Predicting homo pigmentation phenotype through genomic data: From neanderthal to James Watson
Abstract
Background:
Human pigmentation is regulated by several genes acting at different stages of melanin formation. Functional and association studies have elucidated the role of several of these genes in pigmentation phenotypes. Forensic and evolutionary studies can benefit from this knowledge.
Objectives:
To evaluate the reliability of the prediction of pigmentation phenotypes using a large database of genetic markers in individuals with known phenotypes; and from this try to predict the pigmentation phenotype of prehistoric Homo specimens and of contemporary individuals whose visible phenotypes are not known.
Methods:
We compared predicted and observed phenotypic data through an analysis of 124 single nucleotide polymorphisms in 33 genic and seven intergenic regions of 30 subjects, five of them prehistoric, whose complete nuclear genomes are available in UCSC and PSU UCSC public databases.
Results:
For the molecular predicted versus observed phenotypes, the percentage of agreement was as follows: freckles: 91; skin: 64; hair: 44; eyes: 36; total: 59; while the molecular predicted versus probable (no visible observation available; inferences based on ethnic population characteristics) it was, respectively, 83, 60, 42, 67, and 63. The difference between two sets is statistically nonsignificant (P = 0.75).
Conclusion:
To our knowledge, this is the first article to examine the effect of a large number of genetics markers for phenotype prediction. The approach could be useful for forensic applications, as well as for the determination of possible phenotypes of extinct prehistoric individuals. Am. J. Hum. Biol., 2012. © 2012 Wiley Periodicals, Inc.
Number of times cited: 13
- Lian Deng and Shuhua Xu, Adaptation of human skin color in various populations, Hereditas, 10.1186/s41065-017-0036-2, 155, 1, (2017).
- Juan Olvido Perea García, Katrine Rosendal Ehlers and Kristian Tylén, Bodily constraints contributing to multimodal referentiality in humans: The contribution of a de-pigmented sclera to proto-declaratives, Language & Communication, 54, (73), (2017).
- Nádia Carolina de Aguiar Fracasso, Edilene Santos de Andrade, Cláudia Emília Vieira Wiezel, Claudia Caixeta Franco Andrade, Lídia Renata Zanão, Mateus Spinelli da Silva, Leonardo Arduino Marano, Eduardo Antônio Donadi, Erick C. Castelli, Aguinaldo Luiz Simões and Celso Teixeira Mendes-Junior, Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil, Legal Medicine, 25, (43), (2017).
- Irina Morozova, Pavel Flegontov, Alexander S. Mikheyev, Sergey Bruskin, Hosseinali Asgharian, Petr Ponomarenko, Vladimir Klyuchnikov, GaneshPrasad ArunKumar, Egor Prokhortchouk, Yuriy Gankin, Evgeny Rogaev, Yuri Nikolsky, Ancha Baranova, Eran Elhaik and Tatiana V. Tatarinova, Toward high-resolution population genomics using archaeological samples, DNA Research, 23, 4, (295), (2016).
- Riaan F. Rifkin, Laure Dayet, Alain Queffelec, Beverley Summers, Marlize Lategan, Francesco d’Errico and Michael D. Petraglia, Evaluating the Photoprotective Effects of Ochre on Human Skin by In Vivo SPF Assessment: Implications for Human Evolution, Adaptation and Dispersal, PLOS ONE, 10, 9, (e0136090), (2015).
- Ya Hu, Qiliang Ding, Yungang He, Shuhua Xu and Li Jin, Reintroduction of a Homocysteine Level-Associated Allele into East Asians by Neanderthal Introgression, Molecular Biology and Evolution, (msv176), (2015).
- Caio Cesar Silva de Cerqueira, Tábita Hünemeier, Jorge Gomez-Valdés, Virgínia Ramallo, Carla Daiana Volasko-Krause, Ana Angélica Leal Barbosa, Pedro Vargas-Pinilla, Rodrigo Ciconet Dornelles, Danaê Longo, Francisco Rothhammer, Gabriel Bedoya, Samuel Canizales-Quinteros, Victor Acuña-Alonzo, Carla Gallo, Giovanni Poletti, Rolando González-José, Francisco Mauro Salzano, Sídia Maria Callegari-Jacques, Lavínia Schuler-Faccini, Andrés Ruiz-Linares, Maria Cátira Bortolini and Francesc Palau, Implications of the Admixture Process in Skin Color Molecular Assessment, PLoS ONE, 9, 5, (e96886), (2014).
- P. Skoglund, H. Malmstrom, A. Omrak, M. Raghavan, C. Valdiosera, T. Gunther, P. Hall, K. Tambets, J. Parik, K.-G. Sjogren, J. Apel, E. Willerslev, J. Stora, A. Gotherstrom and M. Jakobsson, Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers, Science, 10.1126/science.1253448, 344, 6185, (747-750), (2014).
- John Hawks, Significance of Neandertal and Denisovan Genomes in Human Evolution, Annual Review of Anthropology, 42, 1, (433), (2013).
- Jolanta Draus-Barini, Susan Walsh, Ewelina Pośpiech, Tomasz Kupiec, Henryk Głąb, Wojciech Branicki and Manfred Kayser, Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains, Investigative Genetics, 4, 1, (3), (2013).
- Todd R. Disotell, Archaic human genomics, American Journal of Physical Anthropology, 149, S55, (24-39), (2012).
- M. Meyer, M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J. G. Schraiber, F. Jay, K. Prufer, C. de Filippo, P. H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R. E. Green, K. Bryc, A. W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M. F. Hammer, M. V. Shunkov, A. P. Derevianko, N. Patterson, A. M. Andres, E. E. Eichler, M. Slatkin, D. Reich, J. Kelso and S. Paabo, A High-Coverage Genome Sequence from an Archaic Denisovan Individual, Science, 338, 6104, (222), (2012).
- Wojciech Branicki and Manfred Kayser, Prediction of Human Pigmentation Traits from DNA Polymorphisms, eLS, (1-10), (2015).
