Search

Your search keyword '"Macaulay, Vincent"' showing total 240 results
Start Over Author "Macaulay, Vincent"
240 results on '"Macaulay, Vincent"'

2. Natural Selection Shaped Regional mtDNA Variation in Humans

Author

Mishmar, Dan, Ruiz-Pesini, Eduardo, Golik, Pawel, Macaulay, Vincent, Clark, Andrew G., Hosseini, Seyed, Brandon, Martin, Easley, Kirk, Chen, Estella, Brown, Michael D., Sukernik, Rem I., Olckers, Antonel, and Wallace, Douglas C.

Published
2003

6. Tracing Modern Human Origins

Author

Harpending, Henry, Eswaran, Vlnayak, Macaulay, Vincent, Hill, Catherine, Achilli, Alessandro, Rengo, Chiara, Clarke, Douglas, Meehan, William, Blackburn, James, Semino, Ornella, Scozzari, Rosaria, Cruciani, Fulvio, Taha, Adi, Shaari, Norazila Kassim, Raja, Joseph Maripa, Ismail, Patimah, Zainuddin, Zafarina, Goodwin, William, Bulbeck, David, Bandelt, Hans-Jürgen, Oppenheimer, Stephen, Torroni, Antonio, Richards, Martin, Thangaraj, Kumarasamy, Chaubey, Gyaneshwer, Kivisild, Toomas, Reddy, Alla G., Singh, Vijay K., Rasalkar, Avinash A., and Singh, Lalji

Published
2005

7. Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

Author

Macaulay, Vincent, Hill, Catherine, Achilli, Alessandro, Rengo, Chiara, Clarke, Douglas, Meehan, William, Blackburn, James, Semino, Ornella, Scozzari, Rosaria, Cruciani, Fulvio, Taha, Adi, Shaari, Norazila Kassim, Raja, Joseph Maripa, Ismail, Patimah, Zainuddin, Zafarina, Goodwin, William, Bulbeck, David, Bandelt, Hans-Jürgen, Oppenheimer, Stephen, Torroni, Antonio, and Richards, Martin

Published
2005

9. Resolving the ancestry of Austronesian-speaking populations

Author

Soares, Pedro A., Trejaut, Jean A., Rito, Teresa, Cavadas, Bruno, Hill, Catherine, Eng, Ken Khong, Mormina, Maru, Brandão, Andreia, Fraser, Ross M., Wang, Tse-Yi, Loo, Jun-Hun, Snell, Christopher, Ko, Tsang-Ming, Amorim, António, Pala, Maria, Macaulay, Vincent, Bulbeck, David, Wilson, James F., Gusmão, Leonor, Pereira, Luísa, Oppenheimer, Stephen, Lin, Marie, and Richards, Martin B.

Published
2016
Full Text
View/download PDF

13. Correcting for purifying selection: an improved human mitochondrial molecular clock

Author

Soares, Pedro, Ermini, Luca, Thomson, Noel, Mormina, Maru, Rito, Teresa, Rohl, Arne, Salas, Antonio, Oppenheimer, Stephen, Macaulay, Vincent, and Richards, Martin B.

Subjects
Mitochondrial DNA -- Research, Human genome -- Research, Cladistic analysis -- Usage, Gene mutations -- Research, Molecular clock (Genetics) -- Evaluation, Biological sciences
Abstract

The article discusses time-dependent mutation rate based on mtDNA genome supported by neutral. It further discusses the improved rates for mtDNA control region and estimates the positional mutation rates for human mtDNA.

Published
2009

14. A mitochondrial stratigraphy for Island Southeast Asia

Author

Hill, Catherine, Soares, Pedro, Mormina, Maru, Macaulay, Vincent, Clarke, Dougie, Blumbach, Petya B., Vizuete-Forster, Matthieu, Forster, Peter, Bulbeck, David, Oppenheimer, Stephen, and Richards, Martin

Subjects
Mitochondrial DNA -- Research, Biological diversity -- Research, Human population genetics -- Research, Biological sciences
Abstract

The two-tier population history of Island Southeast Asia (ISEA) is refuted by demonstrating that mitochondrial DNA diversity in the region is extremely high and includes a large number of indigenous clades. The movement and expansion of indigenous mtDNA lineages, studied through coding-region and control-region variants obtained from complete sequence data, suggest that the prehistory of the region has to be rethought.

