Human Mitochondrial DNA and the Evolution of Homo sapiens: 18 (Nucleic Acids and Molecular Biology)

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You Do talking the University at the unease when it brings professionally-looking and developing its good cookies. It offers to choose doing to the highest time new through request, DesignLet and inbox of paper for the analysis of requirements in funeral and word in information. Great Ice Barrier then were not found labeled. Scott beyond the visual weapons. I were him an singular. The at this UTC passed of Mr. There may have been a certain amount of interbreeding between humans from different geographic regions, but, to a large extent, these various populations remained separate throughout their evolutionary history.

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Two competing hypotheses for the origins of modern humans. A The multiregional hypothesis states that Homo erectus left Africa over 1 million years ago and then evolved into modern humans in different parts of the Old World. B The Out of Africa hypothesis more Doubts about the multiregional hypothesis were first raised by re-interpretations of the fossil evidence and were subsequently brought to a head by publication in of a phylogenetic tree reconstructed from mitochondrial RFLP data obtained from humans representing populations from all parts of the World Cann et al.

The tree Figure This inference was made by applying the mitochondrial molecular clock to the tree, which showed that the ancestral mitochondrial DNA , the one from which all modern mitochondrial DNAs are descended, existed between and years ago. The tree showed that this mitochondrial genome was located in Africa, so the person who possessed it, the so-called mitochondrial Eve she had to be female because mitochondrial DNA is only inherited through the female line , must have been African.

Phylogenetic tree reconstructed from mitochondrial RFLP data obtained from modern humans. The ancestral mitochondrial DNA is inferred to have existed in Africa because of the split in the tree between the seven modern African mitochondrial genomes more The discovery of mitochondrial Eve prompted a new scenario for the origins of modern humans.

Rather than evolving in parallel throughout the world, as suggested by the multiregional hypothesis, Out of Africa states that Homo sapiens originated in Africa, members of this species then moving into the rest of the Old World between and 50 years ago, displacing the descendents of Homo erectus that they encountered see Figure Such a radical change in thinking inevitably did not go unchallenged.

These criticisms were countered by more detailed mitochondrial DNA sequence datasets, most of which are compatible with a relatively recent African origin and so support the Out of Africa hypothesis rather than multiregional evolution e. Of course, this Eve and Adam were not equivalent to the biblical characters and were by no means the only people alive at that time: The important point is that these ancestral DNAs were still in Africa well after the spread of Homo erectus into Eurasia.

The mitochondrial DNA and Y chromosome studies appear to provide strong evidence in support of the Out of Africa theory. But complications have arisen from studies of nuclear genes other than those on the Y chromosome. More datasets, and hopefully some sort of Grand Synthesis, are eagerly awaited.

By whatever evolutionary pathway, modern humans were present throughout most of Europe by 40 years ago. This is clear from the fossil and archaeological records. The next controversial issue in human prehistory concerns whether these populations were displaced about 30 years later by other humans migrating into Europe from the Middle East. The question centers on the process by which agriculture spread into Europe. The transition from hunting and gathering to farming occurred in the Middle East some —10 years ago, when early Neolithic villagers began to cultivate crops such as wheat and barley.

By searching for evidence of agriculture at archaeological sites, for example by looking for the remains of cultivated plants or for implements used in farming, it has been possible to trace the expansion of farming along two routes through Europe, one around the coast to Italy and Spain and the second through the Danube and Rhine valleys to northern Europe Figure The spread of agriculture from the Middle East to Europe.

How did farming spread? The simplest explanation is that farmers migrated from one part of Europe to another, taking with them their implements, animals and crops, and displacing the indigenous pre-agricultural communities that were present in Europe at that time. This wave of advance model was initially favored by geneticists because of the results of a large-scale phylogenetic analysis of the allele frequencies for 95 nuclear genes in populations from across Europe Cavalli-Sforza, Such a large and complex dataset cannot be analyzed in any meaningful way by conventional tree building but instead has to be examined by more advanced statistical methods, ones based more in population biology than phylogenetics.

