bluuebunny/crossref_metadata_2025 huggingface dataset:
Mammalian Sex Chromosome Evolution
Authors: Wyckoff Gerald J , Malcom Christine M
Published: October 2009

Although they are highly dissimilar in sequence content in extant organisms, the mammalian sex chromosomes (i.e. the X and Y) evolved from a pair of autosomes. Differentiation of the sex chromosomes during evolution was initiated by the suppression of X–Y recombination. This was followed by the general degeneration of genes on the Y‐chromosome, with specific instances of gene specialization on the nonrecombining portion of the Y.
XandYChromosomes: Homologous Regions
Authors: El‐Mogharbel Nisrine , Graves Jennifer AM
Published: October 2009

The human X and Y chromosomes have quite different deoxyribonucleic acid (DNA) and gene contents, and appear completely cytologically nonhomologous. However, they share many homologous regions, the relics of a process of gradual evolution from a homologous autosomal pair into the differentiated sex chromosome pair they are today.
X‐chromosome Inactivation
Authors: Hore Timothy A , Wakefield Matthew J , Graves Jennifer AM
Published: October 2009

X‐chromosome inactivation is an epigenetic process that silences the majority of genes on one of the two X‐chromosomes in female mammals. This silencing effectively equalizes dosage of X‐linked genes in females with that of males, who only possess one X‐chromosome and a sex‐determining Y‐chromosome.
Chromosome Rearrangement Patterns in Mammalian Evolution
Authors: Wienberg Johannes , Müller Stefan
Published: October 2009

Closely related species often have the same or similar karyotypes. This has been demonstrated in classical genetics with salivary gland chromosomes of different

Drosophila

species, in which the sequence of rearrangements that occurred during evolution can often be traced. Recently, molecular cytogenetics has proved that this is also true for mammalian chromosomes. The inspection of chromosomal changes with molecular defined probes by fluorescence

in situ

hybridization (FISH) allows the interpretation of the single or multiple steps that changed genomes during evolution. Comparative chromosome painting or ‘Zoo‐FISH’ and related techniques are now considered as one of the most powerful approaches in comparative genome studies for the understanding of the mode and tempo of gross genomic changes in primates and other mammals. For many nodes in mammalian phylogeny landmark chromosome rearrangements have now been identified that would discriminate ancestral versus derived chromosome changes and help to elucidate species phylogenies.
Comparative Cytogenetics
Authors: Breen Matthew , Langford Cordelia
Published: October 2009

In the pre‐genomics era, the field of comparative cytogenetics was restricted to the comparison of banded chromosome preparations of the species being studied. The development of molecular biology and subsequent convergence of this field with conventional cytogenetics led to the development of molecular cytogenetics. The application of molecular cytogenetics, in particular multicolour fluorescence
in situ
hybridization (MFISH), has revolutionized our ability to compare genomes at the chromosomal, subchromosomal and molecular levels, leading to much more defined knowledge about the processes of chromosomal rearrangement that have occurred during evolution. In this article we review very briefly some of the work that has led to a greater understanding of the comparative cytogenetics of mammals, in the context of their relationship to the human karyotype.
Chromosomal Rearrangements in Primates
Authors: Stanyon Roscoe , Bigoni Francesca
Published: October 2009

Comparative molecular cytogenetics techniques allow us to trace the chromosome rearrangements which have occurred during primate and human evolution. Technique such as fluorescence

in situ

hybridization (FISH) of whole chromosome paints (WCP) allows us to track interchromosomal rearrangements (translocations). FISH with smaller probes such as bacterial artificial chromosomes (BAC) allows us to study intrachromosomal rearrangements such as inversions. These data show that human chromosomes are amazingly similar to those of great apes and most Old World monkeys. Human chromosomes can be derived from the ancestral primate karyotype by a limited number of rearrangements.
Primate Phylogenetics
Authors: Disotell Todd R
Published: October 2009

Hypotheses of primate phylogenetic relationships have been greatly influenced by molecular systematic approaches. Improved methods of obtaining and amplifying deoxyribonucleic acid (DNA) from a greater number of sources from more species and subspecies, high‐throughput sequencing techniques, the characterization of genomic events such as the insertion of retrotransposons, along with new analytical techniques have allowed inferences to be drawn for most genus‐level branches of the primate phylogenetic tree.
Ethnic Inequalities in Health
Authors: Nazroo James Y
Published: October 2009

The patterning of ethnic inequalities in health is complex, as are possible explanations for the inequalities. Empirical evidence suggests that social inequalities are more relevant than genetic differences.
Clustering of Highly Expressed Genes in the Human Genome
Authors: Gierman Hinco J , Versteeg Rogier
Published: October 2009

A dual mechanism of gene regulation exists in the human genome: Transcription factors determine whether a gene will be expressed and establish a basic level of transcription. In addition, the chromosomal domain in which a gene is positioned exerts a substantial effect and potentiates the ultimate expression level.
Surnames and Genetics
Authors: Jobling Mark A
Published: October 2009

