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Baroque Design: Gratuitous Genomic Complexity

John C. Avise

in Inside the Human Genome: A Case for Non-Intelligent Design

This chapter addresses various gratuitous complexities—inherent in the human genome—that routinely compromise personal health. These range from problems associated with split genes (wherein introns ... More

This chapter addresses various gratuitous complexities—inherent in the human genome—that routinely compromise personal health. These range from problems associated with split genes (wherein introns are interspersed with exons), to various complications from the Byzantine mechanisms of gene regulation and nucleic acid surveillance, to the peculiarities of genomic imprinting, to the astoundingly bizarre structure and function of mitochondrial DNA. To explain these baroque features and their oft‐deleterious health consequences, explanations from theology and philosophy are contrasted with those that emerge from the evolutionary‐genetic sciences.Less

Finding Our Roots: Did “Eve” Know “Adam”?

Norman A. Johnson

in Darwinian Detectives: Revealing the Natural History of Genes and Genomes

Unlike most of our genes, mitochondrial DNA is transmitted solely by mothers; males are a dead-end for the mitochondria. Evolutionary biologists have determined that the most recent common ancestor ... More

Unlike most of our genes, mitochondrial DNA is transmitted solely by mothers; males are a dead-end for the mitochondria. Evolutionary biologists have determined that the most recent common ancestor of all mitochondrial genetic variants was a woman who lived in Africa about 200,000 years ago. That we can trace back all mitochondrial DNA back to a single female (the mitochondrial Eve) is not a surprise. In fact, it is a simple consequence of population genetics. The location in time and place of this common ancestor does inform us about human demography and evolution. However, genetic recombination coupled with evolutionary forces will cause different genes to vary in their evolutionary histories. The mitochondrial “Eve” did not know the common ancestor of Y chromosomes, “Adam”. In fact, it is likely that the Y-chromosome Adam lived tens of thousands of years after the mitochondrial Eve.Less

Mitochondrial DNA Variation in Northern Island Melanesia

Jonathan S. Friedlaender, Françoise R. Friedlaender, Jason A. Hodgson, Stacy McGrath, Matthew Stoltz, George Koki, Theodore G. Schurr, and D. Andrew Merriwether

in Population Genetics, Linguistics, and Culture History in the Southwest Pacific

This chapter reports the mitochondrial DNA diversity in the Southwest Pacific, focusing on the extensive structure of this variation in Northern Island Melanesia. It shows that a constellation of ... More

This chapter reports the mitochondrial DNA diversity in the Southwest Pacific, focusing on the extensive structure of this variation in Northern Island Melanesia. It shows that a constellation of mitochondrial variants in Northern Island Melanesia is particularly old and not found beyond the Wallace Line to the west. These variants must have developed subsequent to initial settlement some 40,000-50,000 years ago. The evidence also suggests a subsequent series of expansions into the region from the west, through the Upper Pleistocene and into the Holocene. The most recent involve haplogroup E and the so-called “Polynesian Motif” (haplogroup B4a1a1). This “Motif” clearly in Near Oceania forms a haplogroup that was introduced from Island Southeast Asia, and is closely associated with the Lapita phenomenon. There are some problems with the distribution of the “Motif” in Island Melanesia that require explanation. Overall, the mitochondrial DNA diversity is organized on a clear island-by-island basis, with the Papuan-speaking groups of the island interiors showing the greatest diversity, and the Oceanic-speaking groups on the coastlines the least.Less

 The Origins and Evolution of Homo sapiens

Paul F. Lurquin and Linda Stone

in Evolution and Religious Creation Myths: How Scientists Respond

The notions of natural selection and drift also apply to humans and their biological and cultural evolution. The science of paleoanthropology explains human evolution through the study of ... More

The notions of natural selection and drift also apply to humans and their biological and cultural evolution. The science of paleoanthropology explains human evolution through the study of intermediate fossil forms. In addition, geneticists have been able to retrace, through the study of mitochondrial DNA and Y-chromosome DNA, the origin and migrations of prehistoric humans. The understanding of human cultural evolution has greatly benefited from the application of evolutionary thinking.Less

Mitochondrial DNA and human evolution

Rebecca L. Cann

in Origins of the Human Brain

Mitochondrial DNA (mtDNA) studies of modern human populations have made unique contributions to the understanding of human evolution due to two important features of this gene: their lack of ... More