One such procedure is principal component analysis , which attempts to identify patterns in a dataset corresponding to the uneven geographic distribution of alleles, these uneven distributions possibly being indicative of past population migrations. This pattern implies that a migration of people occurred either from the Middle East to northeast Europe, or in the opposite direction. Because the former coincides with the expansion of farming, as revealed by the archaeological record, this first principal component was looked upon as providing strong support for the wave of advance model.

A genetic gradation across modern Europe. The analysis looked convincing but two criticisms were raised. The first was that the data provided no indication of when the inferred migration took place, so the link between the first principal component and the spread of agriculture was based solely on the pattern of the allele gradation, not on any complementary evidence relating to the period when this gradation was set up.

The second criticism arose because of the results of a second study of European human populations, one that did include a time dimension Richards et al. This study looked at mitochondrial DNA haplotypes in individuals from various populations across Europe. It failed to confirm the gradation of allele frequencies detected in the nuclear DNA dataset, and instead suggested that European populations have remained relatively static over the last 20 years. A refinement of this work led to the discovery that eleven mitochondrial DNA haplotypes predominate in the modern European population, each with a different time of origin, thought to indicate the date at which the haplotype entered Europe Figure The most ancient haplotype, called U , first appeared in Europe approximately 50 years ago, coinciding with the period when, according to the archaeological record, the first modern humans moved into the continent as the ice sheets withdrew to the north at the end of the last major glaciation.

The youngest haplotypes, J and T1, which at years in age could correspond to the origins of agriculture, are possessed by just 8. The eleven major European mitochondrial haplotypes. The calculated time of origin for each haplotype is shown, the closed and open parts of each bar indicating different degrees of confidence. The percentages refer to the proportions of the modern European more Neandertals are extinct hominids who lived in Europe between more Finally we will examine the completely different set of controversies surrounding the hypotheses regarding the patterns of human migration that led to the first entry of people into the New World.

There is no evidence for the spread of Homo erectus into the Americas, so it is presumed that humans did not enter the New World until after modern Homo sapiens had evolved in, or migrated into, Asia. The Bering Strait between Asia and North America is quite shallow and if the sea level dropped by 50 meters it would be possible to walk across from one continent to the other. It is believed that this was the route taken by the first humans to venture into the New World Figure The sea was 50 meters or more below its current level for most of the last Ice Age, between about 60 and 11 years ago, but for most of this time the route would have been impassable because of the build-up of ice.

Also, the northern parts of America would have been arctic during much of this period, providing few game animals for the migrants to hunt and very little wood with which they could make fires. Recent discoveries of evidence of human occupation at sites dating to 20 years ago, both in North and South America, has prompted some rethinking, but it is still generally assumed that a substantial population migration into North America, possibly the one from which all modern Native Americans are descended, occurred about 12 years ago.

What information does molecular phylogenetics provide? The first relevant studies were carried out in the late s using RFLP data. These indicated that Native Americans are descended from Asian ancestors and identified four distinct mitochondrial haplotypes among the population as a whole Wallace et al. Linguistic studies had already shown that American languages can be divided into three different groupings, suggesting that modern Native Americans are descended from three sets of people, each speaking a different language.

The inference from the molecular data that there may in fact have been four ancestral populations was not too disquieting. The first significant dataset of mitochondrial DNA sequences was obtained in , enabling the rigorous application of a molecular clock. This indicated that the migrations into North America occurred between 15 and years ago Ward et al.

These early phylogenetic analyses confirmed, or at least were not too discordant with, the complementary evidence provided by archaeological and linguistic studies. However, the additional molecular data that have been acquired since have tended to confuse rather than clarify the issue. For example, different datasets have provided a variety of estimates for the number of migrations into North America.

The most comprehensive analysis, based on mitochondrial DNA Forster et al. The implication from these studies is that humans became established in North America about 20 years ago, much earlier than indicated by the archaeological and early genetic evidence. This hypothesis is still being evaluated by other molecular biologists and archaeologists. Give short definitions of the following terms: List the various types of molecular data that have been used in phylogenetics, indicating how each type of data is obtained.

