Genomics in Biological Anthropology: New Challenges, New Opportunities

Book Series: Anthropology : Current and Future Developments

Volume 2

by

Manuela Lima, Amanda Ramos, Cristina Santos

DOI: 10.2174/97816810838581160201
eISBN: 978-1-68108-385-8, 2016
ISBN: 978-1-68108-386-5
ISSN: 2405-7703 (Print)
ISSN: 2405-7711 (Online)



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Molecular methodologies are crucial to our understanding of human population diversity, as well as our evolutionary relationships with...[view complete introduction]

Table of Contents

Foreword

- Pp. i

Esther Rebato

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Preface

- Pp. ii-iii (2)

Manuela Lima, Amanda Ramos and Cristina Santos

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List of Contributors

- Pp. iv-v (2)

Manuela Lima, Amanda Ramos and Cristina Santos

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Human Genomic Projects: Setting the Stage for Genome-Scale Anthropological Studies

- Pp. 3-24 (22)

Cristina Santos, Mafalda Raposo, Amanda Ramos and Manuela Lima

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Complete Mitochondrial DNA through Massively Parallel Sequencing: Methodology and Applications

- Pp. 25-49 (25)

Sofia L. Marques, Ana Goios and Luis Alvarez

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Somatic vs Germinal Mutations in Mitochondrial DNA: Is There Any Relation with Human Health and Aging?

- Pp. 50-64 (15)

Amanda Ramos, Maria Pilar Aluja, Manuela Lima and Cristina Santos

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Human Y Chromosome Mutation Rate: Problems and Perspectives

- Pp. 65-91 (27)

Paolo Francalacci, Daria Sanna and Antonella Useli

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Genomics of Isolated Populations: Inferences for Gene-Finding Studies

- Pp. 92-105 (14)

Manuela Lima

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Complex Human Phenotypes: The Interplay between Genes and Environment

- Pp. 106-137 (32)

Mar Fatjo-Vilas and Barbara Arias

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Ancient DNA: From Single Words to Full Libraries in 30 Years

- Pp. 138-159 (22)

Marc Simon and Assumpcio Malgosa

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Troubles and Efficiency of aDNA

- Pp. 160-182 (23)

Marc Simon and Assumpcio Malgosa

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aDNA Methodological Revolution

- Pp. 183-205 (23)

Marc Simon and Assumpcio Malgosa

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Complicities Between Forensic Anthropology and Forensic Genetics: New Opportunities for Genomics?

- Pp. 206-218 (13)

Eugenia Cunha and Manuela Lima

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Subject Index

- Pp. 219-223 (5)

Manuela Lima, Amanda Ramos and Cristina Santos

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Foreword

The Genome science encompasses many scientific areas and is essential to advancing knowledge of different disciplines as Evolutionary Biology, Genetics, Medicine and Biological Anthropology, among others. With respect to this last discipline, the understanding of our place in nature has benefited in recent years of the Genomic research that is being essential in the analysis of the biological origin of our species, and to measure in a more precise way human biological variation. The main genome projects have had a great impact in Biological Anthropology, and the anthropological studies are benefiting more and more from the genomic data. The developments in genome bioinformatics and computational biology have helped make the advances possible in the field of Anthropological Genetics, as well as in Forensic Anthropology and the population studies. Briefly, the current genomic revolution constitutes a turning point in our understanding of human evolution, and a fascinating insight into what can be revealed from the study of genomes.

The book deals with the genomic approaches in Biological Anthropology and how the DNA markers can provide insight into the processes of evolution and human variability; in addition, explanations of the technological developments and how they affect the fields of Forensic sciences and population studies are shown, alongside the methods of field investigations and their contribution to the Molecular Anthropology. But in turn, this volume reveals how the modern Anthropology can contribute to redefine the ways we have come to understand the genetic issues.

This volume, written by experts in their respective field, provides a rigorous overview about a subject so promising like Genomics and its present and future applications in the study of Human Biology. Through the different chapters authors are providing essential information for the area of Biological Anthropology that could change the traditional vision in this field and contribute to resolve numerous anthropological questions that have not yet been answered.