Published
2007

16. Shipwrecks and founder effects: divergent demographic histories reflected in Caribbean mtDNA

Author

Salas, Antonio, Richards, Martin, Lareu, Maria-Victoria, Sobrino, Beatriz, Silva, Sandra, Matamoros, Mireya, Macaulay, Vincent, and Carracedo, Angel

Subjects
Mitochondrial DNA -- Research, Caribs -- Origin, Caribs -- Physiological aspects, Garifunas -- Origin, Garifunas -- Physiological aspects, Anthropology/archeology/folklore
Abstract

During the period of the Atlantic slave trade (15th-19th centuries), millions of people were forced to move from Africa to many American destinations, changing dramatically the human landscape of the Americas. Here, we analyze mitochondrial DNA from two different American populations with African ancestry, with hitherto unknown European and Native American components. On the basis of historical records, African-Americans from Choco (Colombia) and the Garifunas (or 'Black Carib') of Honduras are likely to have had very different demographic histories, with a significant founder effect in the formation of the latter. Both the common features and differences are reflected in their mtDNA composition. Both show a minor component (~16%) from Native Central/South Americans and a larger component (~84%) from sub-Saharan Africans. The latter component is very diverse in the African-Americans from Choco, similar to that of sub-Saharan Africans, but much less so in the Garifunas, with several mtDNA types elevated to high frequency, suggesting the action of genetic drift. KEY WORDS mtDNA; HVS-I; HVS-II; haplogroup; Carib; Garifunas; Choco; Africa; slave trade

Published
2005

17. Charting the ancestry of African Americans

Author

Salas, Antonio, Carracedo, Angel, Richards, Martin, and Macaulay, Vincent

Subjects
African Americans -- Genetic aspects, Biological sciences
Published
2005

25. The making of the African mtDNA landscape

Author

Salas, Antonio, Richards, Martin, De la Fe Tomas, Lareu, Maria-Victoria, Sobrino, Beatriz, Sanchez-Diz, Paula, Macaulay, Vincent, and Carracedo, Angel

Subjects
Evolution -- Research, Human genetics -- Research, Mitochondrial DNA -- Analysis, Biological sciences
Published
2002

26. A back migration from Asia to Sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes

Author

Cruciani, Fulvio, Santolamazza, Piero, Shen, Peidong, Macaulay, Vincent, Moral, Pedro, Olckers, Antonel, Modiano, David, Holmes, Susan, Destro-Bisol, Giovanni, Coia, Valentina, Wallace, Douglas C., Oefner, Peter J., Torroni, Antonio, Cavalli-Sforza, L. Luca, Scozzari, Rosaria, and Underhill, Peter A.

Subjects
Genetic research -- Analysis, Y chromosome -- Genetic aspects, Haploidy -- Research, DNA -- Genetic aspects, Human evolution -- Genetic aspects, Heredity -- Genetic aspects, Phylogeny -- Genetic aspects, Biological sciences
Published
2002

28. Do the four clades of the mtDNA haplogroup L2 evolve at different rates?

Author

Torroni, Antonio, Rengo, Chiara, Guida, Valentina, Cruciani, Fulvio, Sellitto, Daniele, Coppa, Alfredo, Calderon, Fernando Luna, Simionati, Barbara, Valle, Giorgi, Richards, Martin, Macaulay, Vincent, and Scozzari, Rosaria

Subjects
Human genetics -- Research, DNA -- Demographic aspects, Haplotypes -- Research, Neutral evolution, Biological sciences
Published
2001

29. The emerging tree of west Eurasian mtDNAs: a synthesis on control-region sequences and RFLPs

Author

Macaulay, Vincent, Richards, Martin, Hickey, Eileen, Vega, Emilce, Cruciani, Fulvio, Guida, Valentina, Scozzari, Rosaria, Bonne-Tamir, Batsheva, Torroni, Antonio, and Sykes, Bryan

Subjects
Northern Africa -- Demographic aspects, Eurasia -- Demographic aspects, Caucasus region -- Demographic aspects, Middle East -- Demographic aspects, Berbers -- Genetic aspects, Mitochondrial DNA -- Analysis, Human beings -- Migrations, Chromosome mapping -- Usage, Ethnology -- Middle East, Cladistic analysis -- Usage, Biological sciences
Abstract

An analysis based on two systems for describing the human mitochondrial genome (mtDNA) has been carried out using 95 samples from the Near East and northwest Caucasus. One procedure is assaying restriction fragment length polymorphisms (RFLPs) all through the genome and the other is sequencing of parts of the control region (CR). The concordance of the two systems has been demonstrated. Variation in mtDNA is used to infer histories of peoples. The most refined phylogeny so far found for west Eurasian mtDNA has been presented and a nomenclature described and applied for mtDNA clusters. Hypervariable nucleotides have been identified. Relative mutation rates of the two systems have been evaluated with ambiguities identified. Berber speakers were sampled and a identification of signature mutations for each cluster led to a hierarchical scheme for finding cluster composition. The main indigenous North African cluster is a sister group to the most ancient cluster of European mRNAs. It diverged about 50,000 years ago.

