Moises Coll Macia

Population structure We constructed an unrooted haplotype network for all complete mitochondrial genomes (Late Pleistocene, pre-whaling Holocene, contemporary) individuals using the Median-joining network185 as implemented in PopART.90 Fixation index values (FST) were calculated by pooling individuals into 2,000 year time bins and splitting them into their two respective regions using Arlequin v3.5,91 using default parameters and an input file generated with DnaSP.

Abstract A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis, many of which have been claimed to affect male fertility. Here we examine copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men. Using a subset of 7947 men grouped into 1449 patrilineal genealogies, we infer 57 large scale de novo copy number mutations affecting palindrome 1.

Quantification and statistical analysis Archaic admixture inference The method finds archaic genomic segments in non-Africans by identifying segments with a strong enrichment of single nucleotide variants that are not seen in an unadmixed outgroup population (in this case, Sub-Saharan populations). Non-African variants not present in the outgroup show a 10-fold enrichment in archaic segments because these variants have been accumulated since the common ancestor of archaic and modern humans.