Esther Rebato
Department of Genetics, Physical Anthropology and Animal Physiology
University of the Basque Country (UPV-EHU)
Bilbao
Spain
E-mail: esther.rebato@ehu.es


Preface

Molecular methodologies have been routinely applied in Biological Anthropology to increase our understanding of human diversity and to elucidate the associations within and between human populations, as well as our evolutionary relationships with nonhuman primates. Since the first molecular studies, which date back to the late 1960s, molecular methodologies have been rapidly applied to investigations in the area of Biological Anthropology. The development of the Human Genome Project, concluded in 2004, resulted in the availability of a complete human reference sequence; combined with very important advances in sequencing and bioinformatics technologies, this leads the way to other genome-scale projects.

In Chapter 1 Santos and co-authors present a general characterization of the main genome projects with potential impact in the field of Biological Anthropology, providing examples of questions to which genomic data can now successfully be called upon.

The emergence of genomics has contributed to the availability of databases containing large amounts of information, leading also to the implementation of new mathematical/bioinformatics methods, which have undergone a major expansion in recent years. The analysis of both nuclear and mitochondrial human genomes received new tools of analysis, providing information that now needs to be conciliated with previous classic genetic evidences. Discrepancies between the results obtained with the use of such methodological innovations and the most established methodologies thus constitute a challenge, which anthropologists need to resolve. The transition from traditional approaches to massively parallel sequencing or next-generation sequencing of the mitochondrial DNA (mtDNA) is discussed in Chapter 2, by Marques and collaborators; these authors highlight the need for the development and validation of new routine procedures and optimization of laboratorial protocols.

The expanding amount of data has made it possible to address several important questions in a molecular evolutionary context. In Chapter 3 Ramos and co-workers analyse the contribution of germinal versus somatic heteroplasmy, discussing in its impact in aging and health.

Besides mtDNA, genomics have also been impacting the analysis of yet another monoparental system, the Y chromosome. Because a major goal of Biological Anthropology is to date events related with the present day populations (such as major migratory waves), mutation rate estimations for the Y chromosome are pertinent. In Chapter 4 Francalaci and collaborators address alternative methodologies which use genomic data to estimate such rates.

Information derived from genome projects, namely from the HapMap project is, as previously referred, having a tremendous impact in providing in-depth insights into the genetic makeup of human populations, namely of isolated populations, who are privileged populations for gene-finding studies of both monogenic and multifactorial diseases. In Chapter 5 the characteristics of genetically isolated populations are addressed by Lima and the potential impact of genomic data on gene finding efforts is discussed.

In Chapter 6 Fatjó-Vilas & Arias further address the imports of the genomic era into discoveries concerning the aetiology of multifactorial diseases, focusing on ecogenetics, an area which studies the relationship between genetic and environmental factors, looking for gene-environment interactions.

Ancient DNA has also entered the genomic era; an historical overview of the advances and constraints in the field of ancient DNA analysis is provided by Simon & Malgosa that also discuss, in Chapter 8, the pitfalls of ancient DNA analysis and the strategies to circumvent them. The advances achieved by paleogenetics are also acknowledged by these authors, in Chapter 9.

Human genomics has been impacting several areas, and Forensic Anthropology is no exception. In Chapter 10 the interrelation between Forensic Anthropology and Forensic Genetics is highlighted, arguing that recent genomic tools have the potential to efficiently resolve questions left unanswered by genetics. Genomic resolution is gradually occupying an important place in Biological Anthropology; the process has been relatively simple in several sub-areas of Anthropology, such as population genetics, whereas in other sub-areas, such as Forensic Anthropology, several issues need to be overcome before a routine application of genomic data can be considered.

Initially tailored towards research of human health and disease, genomics has already provided important attention to human origins and variation studies; yet, and although paleogenomics has been dramatically impacting anthropology, genomics as an anthropological subject is still in childhood, and more work has yet to be done.

