern bison populations, in contrast to moose populations. Variation in both isotopes in bison resulted from inter-population differences, while in moose it was mainly an effect of intra-population variation. Almost all modern bison populations differed in δ13C and δ15N from early Holocene bison. Such differences were not observed in moose. It indicates refugee status of European bison. Our results yielded evidence that habitat structure, management and a different history of population recovery have a strong influence on foraging behaviour of large herbivores reflected in stable isotope signatures. Influence of forest structure on carbon isotope signatures of studied herbivores supports the “canopy effect” hypothesis.
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Affiliation(s)
| | - Hervé Bocherens
- Fachbereich Geowissenschaften, Forschungsbereich Paläobiologie, Universität Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Palaeoecology (HEP), Universität Tübingen, Tübingen, Germany
| | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Dorothée G. Drucker
- Fachbereich Geowissenschaften, Forschungsbereich Paläobiologie, Universität Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Palaeoecology (HEP), Universität Tübingen, Tübingen, Germany
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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10
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Burgio KR, Carlson CJ, Tingley MW. Lazarus ecology: Recovering the distribution and migratory patterns of the extinct Carolina parakeet. Ecol Evol 2017; 7:5467-5475. [PMID: 28770082 PMCID: PMC5528215 DOI: 10.1002/ece3.3135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
The study of the ecology and natural history of species has traditionally ceased when a species goes extinct, despite the benefit to current and future generations of potential findings. We used the extinct Carolina parakeet as a case study to develop a framework investigating the distributional limits, subspecific variation, and migratory habits of this species as a means to recover important information about recently extinct species. We united historical accounts with museum collections to develop an exhaustive, comprehensive database of every known occurrence of this once iconic species. With these data, we combined species distribution models and ordinal niche comparisons to confront multiple conjectured hypotheses about the parakeet's ecology with empirical data on where and when this species occurred. Our results demonstrate that the Carolina parakeet's range was likely much smaller than previously believed, that the eastern and western subspecies occupied different climatic niches with broad geographical separation, and that the western subspecies was likely a seasonal migrant while the eastern subspecies was not. This study highlights the novelty and importance of collecting occurrence data from published observations on extinct species, providing a starting point for future investigations of the factors that drove the Carolina parakeet to extinction. Moreover, the recovery of lost autecological knowledge could benefit the conservation of other parrot species currently in decline and would be crucial to the success of potential de‐extinction efforts for the Carolina parakeet.
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Affiliation(s)
- Kevin R Burgio
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
| | - Colin J Carlson
- Department of Environmental Science, Policy and Management University of California Berkeley CA USA
| | - Morgan W Tingley
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
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11
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Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L. Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. Mol Biol Evol 2016; 33:2801-2814. [PMID: 27436010 PMCID: PMC5062319 DOI: 10.1093/molbev/msw144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 × 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (∼150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors. We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource, and pathogen exposure) and on the key gene functions altered by the domestication process.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Supagro, Montferrier-sur-Lez, France IBC, Institut de Biologie Computationnelle, Montpellier, France
| | | | | | - Hugues Parinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Laurence Flori
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France INTERTRYP, CIRAD, IRD, Montpellier, France
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12
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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13
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Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, MacHugh DE, Park SDE, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JAM, Groenen MAM. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity (Edinb) 2016; 118:169-176. [PMID: 27677498 PMCID: PMC5234481 DOI: 10.1038/hdy.2016.79] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/10/2023] Open
Abstract
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.
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Affiliation(s)
- M R Upadhyay
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish Institute of Agricultural Sciences, Uppsala, Sweden
| | - W Chen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, CM Utrecht, The Netherlands
| | | | - D E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - S D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Dublin 2, Ireland
| | - D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - D Matassino
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - F Ciani
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - H-J Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A M van Arendonk
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - M A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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14
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Vai S, Vilaça ST, Romandini M, Benazzo A, Visentini P, Modolo M, Bertolini M, MacQueen P, Austin J, Cooper A, Caramelli D, Lari M, Bertorelle G. The Biarzo case in northern Italy: is the temporal dynamic of swine mitochondrial DNA lineages in Europe related to domestication? Sci Rep 2015; 5:16514. [PMID: 26549464 PMCID: PMC4637886 DOI: 10.1038/srep16514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 11/09/2022] Open
Abstract
Genetically-based reconstructions of the history of pig domestication in Europe are based on two major pillars: 1) the temporal changes of mitochondrial DNA lineages are related to domestication; 2) Near Eastern haplotypes which appeared and then disappeared in some sites across Europe are genetic markers of the first Near Eastern domestic pigs. We typed a small but informative fragment of the mitochondrial DNA in 23 Sus scrofa samples from a site in north eastern Italy (Biarzo shelter) which provides a continuous record across a ≈6,000 year time frame from the Upper Palaeolithic to the Neolithic. We additionally carried out several radiocarbon dating. We found that a rapid mitochondrial DNA turnover occurred during the Mesolithic, suggesting that substantial changes in the composition of pig mitochondrial lineages can occur naturally across few millennia independently of domestication processes. Moreover, so-called Near Eastern haplotypes were present here at least two millennia before the arrival of Neolithic package in the same area. Consequently, we recommend a re-evaluation of the previous idea that Neolithic farmers introduced pigs domesticated in the Near East, and that Mesolithic communities acquired domestic pigs via cultural exchanges, to include the possibility of a more parsimonious hypothesis of local domestication in Europe.
