1
|
Navarro-López B, .Baeta M, Moreno-López O, Kleinbielen T, Raffone C, Granizo-Rodríguez E, Ferragut J, Alvarez-Gila O, Barbaro A, Picornell A, de Pancorbo E M. Y-chromosome analysis recapitulates key events of Mediterranean populations. Heliyon 2024; 10:e35329. [PMID: 39220888 PMCID: PMC11365299 DOI: 10.1016/j.heliyon.2024.e35329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.
Collapse
Affiliation(s)
- B. Navarro-López
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - M. .Baeta
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - O. Moreno-López
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - T. Kleinbielen
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - C. Raffone
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - E. Granizo-Rodríguez
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - J.F. Ferragut
- Departament de Biologia, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Universitat de les Illes Balears, Palma de Mallorca, Illes Balears, Spain
| | - O. Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - A. Barbaro
- Forensic Genetics Section, Studio Indagini Mediche e Forensi (SIMEF), Reggio Calabria, Italy
| | - A. Picornell
- Departament de Biologia, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Universitat de les Illes Balears, Palma de Mallorca, Illes Balears, Spain
| | - M.M. de Pancorbo E
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| |
Collapse
|
2
|
González-Fernández M, Vázquez-Coto D, Albaiceta GM, Amado-Rodríguez L, Clemente MG, Velázquez-Cuervo L, García-Lago C, Gómez J, Coto E. Chromosome-Y haplogroups in Asturias (Northern Spain) and their association with severe COVID-19. Mol Genet Genomics 2024; 299:49. [PMID: 38704518 PMCID: PMC11069473 DOI: 10.1007/s00438-024-02143-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
The main objective of this study was to determine whether the common Y-haplogroups were be associated with the risk of developing severe COVID-19 in Spanish male. We studied 479 patients who required hospitalization due to COVID-19 and 285 population controls from the region of Asturias (northern Spain), They were genotyped for several polymorphisms that define the common European Y-haplogroups. We compared the frequencies between patients and controls aged ≤ 65 and >65 years. There were no different haplogroup frequencies between the two age groups of controls. Haplogroup R1b was less common in patients aged ≤65 years. Haplogroup I was more common in the two patient´s groups compared to controls (p = 0.02). Haplogroup R1b was significantly more frequent among hypertensive patients, without difference between the hypertensive and normotensive controls. This suggested that R1b could increase the risk for severe COVID-19 among male with pre-existing hypertension. In conclusion, we described the Y-haplogroup structure among Asturians. We found an increased risk of severe COVID-19 among haplogroup I carriers, and a significantly higher frequency of R1b among hypertensive patients. These results indicate that Y-chromosome variants could serve as markers to define the risk of developing a severe form of COVID-19.
Collapse
Affiliation(s)
| | - Daniel Vázquez-Coto
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Guillermo M Albaiceta
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Marta G Clemente
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain
| | | | - Claudia García-Lago
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
- Universidad de Oviedo, Oviedo, Spain.
| |
Collapse
|
3
|
García-Fernández C, Lizano E, Telford M, Olalde Í, de Cid R, Larmuseau MHD, M. de Pancorbo M, Calafell F. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition. Sci Rep 2022; 12:20708. [PMID: 36456614 PMCID: PMC9715704 DOI: 10.1038/s41598-022-25200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019-2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
Collapse
Affiliation(s)
- Carla García-Fernández
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Esther Lizano
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marco Telford
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Íñigo Olalde
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Rafael de Cid
- grid.429186.00000 0004 1756 6852Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maarten H. D. Larmuseau
- grid.5596.f0000 0001 0668 7884Laboratory of Human Genetic Genealogy, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.5284.b0000 0001 0790 3681ARCHES–Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, Antwerp, Belgium ,Histories Vzw, Gent, Belgium
| | - Marian M. de Pancorbo
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| |
Collapse
|
4
|
Palencia-Madrid L, Baeta M, Kleinbielen T, Toro-Delgado N, Villaescusa P, Sanchez-Bustamante E, de Pancorbo MM, Luis JR, Ware KE, Somarelli JA, Garcia-Bertrand R, Herrera RJ. Post-Austronesian migrational wave of West Polynesians to Micronesia. Gene 2022; 823:146357. [PMID: 35189246 DOI: 10.1016/j.gene.2022.146357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
Abstract
This study examines Y-chromosome and mtDNA markers in the population of the island of Kiritimati in the context of geographically targeted reference populations from the Pacific. Kiritimati derives its population from the atoll islands of the Gilbert Archipelago and representsa geographicaltransitional region between Micronesia, Polynesia and Melanesia that likely played a critical role during theAustronesian expansion. The large presence(84.1%)of individuals withO-M175, O2a-M324 and O2a2b-P164 sub-haplogroups, 69.9% being O2a2b-P164, the Y-STR homogeneity within O2a2b-P164 and the very recent age of the sub-haplogroup(363-548 years ago)inKiritimati suggestthe arrival ofa genetically homogenous population to the Gilberteses followed by a population expassion.The close Y-STR haplotype affinities with profiles from the Samoa and Tonga Archipelagos point to an unprecedented massive post-Austronesian expansionexodus from West Polynesia.Contrasting the abundance of AustronesianO2a2b-P164 sub-haplogroup, the most abundantMelanesian/Papuansub-haplogroup,C-M130is present at a frequency of 13.5%. Thenetwork topology suggests that C-M130 arrived to theKiribati Archipelago from West Polynesia, specifically from West Samoa, Tonga and/or Tutuila subsequent to the Austronesian expansion about 832-1408 years ago. The haplotype affinities withinO2a2b-P164 argue for anoriginal source in Taiwan and its dispersal to West Polynesia and then to Southeast Micronesia. The present investigation provides an understanding of the genetic composition and complex migration history of an understudied region of the Pacific and provides evidence for recent dispersals towards Micronesia from West Polynesia subsequent to the initial Austronesian expansion.