Mitochondrial DNA (mtDNA) studies of modern human populations have made unique contributions to the understanding of human evolution due to two important features of this gene: their lack of recombination and their rate of mutation. This chapter first examines how rapid evolution and maternal transmission affect phylogenic reconstruction. A human female passes on her mitochondrial genes whereas a human male does not. Since females are almost always sure of maternity, mtDNA is preferred for tracing genealogies in many populations with different cultural norms for mate choice and long-term pair bonds. Mitochondrial DNA is a very sensitive indicator of population history. This chapter presents two reasons that reduce mitochondrial variability compared to other species: genetic bottle-necks and lineage sorting. The human mtDNA tree is also presented. The study has encountered several criticisms in the past. However, these criticisms are answered in this chapter.Less

Ancient DNA Evidence for a Homogeneous Maternal Gene Pool in Sixth Millennium cal bc Hungary and the Central European LBK

Anna Szécsényi-Nagy, Victoria Keerl, János Jakucs, Guido Brandt, Eszter Bánffy, and Kurt W. Alt

in Early Farmers: The View from Archaeology and Science

Two sixth millennium cal BC cultural formations from the Carpathian Basin are discussed: the Linearbandkeramik (LBK) in Transdanubia, and the Szakálhát culture from the Great Hungarian Plain. Our aim ... More

Two sixth millennium cal BC cultural formations from the Carpathian Basin are discussed: the Linearbandkeramik (LBK) in Transdanubia, and the Szakálhát culture from the Great Hungarian Plain. Our aim was to address genetic connections between these cultural units and how they were related to the populations of the central European Neolithic. Mitochondrial data from 33 specimens from the Szakálhát culture were compared with 39 samples from the LBK and analysed in the light of previously published ancient DNA studies. The maternal gene pool of the LBK in Transdanubia and the Szakálhát culture are highly similar to each other. Furthermore, both groups show a remarkable affinity to the LBK and the subsequent fifth–fourth millennia cal BC cultures in central Europe. On the other hand, these Neolithic cultural formations can be clearly distinguished from Mesolithic pan-European hunter-gatherer data as well as from published Iberian Neolithic and central European Late Neolithic cultures.Less

DNA Tests for Genetic Genealogy

Alan McHughen

in DNA Demystified: Unravelling the Double Helix

This chapter covers the different types of direct to consumer DNA tests for genealogy. They are technically similar but a bit different from those used for medical and health conditions, as genealogy ... More

This chapter covers the different types of direct to consumer DNA tests for genealogy. They are technically similar but a bit different from those used for medical and health conditions, as genealogy tests focus on identifying “matches,” or relatives who’ve also tested based on shared SNPs or other similarities. Consumers can choose from autosomal DNA, Y-chromosome, and mtDNA tests, depending on their interests and research goals. Unlike the other tests, genealogy DNA tests compare your results with those of others and predict a relationship based on the amount of DNA you share. This adds an extra layer of complexity but is no less rewarding, and the findings can be no less surprising. Understanding how these tests work and what they show enables consumers to choose the specific ones that will be most helpful in compiling their genetic genealogy.Less

Recent Developments in Forensic DNA Technology

Henry Erlich, Cassandra Calloway, and Steven B. Lee

in Silent Witness: Forensic DNA Evidence in Criminal Investigations and Humanitarian Disasters

The current standard of forensic DNA analysis is genotyping the length polymorphism of STR loci by capillary electrophoresis and analyzing the polymorphism of mitochondrial DNA by Sanger sequencing. ... More

The current standard of forensic DNA analysis is genotyping the length polymorphism of STR loci by capillary electrophoresis and analyzing the polymorphism of mitochondrial DNA by Sanger sequencing. However, the trend of dramatic technological developments begun in the mid 1980s has continued, with the most consequential recent innovations being (1) the development of next generation sequencing (NGS) or massively parallel sequencing (MPS) and (2) the implementation of commercial Rapid DNA instruments that automate genotyping of all CODIS core STR loci from sample to profile in 90 minutes. This chapter reviews the principles, benefits, and applications of NGS or MPS technology, with a focus on the critical features of massively parallel and clonal sequencing and the ability to perform quantitative analysis of mixtures. The potential to analyze degraded DNA by using NGS/MPS to sequence mitochondrial DNA and SNPs is discussed, as are the benefits and limitations of Rapid DNA instruments.Less

Biological Relationships: MISSING LINKS

Elizabeth Weiss and James W. Springer

in Repatriation and Erasing the Past

Weiss and Springer explain the many ways anthropologists determine biological relatedness; DNA, mitochondrial DNA, Y-chromosome DNA, metric and nonmetric cranial and dental traits are all types of ... More