Heritable surnames contain information about the relatedness of individuals within and between populations, and thus can be used to estimate human inbreeding and population structure. These estimates are affected adversely by the failure of underlying assumptions: many surnames have several founders, and the link between surname and inheritance can be broken by nonpaternity and other factors. Associations between patrilinearly inherited surnames and paternally inherited Y‐chromosome haplotypes are now allowing the histories of names to be investigated using molecular genetic methods.
Systemic Lupus Erythematosus: Genetic and Epigenetic View
Authors: Nath Swapan K , Sawalha Amr H
Published: October 2009

Systemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex aetiology, in which susceptibility is determined by the combination of genetic, environmental, epigenetic and stochastic factors. SLE is very heterogeneous in its clinical manifestations and the presence of different autoantibodies may predict different set of clinical outcome. However, despite considerable accumulated knowledge, the detailed pathogenesis of SLE still remains unknown. Several studies have indicated the importance ofdeoxyribonucleic acid(DNA) hypomethylation in the aetiology of SLE. Recent advances in high‐throughput genotyping technologies and high‐density genetic association studies have identified and replicated many SLE susceptibility genes in different populations. In this article, we outline our current understanding of some genetic and epigenetic aspects of SLE.
Genetic Redundancy
Authors: Krakauer David C
Published: October 2009

Genetic redundancy typically relates to the duplication of an open reading frame within a genome. Genetic redundancy is often inferred when the modification or deletion of a portion of genetic material in a duplicated genome results in minimal changes in trait or organismal phenotype in reference to the nonduplicated wildtype. This invariance has been attributed to buffering mechanisms promoted by duplicates and to a number of compensatory pathways independent of the duplicate. Most duplicates are rapidly lost from genomes by mutation and drift.
Gene Clustering in Eukaryotes
Authors: Lawrence Jeffrey G , Blumenthal Thomas
Published: October 2009

Genes are not always organized at random within eukaryotic chromosomes. Multiple mechanisms can lead to the proximity of genes whose products have related functions.
Somatic Hypermutation of Antigen Receptor Genes: Evolution
Authors: Diaz Marilyn , Verkoczy Laurent K
Published: October 2009

Analysis of the pattern of immunoglobulin mutation across species has helped to reveal some of the molecular properties of this process. Strong evidence for the involvement of a cytosine deaminase and error‐prone deoxyribonucleic acid (DNA) polymerases on the DNA encoding the immunoglobulin variable regions confirms earlier predictions made from phylogenetic studies.
Vertebrate Immune System: Evolution
Authors: Hughes Austin L
Published: October 2009

The vertebrates possess unique adaptations for immune defense that have apparently evolved gradually over the long evolutionary history of the vertebrate lineage. Molecular diversity is one of the hallmarks of vertebrate immune mechanisms, and molecular analyses have clearly implicated natural selection as the major factor in promoting molecular diversity and a consequent enhanced immune surveillance.
Dosage Compensation Mechanisms: Evolution
Authors: Marín Ignacio
Published: October 2009

Degeneration of sex‐limited chromosomes favours the emergence of dosage compensation mechanisms able to equalize in both sexes the amount of products derived from sex‐linked genes. These mechanisms are understood in detail in the fly

Drosophila melanogaster

, the nematode

Caenorhabditis elegans

and in eutherian mammals. The three systems, biochemically and evolutionarily unrelated, share a common logic.
Major Histocompatibility Complex (MHC) Genes: Polymorphism
Authors: Meyer Diogo , Mack Steven J
Published: October 2009

The major histocompatibility complex (MHC) contains genes that code for glycoproteins that play key roles in the immune response. Several features of MHC gene polymorphism indicate that diversifying natural selection has acted upon these genes. Different models of diversifying selection may explain the observed variation.
Defensins: Evolution
Authors: Hughes Austin L
Published: October 2009

The α and β defensins are short, cationic peptides that are used in the antibacterial defences of mammals. The α‐ and β‐defensin gene families have diversified as a result of recent gene duplications in several lineages of mammals, and there is evidence that positive Darwinian selection has had a role in their diversification.
Low‐density Lipoprotein Receptor (
LDLR
) Family: Genetics and Evolution
Authors: Schneider Wolfgang Johann
Published: October 2009

The low‐density lipoprotein receptor family comprises a large and growing number of genes, whose products contain a characteristic set of structural domains. Attempts to delineate the evolutionary history of this gene family must take into consideration newly discovered functions, ranging from ligand binding by the extracellular domains to signal transduction through the cytoplasmic regions of the receptors.
Proteases: Evolution
Authors: Southan Christopher
Published: October 2009

Human
proteases
have diverse fold structures, catalytic mechanisms, biochemical functions and evolutionary origins. Most arose by gene duplication, but some arose by horizontal transfer from prokaryotes. Adaptation and diversification of their biological roles have resulted from shifts in substrate specificities, expression patterns and new domain combinations.
Neuropeptides and their Receptors: Evolution
Authors: Hoyle Charles HV
Published: October 2009