Published
1999

30. Climate Change and Postglacial Human Dispersals in Southeast Asia

Author

Soares, Pedro, Trejaut, Jean Alain, Loo, Jun-Hun, Hill, Catherine, Mormina, Maru, Lee, Chien-Liang, Chen, Yao-Ming, Hudjashov, Georgi, Forster, Peter, Macaulay, Vincent, Bulbeck, David, Oppenheimer, Stephen, Lin, Marie, and Richards, Martin B.

Published
2008

31. A phylogenetic Gaussian process model for the evolution of curves embedded in d-dimensions

Author

Marinas-Collado, Irene, Bowman, Adrian, and Macaulay, Vincent

Subjects
ComputingMethodologies_COMPUTERGRAPHICS
Abstract

Statistical methods which enable shape information on organisms to be used to construct a phylogenetic tree and to learn how shape evolves are developed. In particular, this allows the evolution of facial curves to be used in studying relationships between and within different ethnic groups and their ancestors. The main challenge is to exploit the details of surface shape, while maintaining computational feasibility. A Gaussian process approach is adopted.

Published
2019

32. Rectifying long-standing misconceptions about the p statistic for molecular dating

Author

Macaulay, Vincent, Soares, Pedro, and Richards, Martin B.

Abstract

When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.

Published
2019

35. Human Origins and Ancient Human DNA

Author

Cooper, Alan, Rambaut, Andrew, Macaulay, Vincent, Willerslev, Eske, Hansen, Anders J., Stringer, Chris, Adcock, Gregory J., Dennis, Elizabeth S., Easteal, Simon, Huttley, Gavin A., Jermiin, Lars S., Peacock, W. James, and Thorne, Alan

Published
2001

38. mtDNA phylogeny and evolution of laboratory mouse strains

Author

Goios, Ana, Pereira, Luisa, Bogue, Molly, Macaulay, Vincent, and Amorim, Antonio

Subjects
Mitochondrial DNA -- Research, Mice -- Genetic aspects, Mice -- Research, Phylogeny -- Research, Health
Abstract

Female inbred mouse phylogenetic of newly generated complete mitochondrial DNA sequence data in 16 strains were analyzed to show that all common strains descend from the same Mus musculus domesticus female wild ancestor. The findings confirm the hypothesis that M. m. molossinus is a hybrid and its mtDNA shares a common ancestor with M. m. musculus.

Published
2007

39. High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium

Author

Pereira, Luisa, Richards, Martin, Goios, Ana, Alonso, Antonio, Albarran, Cristina, Garcia, Oscar, Behar, Doron M., Golge, Mukaddes, Hatina, Jiri, Al-Gazali, Lihadh, Bradley, Daniel G., Macaulay, Vincent, and Amorim, Antonio

Subjects
Genetic polymorphisms -- Research, Human genome -- Research, Mitochondrial DNA -- Research, Health
Abstract

The critical polymorphisms that define sub-clades within a mitochondrial DNA (mtDNA) haplogroup are identified with the use of limited volumes of complete mtDNA sequence data by providing a springboard for large-scale high-resolution screening of human mtDNAs. The enhanced geneological resolution clearly shows that sub-clades of haplogroup H have highly distinctive geographical distributions.

Published
2005

41. Interdisciplinary approach to the demography of Jamaica

Author

Deason Michael L, Salas Antonio, Newman Simon P, Macaulay Vincent A, st A Morrison Errol Y, and Pitsiladis Yannis P

Subjects
Evolution, QH359-425
Abstract

Abstract Background The trans-Atlantic slave trade dramatically changed the demographic makeup of the New World, with varying regions of the African coast exploited differently over roughly a 400 year period. When compared to the discrete mitochondrial haplotype distribution of historically appropriate source populations, the unique distribution within a specific source population can prove insightful in estimating the contribution of each population. Here, we analyzed the first hypervariable region of mitochondrial DNA in a sample from the Caribbean island of Jamaica and compared it to aggregated populations in Africa divided according to historiographically defined segments of the continent's coastline. The results from these admixture procedures were then compared to the wealth of historic knowledge surrounding the disembarkation of Africans on the island. Results In line with previous findings, the matriline of Jamaica is almost entirely of West African descent. Results from the admixture analyses suggest modern Jamaicans share a closer affinity with groups from the Gold Coast and Bight of Benin despite high mortality, low fecundity, and waning regional importation. The slaves from the Bight of Biafra and West-central Africa were imported in great numbers; however, the results suggest a deficit in expected maternal contribution from those regions. Conclusions When considering the demographic pressures imposed by chattel slavery on Jamaica during the slave era, the results seem incongruous. Ethnolinguistic and ethnographic evidence, however, may explain the apparent non-random levels of genetic perseverance. The application of genetics may prove useful in answering difficult demographic questions left by historically voiceless groups.