Weiss and Springer explain the many ways anthropologists determine biological relatedness; DNA, mitochondrial DNA, Y-chromosome DNA, metric and nonmetric cranial and dental traits are all types of data used to reconstruct who is related to whom. These methods have helped to answer how the Americas were peopled.Less

Genetics in field ecology and conservation

Nancy N. FitzSimmons and Joanna Sumner

in Reptile Ecology and Conservation: A Handbook of Techniques

This chapter discusses the importance of genetics in questions of ecology and conservation, as genetic analyses have provided tremendous insights into the behaviour of reptiles, their evolution, and ... More

This chapter discusses the importance of genetics in questions of ecology and conservation, as genetic analyses have provided tremendous insights into the behaviour of reptiles, their evolution, and the history and dynamics of populations. To that end, the chapter discusses the functions and limitations of certain genetic markers: allozymes and restriction fragment length polymorphisms, mitochondrial DNA (mtDNA) sequencing, nuclear gene sequencing (NGS), nuclear microsatellites, single nucleotide polymorphisms (SNP), and whole genome research. Additionally, this chapter offers some pointers on sampling and labwork, such as the design and considerations for sampling; the process of collection, storage, and preservation; curating; and the subsequent data analysis and management.Less

Extraordinary Population Structure among the Baining of New Britain

Jason A. Wilder and Michael F. Hammer

in Population Genetics, Linguistics, and Culture History in the Southwest Pacific

This chapter examines with four unlinked loci the extent of divergence between two linguistically related Baining groups in New Britain. Although they are linguistically related and are less than 100 ... More

This chapter examines with four unlinked loci the extent of divergence between two linguistically related Baining groups in New Britain. Although they are linguistically related and are less than 100 km apart, they are, by a number of measures, surprisingly different genetically. This difference is explained in terms of male and female demographic distinctions. Early comparisons in global and regional mtDNA and NRY diversity indicate comparatively greater overall mtDNA variability, but greater among-group NRY variation. The chapter suggests that the key factor is the larger effective population size of women (since relatively few men contribute to following generations). This distinction could cause an acceleration in the effects of genetic drift, leading to less overall variation, but proportionately more among-group variation. In the Baining study, evidence is found for a much smaller male effective population size. However, the proportion of males who migrate and successfully reproduce appears to be greater than for females. In considering the surprising degree of overall differentiation between these two Baining groups, the effects of drift are paramount, but there remains the question of whether the differences may be due to the residue of ancient lineage sorting.Less

Ancestry Testing and DNA: Uses, Limits, and Caveat Emptor

Troy Duster

in Race and the Genetic Revolution: Science, Myth, and Culture

This chapter explores the increasing direct consumer use of DNA tests for ancestry tracing as well as its capacities and limits. It also examines the use of Ancestral Informative Markers (AIMs) as a ... More

This chapter explores the increasing direct consumer use of DNA tests for ancestry tracing as well as its capacities and limits. It also examines the use of Ancestral Informative Markers (AIMs) as a new method in determining ancestry. Fundamentally, DNA testing is capable of tracing a person's biological ancestry. However, in order to determine a person's “real” biological lineage, there needs to be a clear distinction between the direct biological ancestors. Many issues emerge as a result of the limitations in tracing the Y chromosome of a male and the mitochondrial DNA (mtDNA) of a female. Unlike the traditional method, the use of AIMs seems likely to be more accurate as it examines a group's relative share of genetic markers found on the autosomes—the nongender chromosomes inherited from both parents. Taken together, these markers appear to yield sufficiently distinctive patters in tested populations.Less

DNA: Up Close and Personal

Alan McHughen

in DNA Demystified: Unravelling the Double Helix

We now look at personal genetics and genomics, especially important with the rise of companies willing to analyze your own DNA (for a small fee, of course), giving you the raw genetic information ... More

We now look at personal genetics and genomics, especially important with the rise of companies willing to analyze your own DNA (for a small fee, of course), giving you the raw genetic information about yourself and your ancestors. Although we previously learned that DNA is “the same” in all species, we now turn to the individual, you, and explore how your DNA base sequence differs from the DNA base sequence of a bacterium, a liverwort, a chimp, and your weird Uncle Jason. This chapter provides the background to appreciate the specific issues related to medical and health issues, and then genealogical studies, coming up in later chapters. For most people, personal genomics testing involves sending a sample of DNA, in the form of spit or a cheek swab, to a lab. What kind of analyses do the labs perform, and what information do they reveal? In addition to full DNA sequence tests, there’s a whole gamut of other DNA tests, including SNP tests, Y-chromosome tests, mtDNA tests, and more. Your DNA base sequence is a gold mine of information unique to you, and it is entirely yours to discover. Whether you are curious about your medical and health genetics, wish to connect with relatives and build a family tree, or are just fascinated at what information your ancestors provided you, these next chapters will help you dig up the hidden secrets of your own genetic heritage.Less

