Inferring recent human population history from a Y chromosome perspective

The Y chromosome is the longest non-recombining DNA sequence of the human genome. This avoidance of recombination, together with its paternal inheritance, makes the Y chromosome a powerful tool with which to study population history, male genealogy, forensics and medical genetics. Besides the progress made in the field during the last two decades, the recent advent of massive parallel sequencing (MPS) has yielded the discovery of thousands of new variants that have allowed to build a more reliable phylogeny and to obtain direct estimates of its mutation rate. In the present thesis, I analyse the Y-chromosome diversity from two different perspectives and with different purposes. First, by targeting specific SNPs and STRs in ~ 2,500 men bearing one of the selected 50 Catalan surnames, we investigated the driving forces behind the origin, systematization, and diffusion of surnames. And then, by using whole Y-chromosome sequences from North African individuals belonging to the most frequent lineage in the area (E-M183), we have been able to refine the phylogeography of this lineage and to shed light on the controversial dates for its origin and spread.El comportament únic del cromosoma Y, heretat per via paterna sense patir recombinació amb cap altre cromosoma, el converteix en un marcador excepcional amb aplicacions en àmbits com la genètica de poblacions humanes, la genealogia o la genètica forense. Tot i el progrés en l’estudi del cromosoma Y realitzat en les últimes dues dècades, el recent desenvolupament de les tecnologies de seqüenciació massiva ha permès el descobriment de milers de noves variants, mitjançant les quals s’ha obtingut una millor reconstrucció filogenètica, així com una estimació directa de la seva taxa de mutació. En aquesta tesi s’analitza la diversitat del cromosoma Y des de dues perspectives diferents i amb els següents propòsits. En primer lloc, mitjançant el genotipat de marcadors específics del cromosoma Y en ~2500 homes portadors d’un dels 50 cognoms catalans escollits, s’han investigat els processos que han donat lloc a l’origen, la sistematització i la difusió dels cognoms. Per altra banda, la seqüenciació de cromosomes Y en homes nord africans pertanyents al llinatge més freqüent en aquesta àrea (E-M183), ha permès un refinament de l’estructura filogeogràfica d’aquest llinatge, així com l’establiment temporal del seu origen i dispersió

People from Ibiza: an unexpected isolate in the Western Mediterranean

In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation.Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). SAB was supported by the Agencia Estatal de Investigación FPI grant BES-2014-06922

People from Ibiza: an unexpected isolate in the Western Mediterranean

In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation.Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). SAB was supported by the Agencia Estatal de Investigación FPI grant BES-2014-06922

Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81)

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), and by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866. NS is supported by a Formació de personal Investigador (FI) fellowship from Generalitat de Catalunya (FI_B00685

Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations

We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium. FST between both populations was 0.0178 for autosomal SNPs, 0.0146 for autosomal STRs, 0.0101 for X-STRs and 0.1866 for Y-STRs. Combined a priori statistics showed quite large; for instance, pooling all the autosomal loci, the a priori probabilities of discriminating a suspect become 1 − (2.3 × 10−70) and 1 − (5.9 × 10−73), for Roma and Catalans respectively, and the chances of excluding a false father in a trio are 1 − (2.6 × 10−20) and 1 − (2.0 × 10−21).Funding was provided by the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), and by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866

Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations

We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium. FST between both populations was 0.0178 for autosomal SNPs, 0.0146 for autosomal STRs, 0.0101 for X-STRs and 0.1866 for Y-STRs. Combined a priori statistics showed quite large; for instance, pooling all the autosomal loci, the a priori probabilities of discriminating a suspect become 1 − (2.3 × 10−70) and 1 − (5.9 × 10−73), for Roma and Catalans respectively, and the chances of excluding a false father in a trio are 1 − (2.6 × 10−20) and 1 − (2.0 × 10−21).Funding was provided by the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), and by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866

Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America

Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6-20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grants CGL2013-44351-P, CGL2016-75389-P), by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and by the Basque Government (IT-424-07). FT was supported by the ERC Advanced Grant Agreement No 295733, ‘LanGeLin’ projec