Collapse
Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Tamara Kleinbielen
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Nerea Toro-Delgado
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Elena Sanchez-Bustamante
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782 Santiago de Compostela, Spain
| | - Kathryn E Ware
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC 27710, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA.
| |
Collapse
|
5
|
Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
Collapse
|
6
|
Villaescusa P, Seidel M, Nothnagel M, Pinotti T, González-Andrade F, Alvarez-Gila O, M de Pancorbo M, Roewer L. A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373. Forensic Sci Int Genet 2020; 51:102427. [PMID: 33254102 DOI: 10.1016/j.fsigen.2020.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (RST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
Collapse
Affiliation(s)
- Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Oscar Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
7
|
Contingency and Agency in the Mountain Landscapes of the Western Pyrenees: A Place-Based Approach to the Long Anthropocene. SUSTAINABILITY 2020. [DOI: 10.3390/su12093882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Regional- and biome-scale paleoecological analyses and archaeological syntheses in the mountain landscapes of the western Pyrenees suggest that the Long Anthropocene began with agropastoral land use at the onset of the Neolithic. Historical and geographic analyses emphasize the marginality of the western Pyrenees and the role of enforced social norms exacted by intense solidarities of kin and neighbors in agropastoral production. Both are satisfying and simple narratives, yet neither offers a realistic framework for understanding complex processes or the contingency and behavioral variability of human agents in transforming a landscape. The Long Anthropocene in the western Pyrenees was a spatially and temporally heterogeneous and asynchronous process, and the evidence frequently departs from conventional narratives about human landscape degradation in this agropastoral situation. A complementary place-based strategy that draws on geoarchaeological, biophysical, and socio-ecological factors is used to examine human causality and environmental resilience and demonstrate their relationship with the sustainability of mountain landscapes of the western Pyrenees over medium to long time intervals.
Collapse
|
8
|
Villaescusa P, Blázquez P, Martínez-Jarreta B, Jiménez S, Álvarez-Gila O, de Pancorbo MM. The impact of haplogroup R1b-DF27 in Hispanic admixed populations from Latin America. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
9
|
Ibarrondo O, Lopez-Oceja A, Baeta M, M de Pancorbo M. A Statistical Method to Enhance the Analysis of the Differences Among High-Resolution Melting (HRM) Curves of PCR-Amplified DNA Fragments. J Food Sci 2019; 84:2719-2728. [PMID: 31578715 DOI: 10.1111/1750-3841.14814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 11/30/2022]
Abstract
Consistent differences among melting curves of PCR-amplified DNA fragments are treated by normalizing the relative fluorescence units (RFU) and performing a clustering analysis, but statistically significant differences among curves are not usually determined. In the present study, an analysis based on functional data analysis (FDA) was implemented to evaluate the existence of statistically significant differences between normalized RFU curves obtained from PCR-HRM (high-resolution melting) analysis by using ANOVA for functional data. The effectiveness of the FDA method was analyzed with data from a set of samples of eight animal species of interest in food analysis, as well as mixtures of DNA from these species, analyzed by PCR-HRM to differentiate them. The statistical method described in this study has been demonstrated to be a robust and precise tool to discriminate among melting curves derived from HRM analysis. This method has advantages over the current comparison methods. PRACTICAL APPLICATION: As long as food fraud and mislabeling exist, new techniques for species identification are needed. High-resolution melting (HRM) has been shown to be a rapid, reliable and inexpensive species identification method. In the present study, functional data analysis (FDA) was applied to HRM curves of DNA from eight animal species used for food, as well as to mixtures of these species in different proportions. FDA has advantages over the usual methods, providing a deeper statistical analysis and facilitating the data interpretation as shown by the HRM analysis for a clearer comparison among individual species and mixtures of species.