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Affiliation(s)
- Stefania Vai
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Sibelle Torres Vilaça
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Matteo Romandini
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | | | - Marta Modolo
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Marco Bertolini
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Peggy MacQueen
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | - Jeremy Austin
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Giorgio Bertorelle
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
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15
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Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A. Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East. PLoS One 2015; 10:e0141170. [PMID: 26513361 PMCID: PMC4626031 DOI: 10.1371/journal.pone.0141170] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/04/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. METHODOLOGY Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. CONCLUSIONS Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- * E-mail:
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Alessandro Fichera
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Milano), Italy
- Fondazione Telethon, Milano, Italy
| | - Silvia Bonfiglio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Anna De Gaetano
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ahmed El-Beltagi
- Animal Production Research Institute (APRI), Ministry of Agriculture, Cairo, Egypt
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Scheu A, Powell A, Bollongino R, Vigne JD, Tresset A, Çakırlar C, Benecke N, Burger J. The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genet 2015; 16:54. [PMID: 26018295 PMCID: PMC4445560 DOI: 10.1186/s12863-015-0203-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication. Results Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE. Conclusions The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0203-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amelie Scheu
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Adam Powell
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
| | - Ruth Bollongino
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Jean-Denis Vigne
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Anne Tresset
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Canan Çakırlar
- University of Groningen, Institute of Archaeology, Poststraat 6, NL-9712 ER, Groningen, Netherlands.
| | - Norbert Benecke
- German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Joachim Burger
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
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18
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Niemi M, Bläuer A, Iso-Touru T, Harjula J, Nyström Edmark V, Rannamäe E, Lõugas L, Sajantila A, Lidén K, Taavitsainen JP. Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses. PLoS One 2015; 10:e0123821. [PMID: 25992976 PMCID: PMC4439080 DOI: 10.1371/journal.pone.0123821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. RESULTS Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). CONCLUSIONS The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.
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Affiliation(s)
- Marianna Niemi
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- University of Helsinki, Department of Forensic Medicine, Helsinki, Finland
- * E-mail:
| | - Auli Bläuer
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | - Terhi Iso-Touru
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | - Janne Harjula
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | | | - Eve Rannamäe
- Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Lembi Lõugas
- Institute of history, Tallinn University, Tallinn, Estonia
| | - Antti Sajantila
- University of Helsinki, Department of Forensic Medicine, Helsinki, Finland
| | - Kerstin Lidén
- Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
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Utsunomiya YT, Pérez O'Brien AM, Sonstegard TS, Sölkner J, Garcia JF. Genomic data as the "hitchhiker's guide" to cattle adaptation: tracking the milestones of past selection in the bovine genome. Front Genet 2015; 6:36. [PMID: 25713583 PMCID: PMC4322753 DOI: 10.3389/fgene.2015.00036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle "hitchhiked" on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field.
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Affiliation(s)
- Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture Beltsville, MA, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista (UNESP) Araçatuba, São Paulo, Brazil
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Incorporation of aurochs into a cattle herd in Neolithic Europe: single event or breeding? Sci Rep 2014; 4:5798. [PMID: 25052335 PMCID: PMC4107343 DOI: 10.1038/srep05798] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/04/2014] [Indexed: 12/02/2022] Open
Abstract
Domestication is an ongoing process continuously changing the lives of animals and humans and the environment. For the majority of European cattle (Bos taurus) genetic and archaeozoological evidence support initial domestication ca. 11'000 BP in the Near East from few founder aurochs (Bos primigenius) belonging to the mitochondrial DNA T macro-haplogroup. Gene flow between wild European aurochs of P haplogroup and domestic cattle of T haplogroup, coexisting over thousands of years, appears to have been sporadic. We report archaeozoological and ancient DNA evidence for the incorporation of wild stock into a domestic cattle herd from a Neolithic lake-dwelling in Switzerland. A complete metacarpus of a small and compact adult bovid is morphologically and genetically a female. With withers height of ca. 112 cm, it is comparable in size with small domestic cattle from contemporaneous sites in the area. The bone is directly dated to 3360–3090 cal BC and associated to the Horgen culture, a period of the secondary products revolution. The cow possessed a novel mtDNA P haplotype variant of the European aurochs. We argue this is either a single event or, based on osteological characteristics of the Horgen cattle, a rare instance of intentional breeding with female aurochs.