Multiple forms of neuropeptides and their receptors have evolved through the processes of genome duplication, gene duplication and point mutation. Some vertebrate peptide lineages have traceable origins in invertebrates, and linkage to homeobox genes may be useful in determining the lineage.
Streptomycetaceae: Life Style, Genome, Metabolism and Habitats
Authors: Schrempf Hildgund
Published: October 2009

A huge number of

Streptomyces

species belong to the family Streptomycetaceae. They are abundant soil bacteria with a highly complex life cycle. They have a large linear chromosomal
deoxyribonucleic acid
(DNA) which can be accompanied by circular and linear plasmids. They have an amazing capacity to contribute to the bioconversion of many different compounds including biopolymers, which are important for recycling processes in nature and have many biotechnological applications. They modify and synthesize thousands of chemically diverged secondary metabolites, many of which inhibit various cellular processes. Numerous of these are in use to cure diseases which are due to pathogenic microorganisms, parasites or the proliferation of tumour cells. Designed tailoring of genes encoding these metabolites has begun to complement traditional screening methods for new biologically active substances.
Reconstructing Ancient
DNA
Sequences
in Silico
Authors: Ma Jian
Published: October 2009

The increasing number of mammalian genome sequences becoming available provides scientists with dramatic opportunities to computationally reconstruct ancestral mammalian genomic sequences by comparing the genomes of living descendants. In this article, we review computational genome reconstruction methods in different scales, from base‐level reconstruction to chromosomal rearrangement reconstruction.
Evolution of the MammalianXChromosome
Authors: Waters Paul D , Robinson Terence J
Published: October 2009

The mammalian X chromosome has a fascinating evolutionary history which is intimately linked to that of the Y chromosome, since both evolved in concert from identical chromosomes. Teasing apart the events of this evolution (and their timing) has been helped greatly by identifying similarities and differences between the X and Y, and by comparing the sex chromosomes of different species.
Comparing the Human and Canine Genomes
Authors: Switonski Marek , Szczerbal Izabela
Published: October 2009

The dog is a unique species due to its phenotypic variability, exceptional among mammals. From the point of view of comparative biomedicine it needs to be emphasized that in numerous breeds specific hereditary diseases occur with high prevalence and many of them have molecular and clinical counterparts in humans. Thus, the dog is a very useful model to study human hereditary diseases and their therapy, including gene therapy. Knowledge on the human and dog genomes is very advanced. Both genomes were sequenced, their high‐density marker genome maps are available and evolutionary conserved segments (CSs) were identified by comparative chromosome painting, marker genome mapping and sequencing.
Comparing the Human and Chimpanzee Genomes
Authors: Uddin Monica , Wildman Derek E , Goodman Morris
Published: October 2009

The idea that chimpanzees share a close relationship with humans extends as far back as the early nineteenth century. However, only during the last 50 years has mounting genetic evidence demonstrated that chimpanzees are more closely related to humans than to gorillas or other apes. Whole‐genome sequences now available for both human and common chimpanzee confirm their close genetic relationship, whereas also identifying differences that may have contributed to the emergence of species‐specific phenotypes. To better understand the potential phenotypic significance of these differences, additional comparative genomic data from other primate, mammalian and vertebrate taxa are required.
The Sequencing of the Rhesus Macaque Genome and its Comparison with the Genome Sequences of Human and Chimpanzee
Authors: Gibbs Richard A , Worley Kim C , Kehrer‐Sawatzki Hildegard , Cooper David N
Published: October 2009

The rhesus macaque (

Macaca mulatta

) diverged from the ancestors of

Homo sapiens

about 25 million years ago. The macaque's genetic and physiological similarity to human is the basis for it becoming the most widely used nonhuman primate in basic and applied biomedical research. The genome sequence of a female rhesus macaque of Indian origin has been determined and compared with the genome sequences of chimpanzee and human. Those studies have revealed the likely structure of ancestral primate genomes and provided evidence both for positive selection and for the lineage‐specific expansion and contraction of gene families during primate evolution. The complete description of the macaque genome has greatly increased the utility of this animal model for biomedical research at the same time as improving our understanding of the basic biology of this highly successful species of Old World monkey.
Comparing the Human and Sea Urchin Genomes
Authors: Cameron R Andrew
Published: October 2009

Sea urchins belong to a group of animals that diverged from the lineage leading to humans very early. In that capacity their genomes reflect basic qualities of this lineage and inform to a deep reach of time the evolutionary changes leading to in the human genome. Surprisingly, the invention of new genes in this evolutionary path is subordinate to the diverse changes in the abundance of genes in existing families.
Evolution of Common Fragile Sites
Authors: Helmrich Anne
Published: October 2009

Common fragile sites are specific
deoxyribonucleic acid
(DNA) breakage‐prone genomic regions in all healthy humans. Their instability is provoked by replication stress combined with an escape of cell cycle checkpoints. Common fragile sites are favoured regions of chromosomal aberration formation in the neoplastic process. They are inherent parts of the genomes of all so far analysed mammalian species, and recent data support their existence also in yeast. The common fragile site locations are highly conserved between human and other primates as well as between human and mouse. There is no evidence of an involvement of common fragile sites as ‘hotspots’ in chromosome evolution.
Nucleotide Sequence Divergence between Humans and Chimpanzees
Authors: Chen Feng‐Chi , Chuang Trees‐Juen
Published: October 2009