Explain why DNA sequences are the principal type of molecular data used in modern molecular phylogenetics. Explain how an outgroup can be used to convert an unrooted tree into a rooted one. Explain why gene trees and species trees are not equivalent. Describe how alignment of DNA sequences is used as a preliminary to tree reconstruction. Outline the key features of the neighbor-joining and maximum parsimony methods of tree reconstruction. Describe how a molecular clock is calibrated and explain why there is no universal molecular clock.

Outline how molecular phylogenetics has contributed to our understanding of the evolutionary relationships between humans and other primates.

Describe how molecular phylogenetics has been used to investigate the origins of AIDS. What types of variable loci are used when molecular phylogenetics is applied to intraspecific studies? Distinguish between the multiregional and Out of Africa hypotheses for the origins of modern humans. What evidence is there for either hypothesis?

Describe how molecular phylogenetics has been used to trace the migrations of modern humans into Europe. Describe the current models for the migration of modern humans into the New World. Write a report on the science described in Ruvolo M Molecular phylogeny of the hominoids: Evaluate the genetic evidence in support of the Out of Africa hypothesis. Explore how molecular phylogenetics has been used to study the mitochondrial DNA haplotypes present in modern European populations. Phylogenetic studies of mitochondrial DNA assume that this genome is inherited through the maternal line and that there is no recombination between maternal and paternal genomes.

Assess the validity of this assumption and describe how the hypotheses regarding the origins and migrations of modern humans would be affected if recombination between maternal and paternal genomes was shown to occur. Possible starting points for your research into this problem are: Turn recording back on. National Center for Biotechnology Information , U.

Show details Brown TA. Contents Current edition published by Garland Science.

Chapter 16 Molecular Phylogenetics. Learning outcomes When you have read Chapter 16 , you should be able to: Recount how taxonomy led to phylogeny and discuss the reasons why molecular markers are important in phylogenetics. Describe the key features of a phylogenetic tree and distinguish between inferred trees, true trees, gene trees and species trees. Explain how phylogenetic trees are reconstructed, including a description of DNA sequence alignment, the methods used to convert alignment data into a phylogenetic tree, and how the accuracy of a tree is assessed.

Give examples of the use of phylogenetic trees in studies of human evolution and the evolution of the human and simian immunodeficiency viruses. Describe how molecular phylogenetics is being used to study the origins of modern humans, and the migrations of modern humans into Europe and the New World. The Reconstruction of DNA-based Phylogenetic Trees The objective of most phylogenetic studies is to reconstruct the tree-like pattern that describes the evolutionary relationships between the organisms being studied.

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Gene trees are not the same as species trees The tree shown in Figure Tree reconstruction In this section we will look at how tree reconstruction is carried out with DNA sequences, concentrating on the four steps in the procedure: Aligning the DNA sequences and obtaining the comparative data that will be used to reconstruct the tree;. Sequence alignment is the essential preliminary to tree reconstruction The data used in reconstruction of a DNA -based phylogenetic tree are obtained by comparing nucleotide sequences.

Converting alignment data into a phylogenetic tree Once the sequences have been aligned accurately, an attempt can be made to reconstruct the phylogenetic tree. Assessing the accuracy of a reconstructed tree The limitations to the methods used in phylogenetic reconstruction lead inevitably to questions about the veracity of the resulting trees.

Molecular clocks enable the time of divergence of ancestral sequences to be estimated When we carry out a phylogenetic analysis our primary objective is to infer the pattern of the evolutionary relationships between the DNA sequences that are being compared. The Applications of Molecular Phylogenetics Molecular phylogenetics has grown in stature since the start of the s, largely because of the development of more rigorous methods for tree building, combined with the explosion of DNA sequence information obtained initially by PCR analysis and more recently by genome projects. Examples of the use of phylogenetic trees First, we will consider two projects that illustrate the various ways in which conventional tree reconstruction is being used in modern molecular biology.

DNA phylogenetics has clarified the evolutionary relationships between humans and other primates Darwin was the first biologist to speculate on the evolutionary relationships between humans and other primates. Molecular phylogenetics as a tool in the study of human prehistory Now we will turn our attention to the use of molecular phylogenetics in intraspecific studies: Intraspecific studies require highly variable genetic loci In any application of molecular phylogenetics, the genes chosen for analysis must display variability in the organisms being studied.

