scholarly journals Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

2018 ◽  
Vol 11 (9) ◽  
pp. 1642-1655 ◽  
Author(s):  
Nuno Miguel Silva ◽  
Jeremy Rio ◽  
Susanne Kreutzer ◽  
Christina Papageorgopoulou ◽  
Mathias Currat
Keyword(s):  
Bayesian Estimation ◽  
Ancient Dna ◽  
Spatially Explicit ◽  
Population Continuity ◽  
Partial Population

scholarly journals Effect of population structure and migration when investigating genetic continuity using ancient DNA

2016 ◽  
Author(s):  
NM Silva ◽  
S Kreutzer ◽  
C Papageorgopoulou ◽  
M Currat
Keyword(s):  
Population Structure ◽  
Ancient Dna ◽  
Isolated Populations ◽  
Hunter Gatherers ◽  
History Of ◽  
Genetic Continuity ◽  
Population Continuity ◽  
Local Hunter ◽  
And Migration ◽  
Genetic Pool

AbstractRecent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially-explicit approach to the previous non-spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter-gatherers as large as 83% cannot be entirely ruled out.

scholarly journals Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis

2014 ◽  
Vol 14 (1) ◽  
pp. 70 ◽  
Author(s):  
Ross Barnett ◽  
Nobuyuki Yamaguchi ◽  
Beth Shapiro ◽  
Simon YW Ho ◽  
Ian Barnes ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Demographic History ◽  
Panthera Leo ◽  
Spatially Explicit ◽  
Genealogical Analysis ◽  
History Of

scholarly journals Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2006) ◽  
pp. e59
Author(s):  
Yvonne L. Chan ◽  
Christian Nileus Kaalstad Anderson ◽  
Elizabeth A. Hadly
Keyword(s):  
Bayesian Estimation ◽  
Ancient Dna ◽  
Population Bottleneck

scholarly journals Bayesian Estimation of Sequence Damage in Ancient DNA

2007 ◽  
Vol 24 (6) ◽  
pp. 1416-1422 ◽  
Author(s):  
Simon Y. W. Ho ◽  
Tim H. Heupink ◽  
Andrew Rambaut ◽  
Beth Shapiro
Keyword(s):  
Bayesian Estimation ◽  
Ancient Dna

scholarly journals Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA

PLoS Genetics ◽  
2006 ◽  
Vol 2 (4) ◽  
pp. e59 ◽  
Author(s):  
Yvonne L Chan ◽  
Christian N. K Anderson ◽  
Elizabeth A Hadly
Keyword(s):  
Bayesian Estimation ◽  
Ancient Dna ◽  
Population Bottleneck

scholarly journals Bayesian Estimation of Sequence Damage in Ancient DNA

2007 ◽  
Vol 24 (7) ◽  
pp. 1576-1576 ◽  
Author(s):  
S. Y. W. Ho ◽  
T. H. Heupink ◽  
A. Rambaut ◽  
B. Shapiro
Keyword(s):  
Bayesian Estimation ◽  
Ancient Dna

scholarly journals Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content

2011 ◽  
Vol 60 (3) ◽  
pp. 366-375 ◽  
Author(s):  
Simon Y. W. Ho ◽  
Robert Lanfear ◽  
Matthew J. Phillips ◽  
Ian Barnes ◽  
Jessica A. Thomas ◽  
...  
Keyword(s):  
Bayesian Estimation ◽  
Information Content ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Substitution Rates
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