Manuela Lima
Department of Biology, University of the Azores
Ponta Delgada, Portugal

Amanda Ramos & Cristina Santos
Universitat Autònoma de Barcelona, Cerdanyola del Vallès
Barcelona, Spain

List of Contributors

Editor(s):
Manuela Lima
Department of Biology
University of the Azores
Ponta Delgada
Portugal


Amanda Ramos
Universitat Autònoma de Barcelona
Cerdanyola del Vallès
Barcelona
Spain


Cristina Santos
Universitat Autònoma de Barcelona
Cerdanyola del Vallès
Barcelona
Spain




Contributor(s):
Amanda Ramos
Unitat Antropologia Biològica, Department BABVE
Universitat Autònoma de Barcelona, Cerdanyola del Vallès
Barcelona
Spain.
/
Department of Biology
University of the Azores
Ponta Delgada
Portugal.
/
Instituto de Investigação e Inovação em Saúde
Universidade do Porto
Port
Portugal.
/
Institute for Molecular and Cell Biology (IBMC)
University of Porto
Porto
Portugal


Ana Goios
i3S-Instituto de Investigação e Inovação em Saúde/IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto
Porto
Portugal


Antonella Useli
Dipartimento di Scienze della Natura e del Territorio
Università di Sassari
07100 Sassari
Italy


Assumpció Malgosa Morera
Departament de Biologia Animal, Biologia Vegetal i Ecologia
Unitat d’Antropologia Biològica, Universitat Autònoma de Barcelona, Bellaterra
Barcelona
Spain


Bárbara Arias
Departament de Biologia Animal, Facultat de Biologia
Universitat de Barcelona
Barcelona
Spain.
/
Institut de Biomedicina de la Universitat de Barcelona (IBUB)
Barcelona
Spain.
/
Instituto de Salud Carlos III
Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)
Madrid
Spain


Cristina Santos
Unitat Antropologia Biològica, Department BABVE
Universitat Autònoma de Barcelona, Cerdanyola del Vallès
Barcelona
Spain


Daria Sanna
Dipartimento di Scienze della Natura e del Territorio
Università di Sassari
07100 Sassari
Italy


Eugénia Cunha
Department of Life Sciences
Center of Functional Ecology, University of Coimbra
Coimbra
Portugal


Luis Alvarez
i3S-Instituto de Investigação e Inovação em Saúde/IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto
Porto
Portugal


Mafalda Raposo
Departamento de Biologia
Universidade dos Açores
Ponta Delgada
Portugal.
/
Instituto de Investigação e Inovação em Saúde
Universidade do Porto
Portugal.
/
Instituto de Biologia Molecular e Celular (IBMC)
Universidade do Porto
Porto
Portugal


Manuela Lima
Department of Biology
University of the Azores
Ponta Delgada
Portugal.
/
Instituto de Investigação e Inovação em Saúde
Universidade do Porto
Port
Portugal.
/
Institute for Molecular and Cell Biology (IBMC)
University of Porto
Porto
Portugal


Marc Simón Martínez
Departament de Biologia Animal, Biologia Vegetal i Ecologia
Unitat d’Antropologia Biològica, Universitat Autònoma de Barcelona, Bellaterra
Barcelona
Spain


Mar Fatjó-Vilas
FIDMAG Germanes Hospitalàries Research Foundation
Sant Boi de Llobregat
Barcelona
Spain.
/
Departament de Biologia Animal, Facultat de Biologia
Universitat de Barcelona
Barcelona
Spain.
/
Institut de Biomedicina de la Universitat de Barcelona (IBUB)
Barcelona
Spain.
/
Instituto de Salud Carlos III
Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)
Madrid
Spain


Maria Pilar Aluja
Unitat Antropologia Biològica, Department BABVE
Universitat Autònoma de Barcelona, Cerdanyola del Vallès
Barcelona
Spain


Paolo Francalacci
Dipartimento di Scienze della Natura e del Territorio
Università di Sassari
07100 Sassari
Italy


Sofia L. Marques
i3S-Instituto de Investigação e Inovação em Saúde/IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto
Porto
Portugal




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