Mitochondrial DNA Haplotypes in Pre-Hispanic Human Remains from Puyil Cave, Tabasco, Mexico

María Teresa Navarro-Romero, María de Lourdes Muñoz, and Enrique Alcalá-Castañeda

in Human Migration: Biocultural Perspectives

Previous data have established direct archaeological evidence that semisedentary forager-farmers in the Mesoamerican region existed during the millennia preceding the onset of sedentary agrarian life ... More

Previous data have established direct archaeological evidence that semisedentary forager-farmers in the Mesoamerican region existed during the millennia preceding the onset of sedentary agrarian life in the Maya area. The present study concerned the identification of the maternal genetic origin of skeletal remains discovered in the Puyil cave through sequence analysis of the mitochondrial DNA. The individuals pertained to the Archaic and Classic periods and the samples were found inside the Puyil cave located in Tabasco, Mexico, an area occupied by Zoque and Maya populations. The technologies used were next-generation sequencing and Sanger sequencing. The analysis was was made possible by the development of haplotype networks for comparing mitochondrial DNA sequences from ancient and contemporary civilizations from the American continent and Asia. The sequences displayed haplogroups A, A2, C1, C1c, and D4, while haplogroup B was absent. The haplotype networks showed a close genetic relationship with Maya populations from Mexico and Guatemala and with contemporary native populations from Bolivia, Brazil, Dominican Republic, China, and Asia. The analysis with ancient mitochondrial DNA study sequences showed evidence of Maya ancestors’ migration from North to South America and through the Caribbean islands. The results of this study confirm that a Maya ancestor of the ancient remains from the Puyil cave is shared with contemporary Maya and that expansion of the founding haplogroups A, C, and D came from Asia.Less

Mitochondrial Disorders

Richard Boles and Kathryn Moseley

in Pediatric and Adult Nutrition in Chronic Diseases, Developmental Disabilities, and Hereditary Metabolic Disorders: Prevention, Assessment, and Treatment

This chapter discusses mitochondrial disorders, including factors to be considered in nutritional evaluation and dietary management.

Settlement Burials at the Karsdorf LBK Site, Saxony-Anhalt, Germany: Biological Ties and Residential Mobility

Guido Brandt, Corina Knipper, Nicole Nicklisch, Robert Ganslmeier, Mechthild Klamm, and Kurt W. Alt

in Early Farmers: The View from Archaeology and Science

The Linearbandkeramik (LBK) settlement of Karsdorf (Saxony-Anhalt, Germany) revealed twenty-four longhouses and thirty-four associated burials. They were investigated in an interdisciplinary study ... More

The Linearbandkeramik (LBK) settlement of Karsdorf (Saxony-Anhalt, Germany) revealed twenty-four longhouses and thirty-four associated burials. They were investigated in an interdisciplinary study focusing primarily on biological relationships and mobility within the community. Males, females, and subadults were buried individually or in groups in pits accompanying longhouses suggesting family relationships. The mitochondrial DNA (mtDNA), however, revealed only few biological relations among them. The rare potential relatives were found in different houses, indicating very low continuity of maternal lineages. Strontium isotope ratios of human tooth enamel point to differentiated land-use patterns or interaction of the Karsdorf community in the Unstrut river valley with people from settlements in typical loess locations. Representatives of both isotope ranges distinguished occur among all burial groups. The integrated interpretation of all data suggests exchange of people within consolidated networks of LBK neighbouring communities.Less

Mitochondrial DNA Analysis and Pre-Hispanic Maya Migrations: Languages and Climate Influence

Maria de Lourdes Muñoz-Moreno, Mirna Isabel Ochoa-Lugo, Gerardo Pérez-Ramírez, Kristine G. Beaty, Adrián Martínez Meza, and Michael H. Crawford

in Human Migration: Biocultural Perspectives

The Maya civilization developed in Mesoamerica persisted approximately 3,000 years and was one of the most advanced of its time. Mayas had the only known full writing system, as well as highly ... More