Chimpanzee, as the closest relative of human, has long been a focus of molecular evolution. In this article, we review recent findings of five major categories of human–chimpanzee genomic divergence, namely nucleotide substitution, insertion/deletion, duplication, pseudogenization and rearrangement. It is demonstrated that nonsubstitution variations greatly increase the complexity and play a critical role in human–chimpanzee genome evolution. These genetic changes may provide some clues to the evolutionary origins of human‐specific traits.
The Rat Genome as a Rodent Model in Evolutionary Studies
Authors: Fechtel Kim
Published: October 2009

The genome sequence of the Brown Norway rat,

Rattus norvegicus

, revealed the precision with which genome analysis could trace the imprint of nucleotide changes associated with the radiation of mammalian species. Analysis of the protein‐coding repertoire and noncoding conserved elements (NCEs) including viable and decayed transposable elements, viruses and simple repeats provide landmarks for reconstructing past evolutionary events. From this analysis, it was possible to posit the configuration of genomes of long‐extinct mammalian ancestors. Application of evolutionary methods to subsets of the rat genome, the orthologues of human disease genes, permits the further validation of the laboratory rat as a model for studies of human pathogenesis.
Transposable Element‐driven Duplications during Hominoid Genome Evolution
Authors: Mishra Bud
Published: October 2009

Hominoid genomes exhibit a significant number of large segmental duplications; these and other similar duplications in mammalian genomes are hypothesized to be mediated by transposable elements such as Alus or L1s in hominoids and rodents, respectively. The true evolutionary mechanisms that sculpted these duplications are emerging to be much more subtle and complex.
Balancing Selection in Human Evolution
Authors: Vallender Eric J , Johnson Welkin E
Published: October 2009

Selection can act to maintain alleles within a population through many mechanisms that, taken together, constitute balancing selection. Over the course of primate and human evolution, balancing selection has repeatedly acted upon the species. Though ancient causes and effects may never be fully known or appreciated, current, ongoing, balancing selection can be observed in the human genome today. This is particularly true in genes related to immune response and pathogen defence, reproductive fitness and environmental stressors. In understanding balancing selection, it is possible to see the history of humanity's natural challenges as well as evolution's response.
Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies
Authors: Thomas Paul D
Published: October 2009

Single nucleotide polymorphisms (SNPs) are common genetic variants within a population. Several SNPs have been implicated directly in human diseases, but their biggest promise lies in their potential as genetic markers for discovering genetic factors in a wide variety of human diseases and other traits. There are two methods for modeling the processes by which population genetic variation has evolved: genealogy, the actual family tree in which genetic variants arose and were inherited from parents to children and phylogeny, a compressed history of how these genetic variants accumulated in lineages of successive copies of
deoxyribonucleic acid
(DNA) sequences. Genealogies and phylogenies are two ways to view the same evolutionary process, and each has specific applications to the discovery of genetic factors in human disease, especially relevant in the genomic era.
Alternative Polyadenylation in the Human Genome: Evolution
Authors: Tian Bin
Published: October 2009

Messenger
ribonucleic acid
(mRNA) polyadenylation is an essential step for the maturation of most eukaryotic mRNAs, and is tightly coupled with termination of transcription. Over half of all human genes have alternative polyadenylation sites, resulting in transcript variants with different 3′ UTR (untranslated region) sequences and, in some cases, protein‐coding regions. Comparative genomic studies are beginning to elucidate the phylogenetics of
cis
‐elements and protein factors involved in the regulation of mRNA polyadenylation, and shed light on the evolution of alternative polyadenylation.
Gene Evolution and Human Adaptation
Authors: Harris Eugene E
Published: October 2009

Regions of the human genome that have been subject to past positive selection contain patterns of genetic variation that are markedly different in specific ways from regions that have not experienced positive selection. By uncovering these so‐called signatures of positive selection in the genome we can discover the unique ways in which humans have evolved.
Dual‐coding Regions in Alternatively Spliced Human Genes
Authors: Liang Han , Landweber Laura F
Published: October 2009

By using different exon combinations, alternatively spliced genes may contain dual‐coding regions, where more than one reading frame encodes amino acid sequences. These special coding regions generate functionally related but distinct protein products and evolve under unusual selective forces.
MicroRNAEvolution in the Human Genome
Authors: Su Bing , Zhang Rui
Published: October 2009

Microribonucleic acids(miRNAs) are a growing class of small RNA [∼22 nucleotide (nt)] that function as negative regulators in the genome by targeting messenger RNA (mRNA) for translational repression, cleavage and destabilization. Hundreds of miRNAs have been identified in the human genome. miRNAs can be conserved or nonconserved according to their cross‐species sequence conservation, and these two classes of miRNAs in the human genome are subject to distinct evolutionary patterns.
Positive Selection and the Evolution of Prodynorphin
Authors: Rockman Matthew V
Published: October 2009

