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DISSECTION of HAPLOGROUP R1b-M269 and FORENSIC APPLICATIONS

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NEW INSIGHTS IN THE PATERNAL GENETIC LANDSCAPE OF SOUTHWESTERN EUROPE: DISSECTION OF HAPLOGROUP R1b-M269 AND FORENSIC APPLICATIONS PATRICIA VILLAESCUSA URBANEJA PhD Thesis Directed by: Professor Doctor María de los Ángeles Martínez de Pancorbo Gómez BIOMICs Research Group Department of Zoology and Animal Biology University of the Basque Country UPV/EHU Vitoria-Gasteiz, 2019 (c)2019 PATRICIA VILLAESCUSA URBANEJA The present work has been carried out thanks to the grant of a predoctoral fellowship, within the program of Training of Research Staff by the University of the Basque Country UPV/EHU, which I have benefited from among the years 2015 and 2019. The funds for the accomplishment of the analysis have come from BIOMICs Research Group, consolidated by the Department of Education, Universities and Research of the Basque Government since 2012 (IT-424-07 and IT-833-13) and of the University of the Basque Country UPV/EHU (ELDUNANOTEK UFI11/32). In addition to that, SGIker (UPV/EHU, MICINN, GV/EJ, FSE) has provided technical and human support, especially from the DNA Bank of the University of the Basque Country UPV/EHU. “El único modo de lograr lo imposible, es convenciéndose de que sí es posible” Alicia, Alicia en el país de las maravillas. Acknowledgements In the first place, I would like to extend my sincere gratitude to all the people who have helped, guided and encouraged me during the long and successful journey that was the path to obtain my doctoral thesis. Without their active support, this project would not have been possible. I am remarkably indebted to my mentor Prof. Dr. Marian Martínez de Pancorbo, who believed in me and gave me the support to obtain my predoctoral fellowship. Her guidance and encouragement during these years have been essential in my training both as a researcher and as a person. In addition to that, I am extremely grateful to my lab colleagues, both present and past, who have shared experiences and accompanied me during the long lab hours. Miriam, Carol, Leire, Andrés, Endika, Maite, Tamara, Lourdes, David, Melania, Majo, Sergio, Amara, among others. Sois los mejores compañeros de laboratorio que podría haber deseado, gracias por los innumerables buenos momentos, y por enseñarme y prestarme ayuda con todas las dudas, tanto profesionales como existenciales, que he tenido a lo largo de estos años. I would also like to thank Prof. Dr. Francesc Calafell, for his kind assistance and successful collaboration throughout the project. I have to express my sincere appreciation to Prof. Dr. Lutz Roewer and to Dr. Maria Geppert for receiving me in Berlin. Thank you so much for your hospitality and guidance. Jessy, Jessman, Sascha, Marion, Steffi, Judith, Petra and the rest of the lab technicians, vielen dank für ihren freundlichen empfang! Last but not least, my gratitude goes to my parents, whose support made this possible, as well as to all of my friends, who both directly or indirectly supported me during these years. Ailander, you have been there for me at all times, making the tough times less hard. No words can express my gratitude to you. Thank you very much! Patricia Villaescusa Urbaneja i ii Abstract The human Y chromosome determines male sex and possess a haploid nature, escaping crossing over during meiosis. These traits make this chromosome male specific, which is transmitted from fathers to sons practically unchanged establishing paternal lineages. In the last years the study of genetic markers located in the human Y chromosome, that is, Y chromosome short tandem repeats (Y-STRs) and single nucleotide polymorphisms (Y-SNPs), has become relevant in the area of Forensic Genetics as a powerful tool to exclude male suspects from the involvement in a crime, identify the paternal lineage and biogeographical ancestry of male perpetrators, as well as to provide investigative clues to find an unknown male perpetrator or contributor or to a crime. In addition to that, the analysis of the Y chromosome can also be applied in other areas like population genetics and genetic genealogy for the study of paternity and/or kinship, detecting past and recent male mediated expansions, familiar searching, and evolutionary studies. Although highly useful, the analysis of the Y chromosome is limited in Forensic Genetics due to its haploidy and inheritance, which makes it less effective for identification purposes in comparison with autosomal markers. Moreover, it cannot distinguish between individuals from the same paternal lineage. However, its utility cannot be disregarded since the vast majority of the crimes where DNA evidence is helpful are committed by male perpetrators. The study of Y-SNPs has revealed that the distribution of paternal lineages, or haplogroups, around the word is restricted to concrete geographic areas at continental and regional level, allowing to reconstruct the evolutionary history of lineages. In this context, the current genetic makeup of Europe has been the object of multiple studies, as a controversy arose around the Paleolithic or Neolithic origin of the most common paternal lineage in West Europe, R1b-M269. The main objective of the present doctoral thesis work focuses on the reconstruction of the most probable evolutionary scenario of the main European paternal lineage R1b-M269 in the Iberian Peninsula and Southwest Europe through the dissection in its subhaplogroups. The analysis of M269 and its sublineages in populations of Southwestern Europe allowed us to further characterize the paternal genetic landscape of that region, revealing a different distribution pattern from the one proposed before by other authors for R1b-S116, one of the main M269 sublineages, and resolving the paragroup S116* by the presence of the Iberian near-specific haplogroup R1b-DF27, which occupies a different geographic area than the other S116 subhaplogroups and is present in the Iberian Peninsula in frequencies over 30-50%. iii On the other hand, the analysis and dissection of DF27 has revealed that this lineage is also present in Latin America due to historical events, and that some of its sublineages display moderate geographic differentiation in Iberia, making DF27 a potentially useful marker in Forensic Genetics for determining Iberian or southwest European paternal biogeographical ancestry. Furthermore, the estimated times to the most recent common ancestor (TMRCA) show that DF27 originated recently, around 4,000-4,200 years ago, at the transition between the Neolithic and the Bronze Age that remodeled the Y chromosome landscape of Europe. In addition to that, in forensic and population genetics the necessity of new multiplex tools that allow the simultaneous genotyping of several genetic markers in a unique reaction has proven to be a critical demand. These multiplex tools can be composed of either Y-STRs and/or Y-SNPs, and are based on capillary electrophoresis, minisequencing, or massive parallel sequencing (MPS) technology, although the last one is not yet implemented in all Forensic Genetics laboratories. To respond to the increasing demand of Y-SNP multiplexes with higher haplogroup resolution, and of Y-STR multiplexes able to resolve the particular cases that the current Y-STR panels are not able to respond to, two novel multiplex panels were developed in the present work. On the one hand, the 15-plex Y-SNP minisequencing panel allows the fine subtyping of the haplogroup DF27, suitable for the inference of Iberian and southwest European paternal biogeographical ancestry. On the other hand, the slowly mutating (SM) Y-STR panel could be helpful in conjunction with current Y-STRs panels for confirming exclusions in kinship cases where minimal discrepancies in one or a few loci are reported using only the regular Y-STR panels, as well as for evolutionary studies. All in all, the studies conducted within the present doctoral thesis work have provided new clues about the evolutionary history of the current paternal genetic landscape of Europe, as well as an extensive genetic reference dataset of forensic and population interest for future applications. iv Resumen El cromosoma Y humano determina el sexo masculino y posee una naturaleza haploide, sin estar sujeto en la mayor parte de su longitud a recombinación, debido a que escapa del entrecruzamiento cromosómico durante la meiosis. Estas características hacen que este cromosoma sea específico del sexo masculino y que se trasmita prácticamente sin cambios de padres a hijos, estableciendo lo que se conoce como linajes paternos. El estudio de los linajes del cromosoma Y, mediante polimorfismos de un solo nucleótido (single nucleotide polimorphism, SNP) en el cromosoma Y (Y-SNP), permite la reconstrucción de la historia evolutiva de los linajes paternos de la especie humana desde sus inicios en África hace al menos 300.000 años. El conocimiento de la estructura y propiedades del cromosoma Y obtenido a través de la genética de poblaciones humanas mediante el análisis de sus marcadores genéticos es la base para el estudio de las migraciones humanas y sus aplicaciones en genética forense y otras áreas afines como la genealogía genética o la genética evolutiva. Estos marcadores pueden ser de dos tipos, los anteriormente mencionados Y-SNPs, y los microsatélites Y-STRs (short tandem repeat, STR). Su estudio permite conocer cuáles son los linajes paternos característicos o presentes en cada población humana y entender cómo se distribuyen en las mismas, permitiendo así diferenciar entre unas poblaciones y otras. Por ello, en los últimos años su estudio es relevante dentro del área de la Genética Forense debido a que el análisis de estos marcadores permite, entre otras cosas, excluir a un sospechoso masculino como contribuyente de restos biológicos presentes en la escena de un delito, identificar el linaje paterno y la ancestralidad biogeográfica de los sospechosos, y proporcionar pistas para la identificación del autor o contribuyente masculino de un delito. Además de sus aplicaciones forenses, los marcadores genéticos del cromosoma Y también pueden aplicarse al estudio de paternidad o parentesco biológico, la búsqueda de familiares desaparecidos y la detección de movimientos migratorios masculinos tanto pasados como recientes.
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  • Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography

    Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography

    Copyright 2003 by the Genetics Society of America Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography Michael E. Weale,* Tina Shah,*,1 Abigail L. Jones,* John Greenhalgh,* James F. Wilson,† Pagbajabyn Nymadawa,‡ David Zeitlin,§ Bruce A. Connell,** Neil Bradman* and Mark G. Thomas*,2 *The Centre for Genetic Anthropology, Department of Biology, University College, London WC1E 6BT, United Kingdom, †Department of Biology, University College, London WC1E 6BT, United Kingdom, ‡Subassembly of Medical Sciences, Mongolian Academy of Sciences, Ulaanbaatar-13, Mongolia, §Centre for Social Anthropology and Computing, Department of Anthropology, University of Kent, Canterbury CT2 7NS, United Kingdom and **Department of Languages, Literatures and Linguistics, York University, Toronto, Ontario M3J 1P3, Canada Manuscript received January 27, 2003 Accepted for publication April 30, 2003 ABSTRACT There has been considerable debate on the geographic origin of the human Y chromosome Alu polymor- phism (YAP). Here we report a new, very rare deep-rooting haplogroup within the YAP clade, together with data on other deep-rooting YAP clades. The new haplogroup, found so far in only five Nigerians, is the least-derived YAP haplogroup according to currently known binary markers. However, because the interior branching order of the Y chromosome genealogical tree remains unknown, it is impossible to impute the origin of the YAP clade with certainty. We discuss the problems presented by rare deep-rooting lineages for Y chromosome phylogeography. HE Y chromosome Alu polymorphism (YAP), first to be cited (e.g., Maca-Meyer et al. 2001; Templeton Tdescribed by Hammer (1994), is a unique event poly- 2002), Underhill and colleagues have shown (through morphism (UEP) marker defining a deep-rooting clade the discovery of the new marker M174: see Figure 1) of the Y chromosome genealogical tree (Figure 1).