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Galván-Femenía I, Graffelman J, Barceló-I-Vidal C. Graphics for relatedness research. Mol Ecol Resour 2017; 17:1271-1282. [PMID: 28374569 PMCID: PMC5624821 DOI: 10.1111/1755-0998.12674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022]
Abstract
Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article was to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS- and IBD-based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP-CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log-ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.
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Affiliation(s)
- Iván Galván-Femenía
- Department of Computer Science, Applied Mathematics and Statistics, Universitat de Girona, Girona, Spain.,Disease Genomics-GCAT Group, Germans Trias Health Research Institute (IGTP)-Program of Predictive and Personalized Medicine of Cancer (PMPPC), Can Ruti Campus, Badalona, Barcelona, Spain
| | - Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Carles Barceló-I-Vidal
- Department of Computer Science, Applied Mathematics and Statistics, Universitat de Girona, Girona, Spain
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Gómez-Carballa A, Moreno F, Álvarez-Iglesias V, Martinón-Torres F, García-Magariños M, Pantoja-Astudillo JA, Aguirre-Morales E, Bustos P, Salas A. Revealing latitudinal patterns of mitochondrial DNA diversity in Chileans. Forensic Sci Int Genet 2015; 20:81-88. [PMID: 26517175 DOI: 10.1016/j.fsigen.2015.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022]
Abstract
The territory of Chile is particularly long and narrow, which combined with its mountainous terrain, makes it a unique scenario for human genetic studies. We obtained 995 control region mitochondrial DNA (mtDNA) sequences from Chileans representing populations living at different latitudes of the country from the North to the southernmost region. The majority of the mtDNA profiles are of Native American origin (∼88%). The remaining haplotypes are mostly of recent European origin (∼11%), and only a minor proportion is of recent African ancestry (∼1%). While these proportions are relatively uniform across the country, more structured patterns of diversity emerge when examining the variation from a phylogeographic perspective. For instance, haplogroup A2 reaches ∼9% in the North, and its frequency decreases gradually to ∼1% in the southernmost populations, while the frequency of haplogroup D (sub-haplogroups D1 and D4) follows the opposite pattern: 36% in the southernmost region, gradually decreasing to 21% in the North. Furthermore, there are remarkable signatures of founder effects in specific sub-clades of Native American (e.g. haplogroups D1j and D4p) and European (e.g. haplogroups T2b3 and K1a4a1a+195) ancestry. We conclude that the magnitude of the latitudinal differences observed in the patterns of mtDNA variation might be relevant in forensic casework.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigación Sanitaria de Santiago and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Fabián Moreno
- Servicio Médico Legal, Ministerio de Justicia, Santiago, Chile
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigación Sanitaria de Santiago and Universidade de Santiago de Compostela (USC), Galicia, Spain; Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Manuel García-Magariños
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain
| | | | | | - Patricio Bustos
- Servicio Médico Legal, Ministerio de Justicia, Santiago, Chile
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigación Sanitaria de Santiago and Universidade de Santiago de Compostela (USC), Galicia, Spain.
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