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21
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New World cattle show ancestry from multiple independent domestication events. Proc Natl Acad Sci U S A 2013; 110:E1398-406. [PMID: 23530234 DOI: 10.1073/pnas.1303367110] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment.
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22
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Larson G, Burger J. A population genetics view of animal domestication. Trends Genet 2013; 29:197-205. [PMID: 23415592 DOI: 10.1016/j.tig.2013.01.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/26/2022]
Abstract
The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emphasising the importance of an explicit hypothesis-testing approach for the inference of the origins and subsequent evolution and demography of domestic animals. By applying next-generation sequencing technology alongside appropriate biostatistical methodologies, a substantially deeper understanding of domestication is on the horizon.
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Affiliation(s)
- Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK.
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23
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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Bollongino R, Burger J, Powell A, Mashkour M, Vigne JD, Thomas MG. Modern taurine cattle descended from small number of near-eastern founders. Mol Biol Evol 2012; 29:2101-4. [PMID: 22422765 DOI: 10.1093/molbev/mss092] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Gravlund P, Aaris-Sørensen K, Hofreiter M, Meyer M, Bollback JP, Noe-Nygaard N. Ancient DNA extracted from Danish aurochs (Bos primigenius): genetic diversity and preservation. Ann Anat 2011; 194:103-11. [PMID: 22188739 DOI: 10.1016/j.aanat.2011.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 10/11/2011] [Accepted: 10/14/2011] [Indexed: 10/15/2022]
Abstract
We extracted DNA from 39 Danish aurochs specimens and successfully amplified and sequenced a 252 base pair long fragment of the multivariable region I of the mitochondrial control region from 11 specimens. The sequences from these specimens dated back to 9830-2865 14Cyr BP and represent the first study of genetic variation of Danish aurochs. In addition, for all specimens we address correlations between the ability to obtain DNA sequences and various parameters such as the age of the sample, the collagen content, the museum storage period, Danish geography and whether the specimens were found in an archeological or geological context. We find that aurochs from southern Scandinavia display a star-shaped population genetic structure, that is indicative of a local and relatively recent diversification from a few ancestral haplotypes that may have originated in the ancestral Western European population before migration northwards during the retreat of the glaciers. Scenarios suggesting several invasions of genetically distinct aurochs are not supported by these analyses. Rather, our results suggest that a single continuous migration northward occurred. Our findings also suggest, although with only limited support, that aurochs in Northwestern Europe underwent a population expansion beginning shortly after the retreat of the glacial ice from Denmark and had a stable population size until the population decline that must have occurred prior to extinction. The absence of haplotypes similar to modern domestic cattle in our aurochs suggests that introgression between these species must have been limited, if it occurred at all. We found that the successful recovery of genetic material for PCR amplification correlates with sample age and local geographic conditions. However, contrary to other studies, we found no significant correlation between length of time in museum storage or the type of the locality in which a specimen was discovered (archeological or geological) and amplification success. Finally, we found large variances in our estimates of collagen content preventing an evaluation of this as an indicator of preservation quality.
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Affiliation(s)
- Peter Gravlund
- The Natural History Museum of Denmark, University of Copenhagen, Denmark.
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26
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Lye GC, Lepais O, Goulson D. Reconstructing demographic events from population genetic data: the introduction of bumblebees to New Zealand. Mol Ecol 2011; 20:2888-900. [PMID: 21645159 DOI: 10.1111/j.1365-294x.2011.05139.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Four British bumblebee species (Bombus terrestris, Bombus hortorum, Bombus ruderatus and Bombus subterraneus) became established in New Zealand following their introduction at the turn of the last century. Of these, two remain common in the United Kingdom (B. terrestris and B. hortorum), whilst two (B. ruderatus and B. subterraneus) have undergone marked declines, the latter being declared extinct in 2000. The presence of these bumblebees in New Zealand provides an unique system in which four related species have been isolated from their source population for over 100 years, providing a rare opportunity to examine the impacts of an initial bottleneck and introduction to a novel environment on their population genetics. We used microsatellite markers to compare modern populations of B. terrestris, B. hortorum and B. ruderatus in the United Kingdom and New Zealand and to compare museum specimens of British B. subterraneus with the current New Zealand population. We used approximate Bayesian computation to estimate demographic parameters of the introduction history, notably to estimate the number of founders involved in the initial introduction. Species-specific patterns derived from genetic analysis were consistent with the predictions based on the presumed history of these populations; demographic events have left a marked genetic signature on all four species. Approximate Bayesian analyses suggest that the New Zealand population of B. subterraneus may have been founded by as few as two individuals, giving rise to low genetic diversity and marked genetic divergence from the (now extinct) UK population.
