Inferences from DNA Data: Population Histories, Evolutionary Processes and Forensic Match Probabilities

Abstract

Summary. We develop a flexible class of Metropolis-Hastings algorithms for drawing inferences about population histories and mutation rates from deoxyribonucleic acid (DNA) sequence data. Match probabilities for use in forensic identification are also obtained, which is particularly useful for mitochondrial DNA profiles. Our data augmentation approach, in which the ancestral DNA data are inferred at each node of the genealogical tree, simplifies likelihood calculations and permits a wide class of mutation models to be employed, so that many different types of DNA sequence data can be analysed within our framework. Moreover, simpler likelihood calculations imply greater freedom for generating tree proposals, so that algorithms with good mixing properties can be implemented. We incorporate the effects of demography by means of simple mechanisms for changes in population size and structure, and we estimate the corresponding demographic parameters, but we do not here allow for the effects of either recombination or selection. We illustrate our methods by application to four human DNA data sets, consisting of DNA sequences, short tandem repeat loci, single-nucleotide polymorphism sites and insertion sites. Two of the data sets are drawn from the male-specific Y-chromosome, one from maternally inherited mitochondrial DNA and one from the β-globin locus on chromosome 11.

The place of the Basques in the European Y-chromosome diversity landscape

“…11.5.1 (SPSS Inc.). To estimate the time to most recent common ancestor (TMRCA) of some subtrees we used Batwing 21 assuming constancy in population size or exponential growth (a ¼ 0.005/generation) and gamma priors for y and o. The mutation rates used were those described 22 for the specific loci used herein, except for those two loci with mean mutation rates of zero where, in order to be conservative, we decided to use the (higher) average rate described for Y-chromosome STR loci.…”

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

“…26 Network analyses were performed using Network version 4.510 and Network Publisher version 1.1.0.6 (http://fluxus-engineering.com). The BATWING program 27 (http://www.mas.ncl.ac.uk/~nijw/) was used to estimate haplogroup coalescent times (Time since the Most Recent Common Ancestor -(TMRCA)). The IM program 28 (http://genfaculty.rutgers.edu/hey/software) was used to estimate divergence times and migration rates.…”

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

“…33 We ran 102 000 Monte Carlo iterations of the coalescent simulation and discarded the first 2000 iterations as burn-in. Population demographic priors were: initial effective population size -gamma(1.1,0.0001), growth rate -gamma(1.01,1), time growth starts (in generations) -uniform(0, time to most recent common ancestor), 34 final population size -uniform(0, 50 000).…”

“…33 We analysed the two Ladin-speaking samples and the Italian-speaking sample individually but, because no differentiation was observed between the two Germanspeaking samples (see above and Table 1), we grouped them together and treated them as a single population (GV). Posterior estimates of current effective population size and population growth rate based on mtDNA and Y-chromosome data are given in Tables 2 and 3 respectively.…”