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Author: Stephen Malone Richards
Publisher:
ISBN:
Category : Bison, Fossil
Languages : en
Pages : 610
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Book Description
The introduction of high throughput sequencing (HTS) in 2005 caused a revolution in the field of ancient DNA (aDNA). Using the large sequencing capacity of HTS, researchers have overcome the abundant environmental contamination present in most aDNA extractions to reconstruct the genomes of long extinct organisms, such as an archaic horse that perished >500,000 years ago. The proliferation of genomes engendered by HTS has also led to the development of potential ancillary technologies for aDNA research such as genotyping microarrays. In this thesis, HTS and genotyping techniques were developed or refined to improve the application of aDNA to larger biological questions in evolution. This thesis successfully: a) describes an in-house hybridization capture system that uses RNA probes generated from long-range PCR amplicons, b) demonstrates that recombinase polymerase amplification is a less biased alternative to PCR in hybridization capture of aDNA, c) develops an analytical approach that improves phylogenies generated with data from the Illumina BovineSNP50 BeadChip (a commercially available genotyping microarray). In contrast, an attempt to determine the identity of modified nucleotides in aDNA with Pacific Bioscience's Single Molecule Real-Time (SMRT) sequencing prove to be unsuccessful and genotyping of ancient bison aDNA with the BovineSNP50 BeadChip generated inconsistent results. Furthermore, a hybridization capture probe design was tested and found to be unsuitable for aDNA enrichment. For the larger biological aspect of this thesis, several of the methods developed were used to study bison, because these animals are ideal models of megafauna evolution. Using the in-house hybridization capture system, whole mitochondrial genomes were enriched from aDNA and used to help identify a new extinct species of bison. Furthermore, the new analytical approach for BovineSNP50 BeadChip data was used to demonstrate a significant genetic split between American woods and plains bison, which supports separating these animals at least at the subspecies level. This genetic split suggests that woods and plains bison should be conserved as separate species, which has considerable economic and political implications.
Author: Stephen Malone Richards
Publisher:
ISBN:
Category : Bison, Fossil
Languages : en
Pages : 610
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Book Description
The introduction of high throughput sequencing (HTS) in 2005 caused a revolution in the field of ancient DNA (aDNA). Using the large sequencing capacity of HTS, researchers have overcome the abundant environmental contamination present in most aDNA extractions to reconstruct the genomes of long extinct organisms, such as an archaic horse that perished >500,000 years ago. The proliferation of genomes engendered by HTS has also led to the development of potential ancillary technologies for aDNA research such as genotyping microarrays. In this thesis, HTS and genotyping techniques were developed or refined to improve the application of aDNA to larger biological questions in evolution. This thesis successfully: a) describes an in-house hybridization capture system that uses RNA probes generated from long-range PCR amplicons, b) demonstrates that recombinase polymerase amplification is a less biased alternative to PCR in hybridization capture of aDNA, c) develops an analytical approach that improves phylogenies generated with data from the Illumina BovineSNP50 BeadChip (a commercially available genotyping microarray). In contrast, an attempt to determine the identity of modified nucleotides in aDNA with Pacific Bioscience's Single Molecule Real-Time (SMRT) sequencing prove to be unsuccessful and genotyping of ancient bison aDNA with the BovineSNP50 BeadChip generated inconsistent results. Furthermore, a hybridization capture probe design was tested and found to be unsuitable for aDNA enrichment. For the larger biological aspect of this thesis, several of the methods developed were used to study bison, because these animals are ideal models of megafauna evolution. Using the in-house hybridization capture system, whole mitochondrial genomes were enriched from aDNA and used to help identify a new extinct species of bison. Furthermore, the new analytical approach for BovineSNP50 BeadChip data was used to demonstrate a significant genetic split between American woods and plains bison, which supports separating these animals at least at the subspecies level. This genetic split suggests that woods and plains bison should be conserved as separate species, which has considerable economic and political implications.
Author: Susanne Hummel
Publisher: Springer Science & Business Media
ISBN: 3662050501
Category : Social Science
Languages : en
Pages : 320
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Book Description
This is the definitive source of information on techniques for the identification and sequencing of old DNA (pieces) and their use in biological and medical research and application. Application of aDNA techniques are useful tools for investigations reaching from evolutionary studies to law enforcement approaches. What brings them together is the interest in specific methods of handling aDNA, i.e. elaborated PCR and sequencing techniques and the interpretation of the results. This books serves as an ideal guideline for it demonstrates how problem-solving strategies can be applied in various areas.
Author: Bernd Herrmann
Publisher: Springer Science & Business Media
ISBN: 1461243181
Category : Science
Languages : en
Pages : 275
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Book Description
Ancient DNA refers to DNA which can be recovered and analyzed from clinical, museum, archaeological and paleontological specimens. Ancient DNA ranges in age from less than 100 years to tens of millions of years. The study of ancient DNA is a young field, but it has been revolutionized by the application of polymerase chain reaction technology, and interest is growing very rapidly. Fields as diverse as evolution, anthropology, medicine, agriculture, and even law enforcement have quickly found applications in the recovery of ancient DNA. This book contains contributions from many of the "first generation" researchers who pioneered the development and application of ancient DNA methods. Their chapters present the protocols and precautions which have resulted in the remarkable results obtained in recent years. The range of subjects reflects the wide diversity of applications that are emerging in research on ancient DNA, including the study of DNA to analyze kinship, recovery of DNA from organisms trapped in amber, ancient DNA from human remains preserved in a variety of locations and conditions, DNA recovered from herbarium and museum specimens, and DNA isolated from ancient plant seeds or compression fossils. Ancient DNA will serve as a valuable source of information, ideas, and protocols for anyone interested in this extraordinary field.
