Since the end of the 1970s, Portugal has had an important role in migratory movements, becoming a destination for immigrants of a wide range of nationalities, mainly from African countries. According to PORDATA, until the end of 2014 there were 40,000 immigrants from Cape Verde, 20,000 from Angola, 18,000 from Guinea-Bissau, and 3,000 from Mozambique living in Portugal, and of those, >80 per cent live in the Lisbon region. This may be one of the main contributors to genetic variation of Lisbon residents in the present and the future. Mitochondrial DNA (mtDNA) has features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. These features are also important in evolutionary and population studies. We aim to characterize mtDNA diversity in immigrants from Portuguese Speaking African Countries (PALOP) living in Lisbon and their potential contribution to genetic variation of Lisbon population. Blood samples were collected from 439 PALOP immigrants living in Lisbon, of which 173 immigrants from Angola, 103 immigrants from Cape Verde, eighty-three immigrants from Mozambique and eighty immigrants from Guinea-Bissau, from January 2000 to December 2016. The control region of the mtDNA was amplified using two pairs of primers—L15971/H016 and L16555/H639, and sequenced by BigDye Terminator v.3.1 Cycle Sequence (AB). Sequenced products were detected in a sequencer Genetic Analyzer 3130 (AB). Finally the results were analysed by Sequencing Analysis v.5.2 software and also compared with Revised Cambridge Reference Sequence (rCRS) using SeqScape v.3 (AB) software. The haplogroups were determined based on Phylotree, build 17. Genetic distances and other genetic parameters were calculated with Arlequin software ver.3.5 and analysed and represented with PhyML 3.0. For each sample, the complete sequence of the control region was obtained. The comparison of the sequences obtained with the rCRS, among the 439 analysed individuals, allowed the identification of 319 different haplotypes, corresponding to 164 different haplogroups distributed by ten macrohaplogroups. Macrohaplogroup L was the most common with 386 haplotypes followed by U with fifteen haplotypes, H with twelve haplotypes, M and T with six haplotypes, K with five, R with four, X and J with two and HV with one. PALOP’s immigrants presented a high number of unique haplotypes, most of them belonging to macrohaplogroup L, originating from sub-Saharan regions of Africa.This macrohaplogroup is uncommon in European and Portuguese populations. Consistent with this, phylogenetic analysis showed the establishment of two distinct groups, one composed of the Portuguese population and another of the African populations. In comparing the different immigrant populations living in Lisbon, the genetically closest community to the Portuguese population is Mozambique and the furthest is Cape Verde, followed by Guinea-Bissau and Angola. Our results show that the PALOP immigrants living in Lisbon are genetically heterogeneous. The increase in genetic diversity in Lisbon due to immigrants from PALOP countries may have a major impact on haplotypic and allelic frequencies, on which all forensic and medico-legal investigations are based