Positive natural selection has shaped thecis‐regulation of humanprodynorphin, the precursor molecule for a suite of opioid neuropeptides with roles in perception. Population genetic data suggest that after the split between the human and chimpanzee lineages, selection drove multiple substitutions in a regulatory element upstream ofprodynorphin. The substitutions fall within acis‐regulatory tandem repeat polymorphism segregating in contemporary populations. The repeat polymorphism is also seen by selection, and differing repeat allele frequencies in different parts of the globe reflect the varying pattern of positive selection.
Selection Operating on Protein‐coding Genes in the Human Genome
Authors: Meyer Diogo , Harris Eugene E
Published: October 2009

The dominant selective force acting on protein‐coding regions throughout the human genome is purifying selection, which removes deleterious mutations. The fraction of substitutions that were positively selected, and can therefore be considered to be adaptive, can be estimated using methods based on comparisons of the relative amounts of change at two classes of sites – sites which if changed produce amino acid changes and sites which if changed do not lead to amino acid changes. Current estimates find very low estimates of adaptive evolution in protein‐coding regions during human evolution.
The Contribution of Transposable Elements to Human Proteins
Authors: Volff Jean‐Nicolas
Published: October 2009

The human genome contains hundreds of genes with protein‐coding exons and even complete open reading frames derived from transposable elements. These genes are involved in major biological processes such as immunity, replication, reproduction, cell proliferation and apoptosis. This demonstrates the importance of transposable elements as a genomic pool of coding sequences for the creation and evolution of gene functions.
Are Humans Still Evolving?
Authors: Reed Floyd A
Published: October 2009

The question of whether or not humans are still evolving often captures the popular imagination and regularly leads to conflicting claims. Here, some of the evolutionary forces predicted to act upon current and future human populations are reviewed. It is postulated that the increasing movement and panmixia of humans, coupled with an unprecedented increase in the global size of the human population, are predictive of an unparalleled intensification of natural selection in the near future. However, regardless of which forces eventually prevail in the coming millennia, the idea that human evolution will somehow cease is one that is increasingly difficult to sustain.
Human Population Stratification and its Assessment by Microarray Genotyping
Authors: Bauchet Marc
Published: October 2009

Population stratification is an important phenomenon in biomedical research and anthropology. The recent microarray technology allows genome‐wide assessment of this structure and opens new avenues for understanding and using the rich diversity of the human genome across populations.
Genetic Disease in the Ashkenazim: Role of a Founder Effect
Authors: Kedar‐Barnes Inbal , Rozen Paul , Shohat Mordechai , Baris Hagit N
Published: October 2009

One in four Ashkenazi Jews is a carrier of a genetic disorder. More than 20 recessive genetic disorders are known to be prevalent in this population. Among these are four lysosomal storage diseases (LSD) and it has been suggested that carrier advantage is the driving force. For the most part the prevalence can be explained by genetic drift and consanguinity. Here we define the origin of the Ashkenazi Jews and the histories of some of the common genetic disorders. Nowadays, we will also outline the common practice for genetic screening in the Ashkenazi Jewish population in Israel nowadays.
Genetic Diversity in Africa
Authors: Sanchez‐Mazas Alicia , Poloni Estella S
Published: October 2009

Africa exhibits a high level of human genetic variation, the origin of which is still not fully understood. However, the results brought by the study of several independent genetic polymorphisms in relation to other disciplines indicate that this continent has undergone major population movements possibly linked to the diffusion of the main linguistic phyla.
Genetic Diversity in the German Population
Authors: Krawczak Michael , Lu Timothy T , Willuweit Sascha , Roewer Lutz
Published: October 2009

Throughout most of recent human history, Germany has experienced major demographic transitions that are also reflected by its current population genetic structure. While the Y‐chromosomal gene pool appears to be considerably stratified and the mitochondrial genome is highly homogeneous, variation on autosomes and on the X‐chromosome both exhibit an intermediate level of heterogeneity between subpopulations.
Genetics and the Origins of the Finns
Authors: Norio Reijo
Published: October 2009

The population of Finland initiated from neighbouring south‐eastern areas 10 000 years ago when the glacial ice melted, and it developed further from several European sources, among them the Ukrainian and Iberian refuges.

According to nuclear gene studies, the Finns belong to the European family, with some eastern components. In mitochondrial
deoxyribonucleic acid
(mtDNA) studies, the Finns are indistinguishable from other Europeans. High values of Y‐chromosomal C>T transition point to male population movements on the east–west axis.