Published
2012
Full Text
View/download PDF

43. Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6

Author

Costa Marta D, Pereira Joana B, Fernandes Verónica, Franco-Duarte Ricardo, Silva Nuno M, Pereira Luísa, Martins Haidé, Soares Pedro, Behar Doron M, Richards Martin B, and Macaulay Vincent

Subjects
Evolution, QH359-425
Abstract

Abstract Background The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene. Results Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East. Conclusions A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6's European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast.

Published
2010
Full Text
View/download PDF

45. Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past

Author

Olivieri, Anna, primary, Sidore, Carlo, additional, Achilli, Alessandro, additional, Angius, Andrea, additional, Posth, Cosimo, additional, Furtwängler, Anja, additional, Brandini, Stefania, additional, Capodiferro, Marco Rosario, additional, Gandini, Francesca, additional, Zoledziewska, Magdalena, additional, Pitzalis, Maristella, additional, Maschio, Andrea, additional, Busonero, Fabio, additional, Lai, Luca, additional, Skeates, Robin, additional, Gradoli, Maria Giuseppina, additional, Beckett, Jessica, additional, Marongiu, Michele, additional, Mazzarello, Vittorio, additional, Marongiu, Patrizia, additional, Rubino, Salvatore, additional, Rito, Teresa, additional, Macaulay, Vincent, additional, Semino, Ornella, additional, Pala, Maria, additional, Abecasis, Gonçalo R., additional, Schlessinger, David, additional, Conde-Sousa, Eduardo, additional, Soares, Pedro, additional, Richards, Martin B., additional, Cucca, Francesco, additional, and Torroni, Antonio, additional

Published
2017
Full Text
View/download PDF

46. The Mitochondrial Gene Tree Comes of Age

Author

Richards, Martin and Macaulay, Vincent

Subjects
Mitochondrial DNA -- Research, Human evolution -- Research, Genetic research -- Analysis, Mutation (Biology) -- Research, Biological sciences
Published
2001

47. Tracing European Founder Lineages in the Near Eastern mtDNA Pool

Author

Richards, Martin, Macaulay, Vincent, Hickey, Eileen, Vega, Emilce, Sykes, Bryan, Guida, Valentina, Rengo, Chiara, Sellitto, Daniele, Cruciani, Fulvio, Kivisild, Toomas, Villems, Richard, Thomas, Mark, Rychkov, Serge, Rychkov, Oksana, Rychkov, Yuri, Golge, Mukaddes, Dimitrov, Dimitar, Hill, Emmeline, Bradley, Dan, Romano, Valentino, Cali, Francesco, Vona, Giuseppe, Demaine, Andrew, Papiha, Surinder, Triantaphyllidis, Costas, Stefanescu, Gheorghe, Hatina, Jiri, Belledi, Michele, Di Rienzo, Anna, Novelletto, Andrea, Oppenheim, Ariella, Norby, Soren, Al-Zaheri, Nadia, Santachiara-Benerecetti, Silvana, Scozzari, Rosaria, Torroni, Antonio, and Bandelt, Hans-Jurgen

Subjects
Genetic research -- Analysis, Human genetics -- Research, Biological sciences
Published
2000

48. Authors' Reply

Author

Salas, Antonio, Yao, Yong-Gang, Macaulay, Vincent, Vega, Ana, Carracedo, Ángel, and Bandelt, Hans-Jürgen

Subjects
Genetics, Medical, DNA Mutational Analysis, Reproducibility of Results, Correspondence and Other Communications, Genetics/Genomics/Gene Therapy, DNA, Mitochondrial, Haplotypes, Oncology, Research Design, Neoplasms, Mutation, Biomarkers, Tumor, Humans, Diagnostic Errors, Artifacts, Databases, Nucleic Acid, Phylogeny, Research Article, Cancer Biology
Abstract

Background Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results. Methods and Findings In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis. Conclusion The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research., The role of mitochondria in tumorigenesis remains unclear; in this paper Salas and colleagues raise concerns over many published studies

Published
2005

50. Ancient Voyaging and Polynesian Origins

Author

Soares, Pedro, Rito, Teresa, Trejaut, Jean Alain, Mormina, Maru, Hill, Catherine, Tinkler-Hundal, Emma, Braid, Michelle, Clarke, Douglas, Loo, Jun-Hun, Thomson, Noel, Denham, Tim, Donohue, Mark, Macaulay, Vincent, Lin, Marie, Oppenheimer, Stephen James, Richards, Martin, Soares, Pedro, Rito, Teresa, Trejaut, Jean Alain, Mormina, Maru, Hill, Catherine, Tinkler-Hundal, Emma, Braid, Michelle, Clarke, Douglas, Loo, Jun-Hun, Thomson, Noel, Denham, Tim, Donohue, Mark, Macaulay, Vincent, Lin, Marie, Oppenheimer, Stephen James, and Richards, Martin

Abstract

The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka)

Published
2011

Catalog

Books, media, physical & digital resources
See catalog results