Time estimates using rho (ρ) and maximum likelihood (ML) and estimated migration times using founder analysis. from Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one substitution every 3,624 years, corrected for purifying selection, and a synonymous rate of one substitution every 7,884 years. The full set of dated founders is shown for each model tested

Maximum-parsimony tree of haplogroup JT and list of samples used. from Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

The tree is annotated for synonymous (in red followed by the letter s), non-synonymous (in blue followed by ns), tRNA (coloured in orange), rRNA (in yellow) and control region (in black) nucleotides changes. All the nucleotide substitutions that are recurrent in the tree are underlined and reversions are marked with an exclamation mark (!)

Methods and supplementary images. from Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

Founder analysis results for whole mtDNA genomes with probabilistic distribution across migration times scanned at 200-year intervals from 0-70 ka from Mediterranean Europe to northern/central Europe, from the Near East to northern/central Europe and all reverse analyses. BSPs indicating the median of the effective population size through time based on haplogroup J (left panel) and T (right panel), assuming a generation time of 25 years