The Finnish Disease Heritage (FDH) means overrepresentation of approximately 40 rare recessive disorders. It is due to national isolation between Sweden and Russia and regional isolation from 500‐year‐old internal migrations. This rare disease flora enjoys favourable conditions for clinical and molecular genetic research.
Genetics and the Origins of the Polynesians
Authors: Chambers Geoffrey K
Published: October 2009

The origin of the Polynesian people who settled in Remote Oceania is a long‐standing mystery. Surveys of genetic variation in these populations have helped to distinguish between competing theories arising from anthropology and linguistics. The genetic data show how maternal and paternal lineages combined around 3000 ybp (years before present) giving rise to a new people who spoke Austronesian languages and developed a sophisticated technology for oceanic voyaging.
An Evolutionary Genetic Framework for Heritable Disorders
Authors: Keller Matthew C
Published: October 2009

Natural selection is expected to drive the frequencies of heritable, fitness‐harming states to very low levels, yet many heritable disorders – and especially mental disorder – are common in the human population. These two statements are sometimes interpreted to imply that disorders have not been under natural selection, but this need not be the case. Evolutionary genetics provides three broad classes of models, none of them mutually exclusive, for understanding why disorder risk alleles have persisted in the human population despite natural selection.
Human Genetics and Languages
Authors: Comas David , Bosch Elena , Calafell Francesc
Published: October 2009

The similarities between the mode of inheritance and evolution of genes and languages have fostered interest in the joint analysis of both disciplines. The correlation between genes and languages was firstly demonstrated by Cavalli‐Sforza and collaborators comparing a tree build from ‘classical’ genetic markers to a linguistic tree of languages. Several criticisms to this correlation have been raised and a large number of exceptions have been described. It has been shown that the most plausible factor that influences in the correlation of genes and languages is geography. However, the information provided by genetics and linguistics, as well as the one provided by other disciplines, will allow us to reconstruct the history of humankind.
Molecular Clocks: Determining the Age of the Human–Chimpanzee Divergence
Authors: Jensen‐Seaman Michael I , Hooper‐Boyd Kathryn A
Published: October 2009

The approximate clocklike nature of the accumulation of nucleotide substitutions (the ‘molecular clock’) allows for the estimation of the time of divergence between modern species, dependent on calibrating the clock with known divergence dates from the fossil record. The molecular clock gives dates of approximately 6–8 million years ago for the human–chimpanzee divergence, in general agreement with the palaeontological evidence.
Origins of the Australian and New Guinean Aborigines
Authors: van Holst Pellekaan Sheila M
Published: October 2009

Mitochondrial
deoxyribonucleic acid
(mtDNA) and Y chromosome studies indicate deep ancestry for both Australia and New Guinea peoples, with evidence for limited, shared genetic connection as well as ancient maternal lineages specific to both places. Several entry points into Sahul might explain haplotype distribution. Migration by northern as well as by a southern coastal route remain possible scenarios, as no single regional source population is identifiable.
Origins of the Austro‐Asiatic Populations
Authors: Mohan Reddy B , Kumar Vikrant
Published: October 2009

The Austro‐Asiatic linguistic family, which is considered to be the oldest of all the families in South Asia, has substantial presence in Southeast Asia. The origin and expansion of the Austro‐Asiatic populations have been a contentious issue and so far there has been no formidable archaeological or linguistic evidence in favour of any of the hypotheses suggested. In recent years there has been a couple of genetic studies assessing the genetic unity, history and migration of Austro‐Asiatic groups. In this article we examine different hypotheses, based on both the genetic and nongenetic evidences. We infer a common paternal origin of Austro‐Asiatics and the migration of paternal ancestors of Austro‐Asiatic populations from East to South Asia, followed by the origin of Austro‐Asiatic languages which subsequently spread to Southeast Asia, with primarily male‐mediated migrations.
On Sequence Variants that Influence the Risk of Common Diseases
Authors: Stefánsson Kári , Gulcher Jeffrey R
Published: October 2009

Sequence variants impacting risk of common diseases have the following characteristics: Most of the risk of common diseases is conferred by common variants of modest effect although there are rare variants of large effect that account for a small minority of cases. The risk variants are rarely in coding sequences. They generally influence expression of genes and in that determine where on the spectrum of physiologic function an individual falls. The risk variants are common because they have been under selection and carried with them advantage at some point in time or other alleles at their loci have conferred disadvantage.
Evolution of Gene Deserts in the Human Genome
Authors: Taylor James
Published: October 2009

‘Gene deserts’ are improbably large regions of the human genome that contain no genes. The evolutionary origin of these regions is still unknown, but experimental and computational evidence suggests there are multiple classes of gene deserts in the human genome, each with different evolutionary origins and functional associations.
Gene Conversion during Primate Evolution
Authors: Satta Yoko
Published: October 2009

Gene conversion is a nonreciprocal recombination process. This originally represented a distortion of segregation of alleles in gametocytes. In evolutionary studies, however, this often means ‘the transfer of
deoxyribonucleic acid
(DNA) sequence information from one locus to another’. In evolutionary processes the gene conversion is frequently observed between tandemly duplicated sequences or between homologous sequences on a same chromosome. Significant roles of gene conversion between functional loci are generally in keeping their sequence and functional similarity in the ‘coevolution’ of interacting molecules. In addition, gene conversion often takes place between a functional gene and pseudogene. This mainly causes diseases, especially in humans.
Biased Gene Conversion and its Impact on Human Genome Evolution
Authors: Galtier Nicolas , Duret Laurent
Published: October 2009