The Maya civilization developed in Mesoamerica persisted approximately 3,000 years and was one of the most advanced of its time. Mayas had the only known full writing system, as well as highly developed mathematical and astronomical systems. They also developed sophisticated architecture and arts. The Maya area of settlement ranged from the Yucatan Peninsula through Guatemala, Belize, and part of the Mexican states of Tabasco and Chiapas, as well as parts of Honduras and El Salvador. The Maya civilization reached its peak of power and influence in the Preclassic period, from 2000 BCE to 250 CE. Despite the profound impact of the Mayan civilization on Mesoamerica and neighboring populations, studies of genetic variation of ancient Maya populations in pre-European times are scarce. Therefore, this work examines evidence in ancient DNA from archaeological sites in the states of Yucatan, Chiapas, Quintana Roo, and Tabasco. We report data analysis from sequences of the mtDNA hypervariable region I (HV1) from bone remains found in excavations of archaeological sites of the Maya region and their relationship with ancient and contemporary communities in this region, including Central and South America, as well as with Asia and Beringia. We discuss the results in the light of the influence of climate change in the area and relate them to evidence from language change. Gene flow within the Maya area occurred with a directional flow to South America in the Preclassic and Classic eras of the Mesoamerican chronology. This is supported by historical documentation, that has shown that the ancestors of the Maya civilization entered the Yucatan Peninsula after the first movement of people from Northern Asia into the Americas, with later migrations of the Maya ancestors to Mesoamerica, through Central America and the Caribbean, and toward the northern portions of South America.Less

Evolutionary relationships, questions and methods of otter ecology

Hans Kruuk

in Otters: Ecology, behaviour and conservation

This chapter describes otter phylogeny, including the latest analyses of mitochondrial DNA. They are Mustelids, originating some 11-14 million years ago in the Miocene in south-east Asia, main ... More

This chapter describes otter phylogeny, including the latest analyses of mitochondrial DNA. They are Mustelids, originating some 11-14 million years ago in the Miocene in south-east Asia, main branches being Lutra and Lontra. A rapid species divergence was followed by long-persisting genera. Some intra-specific variation is described. Central questions posed in this book address the relationship between resources and otter numbers, energetics relating to resource exploitation (with thermo-regulation in cold water), and social aspects of distribution in their habitat, mortality, and reproduction. Research methodology to study these questions is described, including individual recognition in the field, trapping, radio-tracking, and pitfalls when using indirect methods such as faecal analysis and distribution of scent-marks. Some study areas are described.Less

An Introduction to the Genus Bibitnys (Rodentia: Sigmodontinae): Phylogenetic Position and Alpha Taxonomy

Guillermo D’Elia, Ulyses F. J. Pardiñas, and Philip Myers

in Mammalian Diversification: From Chromosomes to Phylogeography

This chapter considers the position of the genus Bibimys relative other sigmodontine rodents. It analyzes mitochondrial DNA sequences and provides evidence against the inclusion of Bibimys within the ... More

This chapter considers the position of the genus Bibimys relative other sigmodontine rodents. It analyzes mitochondrial DNA sequences and provides evidence against the inclusion of Bibimys within the Scapteromini. The chapter also questions the validity of the three species currently assigned to Bibimys and stresses the need for continued taxonomic, systematic, and phylogenetic analysis of Neotropical sigmodontine rodents.Less

Unangan (Aleut) Migrations: Causes and Consequences

Michael H. Crawford, Sarah Alden, Randy E. David, and Kristine Beaty

in Human Migration: Biocultural Perspectives

There were diverse causes and demographic and evolutionary consequences of migration of the Unangan (a.k.a. Aleut) people in their expansion from Siberia through the Aleutian archipelago. The causes ... More

There were diverse causes and demographic and evolutionary consequences of migration of the Unangan (a.k.a. Aleut) people in their expansion from Siberia through the Aleutian archipelago. The causes included subsistence patterns, volcanic eruptions that destroyed island econiches, climatic changes that calmed the seas and made interisland migrations possible, and cultural contacts as well as forcible relocations. The consequences of the migrations included an intimate relationship between genetics, as revealed by mitochondrial DNA, and geography; loss of genetic diversity due to population fission along kin groups; creation of genetic barriers due to periodic climatic limitations to migrations; population genetic differentiation due to kin migration and founder effect; and admixture with Russian administrators and military in the western and central islands and with fishermen of English and Scandinavian ancestry in the eastern islands.Less