Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing

Abstract

The human genetic diversity around the world was studied through several high variable genetic markers. In South America the demic consequences of admixture events between Native people, European colonists and African slaves have been displayed by uniparental markers variability. The mitochondrial DNA (mtDNA) has been the most widely used genetic marker for studying American mixed populations, although nuclear markers, such as microsatellite loci (STRs) commonly used in forensic science, showed to be genetically and geographically structured. In this work, we analyzed DNA from buccal swab samples of 296 individuals across Peru: 156 Native Amazons (Ashaninka, Cashibo and Shipibo from Ucayali, Huambiza from Loreto and Moche from Lambayeque) and 140 urban Peruvians from Lima and other 33 urban areas. The aim was to evaluate, through STRs and mtDNA variability, recent migrations in urban Peruvian populations and to gain more information about their continental ancestry. STR data highlighted that most individuals (67%) of the urban Peruvian sample have a strong similarity to the Amazon Native population, whereas 22% have similarity to African populations and only ~1% to European populations. Also the maternally-transmitted mtDNA confirmed the strong Native contribution (~90% of Native American haplogroups) and the lower frequencies of African (~6%) and European (~3%) haplogroups. This study provides a detailed description of the urban Peruvian genetic structure and proposes forensic STRs as a useful tool for studying recent migrations, especially when coupled with mtDNA.

Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms

“…The presence of se 302 , se 428 , Se 357,739,960 may suggest gene flows from Europeans, Africans, and South Asians to this population. However, recent studies suggested that no apparent gene flows from South Asians to this population occurred . In addition, although se 302 is prevalent in South Asians, this allele is also detected in some other populations with quite low frequency, for example, Europeans from Northern Portugal and Kenyans but not other admixed Americans (1000 Genomes Consortium Phase 3 data).…”

Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods

“…The separation and detection were conducted with an Applied Biosystems ® 3130xl Genetic Analyzer (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer's protocols [12,18]. The collection and the analysis of the data obtained by capillary electrophoresis were assessed by GeneMapper ® software v.1.4 (Applied Biosystems, Waltham, MA, USA) [19,20]. To evaluate concordance, conventional DNA testing and allele calls were compared to the results of the ANDE System [12].…”

Autosomal STR and SNP characterization of populations from the Northeastern Peruvian Andes with the ForenSeq™ DNA Signature Prep Kit

“…[11,17,18]. In Peru, with few exceptions [19,20], published autosomal STR reference data are scarce and available mostly from large cosmopolitan areas (e.g. Lima, Trujillo).…”

“…In addition to these, forensic genetic parameters were also calculated for the combined set from the Northeastern Peruvian Andes. To gain a better insight of the possible genetic subdivision in Peru, we characterize the genetic differentiation between our rural Northeastern Peruvian Andes set and that of the admixed cosmopolitan populations described in [19,21].…”