Gene conversion between the maternal and paternal alleles occurs during meiosis as part of the complex molecular process of homologous recombination. Consequently, the transmission of alleles can be non‐Mendelian for loci located near recombination initiation sites. A large body of evidence suggests that such events of meiotic gene conversion are GC‐biased: AT/GC heterozygotes produce an elevated proportion of GC gametes, resulting in an evolutionary advantage for GC over AT alleles. This neutral biased gene conversion (BGC) process has surprisingly strong consequences on the evolution of genomic landscapes in human.
Pseudogene Evolution in the Human Genome
Authors: Zhang Zhaolei , Zheng Deyou
Published: October 2009

Pseudogenes are those regions in the genome that have sequence similarity to functional genes but have decayed and do not have obvious functions. It is estimated that the human genome contain more than 10 000 easily recognizable pseudogenes and many more fragmented sequences, mainly arose through one of the following three mechanisms: duplication, retrotranposition and spontaneous loss of function.
Simple Sequence Repeats in the Human Genome: Evolution
Authors: Riley Donald E , Krieger John N
Published: October 2009

Recent evolutionary findings suggest important functions for even‐numbered, simple sequence repeats (SRs). During evolution, weak‐folding SRs whose single‐stranded forms were incapable of forming classically paired duplex stems, replaced other weak‐folding repeats. Strong‐folding repeats replaced other strong‐folding repeats. Among untranslated regions, SRs were associated with genes encoding membrane‐related functions and genes encoding transcription factors. Among all possible SR sequences, evolution selected primarily weak‐folding repeats. The evolution of many of the differences comparing human SR usage with other mammals can now be mapped using publically available genome sequences. Human SR sites evolved by a variety of pathways.
Ultraconserved
DNA
Sequence Elements in the Human Genome
Authors: Lee Alison P , Venkatesh B
Published: October 2009

Ultraconserved elements are
deoxyribonucleic acid
(DNA) sequences at least 200 base pairs in length and perfectly conserved in human, mouse and rat genomes. These elements are under extreme purifying selection and are implicated in functions such as transcriptional enhancers, exons of noncoding ribonucleic acid (RNA) transcripts and alternatively spliced ‘poison cassette exons’ that regulate the expression of certain classes of proteins.
Mitochondrial Genome Sequences and Their Phylogeographic Interpretation
Authors: Macaulay Vincent , Richards Martin
Published: October 2009

The strong phylogenetic signal provided by complete mitochondrial
deoxyribonucleic acid
(mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans.
Comparative Genetics of Trinucleotide Repeats in the Human and Ape Genomes
Authors: Mularoni Loris , Toll‐Riera Macarena , Albà M Mar
Published: October 2009

The genome of humans and other apes shows important differences in trinucleotide repeat sequences. This has implications for the evolution of protein function and susceptibility to repeat expansion disease.
Comparison of Rates and Patterns of Meiotic Recombination between Humans and Chimpanzees
Authors: Freudenberg Jan
Published: October 2009

Meiotic recombination events were found to be concentrated in relatively small genomic regions that were termed recombination hotspots. Surprisingly, the genomic locations of recombination hotspots are hardly conserved between human and chimpanzee, rendering individual hotspots as evolutionarily transient features. Based on the theoretical advantages of recombination one may thus hypothesize coevolution of gene sequences and recombination modifiers. Consistently, human recombination hotspot predictions were found enriched at central nervous system (CNS) gene loci and those regions that showed accelerated sequence evolution in hominids.
Evolution of Microsatellite DNA
Authors: Vargas Jentzsch Iris M , Bagshaw Andrew , Buschiazzo Emmanuel , Merkel Angelika , Gemmell Neil J
Published: October 2009

Microsatellites are highly mutable tandemly repeated sequences that are ubiquitously distributed in bacterial and eukaryotic genomes. Microsatellites became the preferred molecular marker for a variety of applications under the basic assumption that they are selectively neutral. However, the simplicity of this assumption contrasts with the observed variability of mutation rates across microsatellite loci and with the increasing evidence supporting microsatellite functionality. The evolutionary importance of microsatellites is only recently being uncovered with the intense study of their impact on the regulation of gene expression and the interaction among genomic structures.
Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection
Authors: Kimura Ryosuke , Ohashi Jun
Published: October 2009

The recent availability of human genomic data has driven genome‐wide scans for natural selection with different approaches based on comparative genetics and population genetics. Such studies have provided many candidates for targets of positive selection in the human genome, but the results should be interpreted with caution because of the inevitability of false positives. Here, approaches for identifying positive selection in the human genome are reviewed, and, especially, an up‐to‐date approach based on haplotype variation and linkage disequilibrium is explained in detail.
Indels in the Evolution of the Human and Chimpanzee Genomes
Authors: Wetterbom Anna , Cavelier Lucia , Bergström Tomas F
Published: October 2009