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Affiliation(s)
- G C Lye
- School of Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK.
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The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy. BMC Evol Biol 2011; 11:32. [PMID: 21281509 PMCID: PMC3039592 DOI: 10.1186/1471-2148-11-32] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 01/31/2011] [Indexed: 01/17/2023] Open
Abstract
Background Bos primigenius, the aurochs, is the wild ancestor of modern cattle breeds and was formerly widespread across Eurasia and northern Africa. After a progressive decline, the species became extinct in 1627. The origin of modern taurine breeds in Europe is debated. Archaeological and early genetic evidence point to a single Near Eastern origin and a subsequent spread during the diffusion of herding and farming. More recent genetic data are instead compatible with local domestication events or at least some level of local introgression from the aurochs. Here we present the analysis of the complete mitochondrial genome of a pre-Neolithic Italian aurochs. Results In this study, we applied a combined strategy employing both multiplex PCR amplifications and 454 pyrosequencing technology to sequence the complete mitochondrial genome of an 11,450-year-old aurochs specimen from Central Italy. Phylogenetic analysis of the aurochs mtDNA genome supports the conclusions from previous studies of short mtDNA fragments - namely that Italian aurochsen were genetically very similar to modern cattle breeds, but highly divergent from the North-Central European aurochsen. Conclusions Complete mitochondrial genome sequences are now available for several modern cattle and two pre-Neolithic mtDNA genomes from very different geographic areas. These data suggest that previously identified sub-groups within the widespread modern cattle mitochondrial T clade are polyphyletic, and they support the hypothesis that modern European breeds have multiple geographic origins.
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Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, Stock F, Gama LT, Penedo MCT, Bradley DG, Lenstra JA, Nijman IJ. Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation. PLoS One 2011; 6:e15922. [PMID: 21253012 PMCID: PMC3016991 DOI: 10.1371/journal.pone.0015922] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/29/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.
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Affiliation(s)
- Ceiridwen J. Edwards
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Research Laboratory for Archaeology, University of Oxford, Oxford, United Kingdom
| | - Catarina Ginja
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | | | - Anne Tresset
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, CNRS Muséum National d'Histoire Naturelle, Paris, France
| | - Frauke Stock
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Luis T. Gama
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - M. Cecilia T. Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Isaäc J. Nijman
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One 2010; 5:e15760. [PMID: 21209945 PMCID: PMC3011016 DOI: 10.1371/journal.pone.0015760] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. METHODOLOGY The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. CONCLUSIONS Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl EM. An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One 2010; 5. [PMID: 20927390 PMCID: PMC2946917 DOI: 10.1371/journal.pone.0013042] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/10/2010] [Indexed: 11/19/2022] Open
Abstract
Background PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface contamination, (iii) carry-over contamination, and (iv) contamination of reagents. Methodology/Principal Findings Here we performed a quantitative evaluation of current decontamination methods for these last three sources of contamination, and developed a new procedure to eliminate contaminating DNA contained in PCR reagents. We observed that most current decontamination methods are either not efficient enough to degrade short contaminating DNA molecules, rendered inefficient by the reagents themselves, or interfere with the PCR when used at doses high enough to eliminate these molecules. We also show that efficient reagent decontamination can be achieved by using a combination of treatments adapted to different reagent categories. Our procedure involves γ- and UV-irradiation and treatment with a mutant recombinant heat-labile double-strand specific DNase from the Antarctic shrimp Pandalus borealis. Optimal performance of these treatments is achieved in narrow experimental conditions that have been precisely analyzed and defined herein. Conclusions/Significance There is not a single decontamination method valid for all possible contamination sources occurring in PCR reagents and in the molecular biology laboratory and most common decontamination methods are not efficient enough to decontaminate short DNA fragments of low concentration. We developed a versatile multistrategy decontamination procedure for PCR reagents. We demonstrate that this procedure allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA.
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Affiliation(s)
- Sophie Champlot
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
| | - Camille Berthelot
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
| | - E. Andrew Bennett
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
| | - Thierry Grange
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, Paris, France
- * E-mail:
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Ajmone-Marsan P, Garcia JF, Lenstra JA. On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol 2010. [DOI: 10.1002/evan.20267] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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