Author: Erika Hagelberg
Publisher:
ISBN: 9781782521099
Category : DNA, Fossil
Languages : en
Pages :
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Book Description
Author: Alexander Immel
Publisher:
ISBN:
Category :
Languages : de
Pages : 0
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Book Description
Ancient DNA has become an indispensable resource of fundamental research. Especially the combination of DNA capture methods and Next Generation Sequencing (NGS) has allowed to exploit the full potential of ancient DNA. In this dissertation I present three studies which involve capture of ancient DNA to answer different scientific questions. In my first study I bioinformatically reconstruct the mitochondrial genome of the extinct giant deer Megaloceros giganteus after applying mitochondrial DNA capture and sequencing. Using the giant deer's reconstructed mitochondrial genome I then apply phylogenetic analyses that allow to resolve the giant deer's placement within the cervid family tree and reaffirm the fallow deer being its closest extant relative. Mitochondrial DNA capture also provides the basis for the next study, in which I investigate the effects of X-rays on ancient DNA. Different radiation settings are explored including those commonly used in computed tomography (CT) of anthropological and palaeontological specimens. The results allow to define 200 Gray (Gy) as the maximum absorbed X-ray dose which can still be regarded harmless to ancient DNA molecules. No X-radiation induced effects can be observed below this threshold. In my third study I develop and apply capture of 488 human immunity genes in order to compare the immunogenetic makeup of Late Medieval plague (Yersinia pestis) victims and their modern day successors from Ellwangen, Southern Germany. Applying bioinformatic tools allows me to investigate kinship within both populations, determine genetic continuity between past and present, and reconstruct the Human Leukocyte Antigen (HLA) allelic profiles of both populations. While the majority of HLA alleles do not differ in their frequencies, HLA-B51:01 and HLA-DRB113 show significant frequency differences between both populations, potentially indicative of selective pressure through Yersinia pestis.
Author: Nic Rawlence
Publisher: Frontiers Media SA
ISBN: 2889669335
Category : Science
Languages : en
Pages : 183
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Book Description
Author: Beth Alison Shapiro
Publisher:
ISBN: 9781617795169
Category : Nature
Languages : en
Pages : 247
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Book Description
Ancient DNA presents an overview of the many of the protocols commonly used to study ancient DNA. These include laboratory instructions, extraction protocols, laboratory techniques, and suggestions for appropriate analytical approaches to make sense of the sequences obtained.
Author: Beth Shapiro
Publisher: Humana Press
ISBN: 9781493991754
Category : Science
Languages : en
Pages : 216
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Book Description
This fully updated second edition explores protocols that address the most challenging aspects of experimental work in ancient DNA, such as preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules for sequencing library preparation. The volume also examines the analysis of high-throughput sequencing data recovered from ancient specimens, which, because of the degraded nature of ancient DNA and common co-extraction of contaminant DNA, has challenges that are unique compared to data recovered from modern specimens.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Ancient DNA: Methods and Protocols, Second Edition aims to serve both experts and beginners by presenting protocols in a manner that makes them easily accessible for everyday use in the lab.
Author: Hirak Ranjan Dash
Publisher: Springer
ISBN: 9811315833
Category : Medical
Languages : en
Pages : 325
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Book Description
This book describes the basics and various applications of DNA fingerprinting, including in actual case studies. The book is divided in four modules; Module 1: Basics of DNA Fingerprinting, Module 2: Applications of DNA Fingerprinting, Module 3: DNA Fingerprinting: Case Studies, and Module 4: Future of DNA Fingerprinting. Each module consists of 4 to 5 chapters, written by reputed researchers, academics and forensic scientists from around the globe. The respective chapters cover e.g. related fields, the tools and techniques used, various genotyping kits, real-world case studies, ancient DNA and wild life forensics, molecular diagnosis of human diseases, legal aspects, microbial forensics and the economics of the DNA fingerprinting technique. The book offers a practical guide for professionals, graduate and post-graduate students in the fields of Forensic Science, Medicine, Genetics, Anthropology, Microbiology, and Zoology. It also serves as a useful reference resource, summarizing major technological advances in the field of DNA fingerprinting, the problems faced in this field of science and possible new solutions to these problems. Presently, DNA fingerprinting is utilized in solving the majority of criminal cases; as such, the book is also helpful for investigating agencies, as it includes representative case studies.
Author: M. Anne Katzenberg
Publisher: John Wiley & Sons
ISBN: 1119151619
Category : Social Science
Languages : en
Pages : 688
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Book Description
An Indispensable Resource on Advanced Methods of Analysis of Human Skeletal and Dental Remains in Archaeological and Forensic Contexts Now in its third edition, Biological Anthropology of the Human Skeleton has become a key reference for bioarchaeologists, human osteologists, and paleopathologists throughout the world. It builds upon basic skills to provide the foundation for advanced scientific analyses of human skeletal remains in cultural, archaeological, and theoretical contexts. This new edition features updated coverage of topics including histomorphometry, dental morphology, stable isotope methods, and ancient DNA, as well as a number of new chapters on paleopathology. It also covers bioarchaeological ethics, taphonomy and the nature of archaeological assemblages, biomechanical analyses of archaeological human skeletons, and more. Fully updated and revised with new material written by leading researchers in the field Includes many case studies to demonstrate application of methods of analysis Offers valuable information on contexts, methods, applications, promises, and pitfalls Covering the latest advanced methods and techniques for analyzing skeletal and dental remains from archaeological discoveries, Biological Anthropology of the Human Skeleton is a trusted text for advanced undergraduates, graduate students, and professionals in human osteology, bioarchaeology, and paleopathology.