Mutations in thedeoxyribonucleic acid(DNA) cause genomic divergence between species and provide a starting point for evolutionary change. There are several sources of sequence variation and here we will focus on insertions and deletions (indels). Such events occur frequently in genomic alignments of humans and chimpanzees and the indel divergence is estimated to 3–5%. In this article, we will discuss some causes behind indels and the possible impact of indels on the evolution of primate genomes. In addition, we will provide some examples of indels that may affect protein function as well as alternative splicing.
Spectrum of Mutations in the Human Genome Inferred by Single Nucleotide Polymorphisms
Authors: Zhongming Zhao
Published: October 2009

The spectrum of mutations in the human genome inferred by single nucleotide polymorphisms (SNPs) may be measured by three approaches: directly observed frequencies of nucleotide changes, relative frequencies of nucleotide changes by normalizing the nucleotide content and frequencies of nucleotide changes after excluding the CpG effect. The spectrum of mutations indicates that point mutation does not occur randomly in the human genome and varies between the categorized genomic regions.
Modelling Cancer in
Drosophila
Authors: Brumby Anthony M , Richardson Helena E
Published: October 2009

Ever since the discovery of neoplastic and metastatic overgrowths in
Drosophila melanogaster
, the fly has been recognized as an excellent model organism for studying tumorigenesis. Recently, however, its relevance has become even more pronounced with the modelling of neoplasias in somatic clones of tissue using cooperative interactions between tumour suppressors and homologues of known mammalian oncogenes. The realization that many
Drosophila
neoplasias can be understood with respect to aberrant differentiation of stem cell progeny, together with the growing trend to postulate a stem cell origin of mammalian cancers, further highlight the enormous potential of fly cancer models to greatly increase our understanding of how human cancers develop.
Micro
RNAs
in Development and Disease
Authors: Staton Alison A , Giraldez Antonio J
Published: October 2009

Micro
ribonucleic acids
(miRNAs) are small RNAs responsible for selective repression and degradation of mRNAs. Regulation by miRNAs during development facilitates the transition from one stage to the next and can control specialized characteristics of mature cells. When this regulation is disrupted, cancer can result through increases in proliferation and defects in differentiation.
Cell Migration during Development
Authors: Crabbe Ellen , Vleminckx Kris
Published: October 2009

Cell migration is essential during the establishment of a three‐dimensional and multilayered organism. These migratory processes are highly coordinated both in time and space through various intercellular and cell–substrate interactions providing specific permissive, attractive and repulsive guidance cues.
Methods for Live Microscopy ofDrosophilaSpermatocytes
Authors: Savoian Matthew S , Glover David M
Published: October 2009

Drosophilais a genetically tractable system well suited for cell cycle investigations. The combination of live cell imaging and the variety of different cell types available, in particular, the easily cultured, exceptionally large and flat, primary spermatocyte, offer powerful tools for studying dynamic cell division events.
Evolutionary History and Impact of Human
DNA
Transposons
Authors: Feschotte Cédric
Published: October 2009

Deoxyribonucleic acid
(DNA) transposons are mobile elements that move via a DNA intermediate. The human genome harbours over 300 000 DNA transposon copies, accounting for approximately 3% of the total genomic DNA. Nearly one‐third of these elements are specific to the primate lineage, but there is no evidence for transposition activity within the last 40 million years. However, there is growing evidence that DNA transposons have contributed in shaping the current genome architecture of humans and have been a recurrent source of new regulatory and coding DNA throughout mammalian evolution.
Human‐specific Changes of Genome Structure
Authors: Harris R Alan , Milosavljevic Aleksandar
Published: October 2009

Genomic changes occur along a size continuum ranging from small‐scale base substitutions to large‐scale cytogenetically detectable chromosome rearrangements. Intermediate‐scale changes between these two extremes are the least studied group of genomic changes. The genomic triangulation method was developed to detect intermediate‐scale changes by integrating genomic sequence and mapping data from human, chimpanzee and rhesus macaque. Human‐specific genomic changes associate with segmental duplications (SDs), involve numerous genes and may result in human‐specific phenotypic traits.
Chromatin Structure and Human Genome Evolution
Authors: Semple Colin AM
Published: October 2009

Functional and comparative genomics have provided data on the evolution and function of the human genome, but we still know relatively little about its spatial organization. What is the three‐dimensional structure of the genome? How and when does this structure vary? It has long been suspected that the structural organization of the genome might impose constraints on its evolution. Recent genome‐wide data on chromatin structure have revealed the complex physical landscape of the human genome, and have yielded unexpected insights into the evolution of chromosome architecture, gene order and patterns of mutation and selection.
Evolution of Skin Pigmentation Differences in Humans
Authors: Norton Heather L
Published: October 2009

The distribution of human skin pigmentation variation is highly correlated with the intensity of ultraviolet radiation (UVR). Several hypotheses propose that this strong relationship between skin colour and UVR is best explained by natural selection. The identification of a large number of genes involved in the pigmentary system now enables researchers to test these hypotheses within an evolutionary genetics framework. Genetic data indicate that the light pigmentation that characterizes populations in Europe and East Asia has evolved independently through positive selection, and that functional variation in pigmentation genes in high UVR populations has likely been subject to purifying selection.