Collapse
Affiliation(s)
- Oliver Ibarrondo
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Andrés Lopez-Oceja
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Miriam Baeta
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Marian M de Pancorbo
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| |
Collapse
|
10
|
Hernández CL, Dugoujon JM, Sánchez-Martínez LJ, Cuesta P, Novelletto A, Calderón R. Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world. Ann Hum Biol 2019; 46:63-76. [PMID: 30822152 DOI: 10.1080/03014460.2019.1587507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. AIM To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. SUBJECT AND METHODS Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. RESULTS Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. CONCLUSION The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
Collapse
Affiliation(s)
- Candela L Hernández
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Jean-Michel Dugoujon
- b CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS) , Université Paul Sabatier Toulouse III , Toulouse , France
| | - Luis J Sánchez-Martínez
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Pedro Cuesta
- c Centro de Proceso de Datos , Universidad Complutense , Madrid , Spain
| | | | - Rosario Calderón
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| |
Collapse
|
11
|
Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes. Int J Legal Med 2018; 133:17-23. [PMID: 30229332 DOI: 10.1007/s00414-018-1936-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.
Collapse
|
12
|
Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
Collapse
Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
| |
Collapse
|
13
|
Assessment of a subset of Slowly Mutating Y-STRs for forensic and evolutionary studies. Forensic Sci Int Genet 2018; 34:e7-e12. [DOI: 10.1016/j.fsigen.2018.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 11/22/2017] [Accepted: 03/19/2018] [Indexed: 11/21/2022]
|
14
|
Larmuseau MHD, Calafell F, Princen SA, Decorte R, Soen V. The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:219-227. [PMID: 29327450 DOI: 10.1002/ajpa.23409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/28/2017] [Accepted: 01/01/2018] [Indexed: 11/08/2022]
Abstract
OBJECTIVES War atrocities committed by the Spanish army in the Low Countries during the 16th century are so ingrained in the collective memory of Belgian and Dutch societies that they generally assume a signature of this history to be present in their genetic ancestry. Historians claim this assumption is a consequence of the so-called "Black Legend" and negative propaganda portraying and remembering Spanish soldiers as extreme sexual aggressors. The impact of the presence of Spaniards during the Dutch Revolt on the genetic variation in the Low Countries has been verified in this study. MATERIALS AND METHODS A recent population genetic analysis of Iberian-associated Y-chromosomal variation among Europe is enlarged with representative samples of Dutch (N = 250) and Flemish (N = 1,087) males. Frequencies of these variants are also compared between donors whose oldest reported paternal ancestors lived in-nowadays Flemish-cities affected by so-called Spanish Furies (N = 116) versus other patrilineages in current Flemish territory (N = 971). RESULTS The frequencies of Y-chromosomal markers Z195 and SRY2627 decline steeply going north from Spain and the data for the Flemish and Dutch populations fits within this pattern. No trend of higher frequencies of these variants has been found within the well-ascertained samples associated with Spanish Fury cities. DISCUSSION Although sexual aggression did occur in the 16th century, these activities did not leave a traceable "Spanish" genetic signature in the autochthonous genome of the Low Countries. Our results support the view that the 'Black Legend' and historical propaganda on sexual aggression have nurtured today's incorrect assumptions regarding genetic ancestry.
Collapse
Affiliation(s)
- Maarten H D Larmuseau
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Sarah A Princen
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium
| | - Violet Soen
- Early Modern History (15th-18th Centuries), Faculty of Arts, KU Leuven, Leuven, Belgium
| |
Collapse
|
15
|
Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing. Forensic Sci Int Genet 2017; 31:e12-e16. [PMID: 29089250 DOI: 10.1016/j.fsigen.2017.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/10/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022]
Abstract
Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the 'jungle' of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the 'Minimal Reference Y-tree', was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.
Collapse
|
16
|
Solé-Morata N, Villaescusa P, García-Fernández C, Font-Porterias N, Illescas MJ, Valverde L, Tassi F, Ghirotto S, Férec C, Rouault K, Jiménez-Moreno S, Martínez-Jarreta B, Pinheiro MF, Zarrabeitia MT, Carracedo Á, de Pancorbo MM, Calafell F. Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ. Sci Rep 2017; 7:7341. [PMID: 28779148 PMCID: PMC5544771 DOI: 10.1038/s41598-017-07710-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/28/2017] [Indexed: 11/28/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Neus Solé-Morata
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carla García-Fernández
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Neus Font-Porterias
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - María José Illescas
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Laura Valverde
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Claude Férec
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France.,Université de Bretagne Occidentale, Brest, France.,Etablissement Français du Sang-Bretagne, Brest, France
| | - Karen Rouault
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France
| | - Susana Jiménez-Moreno
- Forensic and Legal Medicine Area, Department of Pathology and Surgery, University Miguel Hernández, Elche, Spain
| | | | - Maria Fátima Pinheiro
- Forensic Genetics Department, National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | | | - Ángel Carracedo
- Genomic Medicine Group, CIBERER- University of Santiago de Compostela, Galician Foundation of Genomic Medicine (SERGAS), Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| |
Collapse
|