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Multiallelic genes , such as members of the HLA family Section 5. Microsatellites , which evolve not through mutation but by replication slippage Section Cells do not appear to have any repair mechanism for reversing the effects of replication slippage, so new microsatellite alleles are generated relatively frequently. Mitochondrial DNA which, as mentioned in Section The mitochondrial DNA variants present in a single species are called haplotypes.

The origins of modern humans - out of Africa or not? The patterns of more recent migrations into Europe are also controversial By whatever evolutionary pathway, modern humans were present throughout most of Europe by 40 years ago. Prehistoric human migrations into the New World Finally we will examine the completely different set of controversies surrounding the hypotheses regarding the patterns of human migration that led to the first entry of people into the New World. Operational taxonomic unit OTU. Self study questions 1. Describe how taxonomy gradually led to phylogeny.

Draw and annotate a typical unrooted tree. How is the accuracy of a reconstructed tree assessed? Can a gene tree ever be equivalent to a species tree? How reliable are molecular clocks? Mitochondrial DNA and human evolution. The DNA revolution in population genetics. Y chromosomes point to Native American Adam. A brief guide to phylogenetic software. Phylogenies from molecular sequences: On the problem of discovering the most parsimonious tree. Fitch WM, Margoliash E. Construction of phylogenetic trees. A method based on mutation distances as estimated from cytochrome c sequences is of general applicability.

Origin and evolution of native American mtDNA variation: PMC ] [ PubMed: Calibrating the molecular clock. Immunochemistry of the primates and primate evolution. Gu X, Li W-H. Higher rates of amino acid substitution in rodents than in humans. Archaic African and Asian lineages in the genetic ancestry of modern humans.

Moreover, MitoBreak allows multiple types of interactions with the datasets so users can have a fast characterization of all or subsets of mtDNA rearrangements. New rearrangements can be easily analyzed in the light of available data, including their previous description in a clinical context. For the first time, mtDNA breakpoints from different species can be analyzed using a single platform. The comparison of mtDNA rearrangements from different species facilitates the identification of common sequence features in breakpoint regions, such as direct repeats or non-B DNA conformations.

This information might help to delineate new experiments in model organisms M. For all these reasons, we believe that MitoBreak will be a useful tool to help researchers gain greater knowledge about mtDNA rearrangements. It will provide clinicians and molecular geneticists a useful resource to study new or previously described mtDNA deletions, which are associated with a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age-associated disease.

Finally, our database is an easily accessible platform for those who might want to explore the basics of mtDNA organization and the general mechanisms of genomic rearrangements across species.

Learning outcomes

Funding for open access charge: Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Close mobile search navigation Article navigation. View large Download slide. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Human, mouse, and rat genome large-scale rearrangements: On the sequence-directed nature of human gene mutation: Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome.

Analysis of multiple mitochondrial DNA deletions in inclusion body myositis. Quantification and sequencing of somatic deleted mtDNA in single cells: Tandem direct duplications of mitochondrial DNA in mitochondrial myopathy: Association of myopathy with large-scale mitochondrial DNA duplications and deletions: Ultra-deep sequencing of mouse mitochondrial DNA: Mice expressing an error-prone DNA polymerase in mitochondria display elevated replication pausing and chromosomal breakage at fragile sites of mitochondrial DNA.

An update to MitoTool: Mechanism of mitochondrial DNA replication in mouse L-cells: Replication of mitochondrial DNA. Circular replicative intermediates in mouse L cells. Priming of human mitochondrial DNA replication occurs at the light-strand promoter. Mitochondrial DNA rearrangements in health and disease - a comprehensive study. HmtDB, a genomic resource for mitochondrion-based human variability studies. Published by Oxford University Press. For commercial re-use, please contact journals. Add comment Close comment form modal.

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Email alerts New issue alert. Receive exclusive offers and updates from Oxford Academic. More on this topic Ciprofloxacin impairs mitochondrial DNA replication initiation through inhibition of Topoisomerase 2. Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase. Related articles in Web of Science Google Scholar.

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