Genes

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Open AccessArticle

Population Genomics of Secondary Contact

by Anthony Geneva and Daniel Garrigan

Genes 2010, 1(1), 124-142; https://doi.org/10.3390/genes1010124 - 25 Jun 2010

Cited by 7 | Viewed by 10107

One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from an [...] Read more.

One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from an endemic population. The simulated coalescent histories are sampled from models that describe the evolution of entire chromosomes, thereby allowing the expected length of introgressed haplotypes to be estimated. The results indicate that our ability to identify reticulate evolution from genetic data is highly variable and depends critically upon the duration of the period of allopatry, the timing of the secondary contact event, as well as the sizes of the populations at the time of contact. One particularly interesting result arises when secondary contact occurs close to the time of a severe founder event, in this case, genetic introgression can be substantially more difficult to detect. However, if secondary contact occurs after such a founding event, when the range of the colonizing population increases, introgression is more readily detectable across the genome. This result may have important implications for our ability to detect introgression between ancestrally bottlenecked modern human populations and archaic hominin species, such as Neanderthals. Full article

(This article belongs to the Special Issue Reticulate Evolution)

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Open AccessReview

An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites

by Jillian T. Detwiler and Charles D. Criscione

Genes 2010, 1(1), 102-123; https://doi.org/10.3390/genes1010102 - 09 Jun 2010

Cited by 61 | Viewed by 10726

Abstract

Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus [...] Read more.

Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus on what is known about how introgression and hybridization have influenced the evolution of protozoan and helminth parasites of animals. There are reports of genome or gene introgression from distantly related taxa into apicomplexans and filarial nematodes. Most common are genetic based reports of potential hybridization among congeneric taxa, but in several cases, more work is needed to definitively conclude current hybridization. In the medically important Trypanosoma it is clear that some clonal lineages are the product of past hybridization events. Similarly, strong evidence exists for current hybridization in human helminths such as Schistosoma and Ascaris. There remain topics that warrant further examination such as the potential hybrid origin of polyploid platyhelminths. Furthermore, little work has investigated the phenotype or fitness, and even less the epidemiological significance of hybrid parasites. Full article

(This article belongs to the Special Issue Reticulate Evolution)

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188 KiB

Open AccessReview

The Application of Next Generation Sequencing in DNA Methylation Analysis

by Yingying Zhang and Albert Jeltsch

Genes 2010, 1(1), 85-101; https://doi.org/10.3390/genes1010085 - 04 Jun 2010

Cited by 45 | Viewed by 16847

Abstract

DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly [...] Read more.

DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states. Full article

(This article belongs to the Special Issue Next Generation DNA Sequencing)

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Open AccessReview

Next Generation Sequencing of miRNAs – Strategies, Resources and Methods

by Susanne Motameny, Stefanie Wolters, Peter Nürnberg and Björn Schumacher

Genes 2010, 1(1), 70-84; https://doi.org/10.3390/genes1010070 - 03 Jun 2010

Cited by 104 | Viewed by 24393

Abstract

miRNAs constitute a family of small RNA species that have been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have arisen to identify and quantify miRNAs and elucidate their [...] Read more.

miRNAs constitute a family of small RNA species that have been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have arisen to identify and quantify miRNAs and elucidate their function. The unprecedented sequencing depth reached by next generation sequencing technologies makes it possible to get a comprehensive miRNA landscape but also poses new challenges for data analysis. We provide an overview of strategies used for miRNA sequencing, public miRNA resources, and useful methods and tools that are available for data analysis. Full article

(This article belongs to the Special Issue Next Generation DNA Sequencing)

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Open AccessReview

Next Generation DNA Sequencing and the Future of Genomic Medicine

by Matthew W. Anderson and Iris Schrijver

Genes 2010, 1(1), 38-69; https://doi.org/10.3390/genes1010038 - 25 May 2010

Cited by 47 | Viewed by 23984

Abstract

In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis [...] Read more.

In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpretation, laboratory workflow, data storage, and ethical considerations. This review describes the current high-throughput sequencing platforms commercially available, and compares the inherent advantages and disadvantages of each. The potential applications for clinical diagnostics are considered, as well as the need for software and analysis tools to interpret the vast amount of data generated. Finally, we discuss the clinical and ethical implications of the wealth of genetic information generated by these methods. Despite the challenges, we anticipate that the evolution and refinement of high-throughput DNA sequencing technologies will catalyze a new era of personalized medicine based on individualized genomic analysis. Full article

(This article belongs to the Special Issue Next Generation DNA Sequencing)

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387 KiB

Open AccessArticle

An Examination of KCNE1 Mutations and Common Variants in Chronic Tinnitus

by Philipp G. Sand, Alexander Luettich, Tobias Kleinjung, Goeran Hajak and Berthold Langguth

Genes 2010, 1(1), 23-37; https://doi.org/10.3390/genes1010023 - 28 Apr 2010

Cited by 19 | Viewed by 9672

Abstract

Chronic tinnitus is a highly prevalent and often incapacitating condition frequently associated with sensorineural hearing loss. While its etiology remains incompletely understood there is a growing awareness of genetic factors that predispose to, or aggravate chronic tinnitus. Candidate genes for the disorder include [...] Read more.

Chronic tinnitus is a highly prevalent and often incapacitating condition frequently associated with sensorineural hearing loss. While its etiology remains incompletely understood there is a growing awareness of genetic factors that predispose to, or aggravate chronic tinnitus. Candidate genes for the disorder include KCNE1, a potassium channel subunit gene that has been implicated in maturation defects of central vestibular neurons, in Menière's disease, and in noise-induced hearing loss. 201 Caucasian outpatients with a diagnosis of chronic tinnitus were systematically screened for mutations in the KCNE1 open reading frame and in the adjacent sequence by direct sequencing. Allele frequencies were determined for 46 known variants, plus two novel KCNE1 mutations. These comprised one missense substitution (V47I) in the highly conserved region encoding the KCNE1 transmembrane domain, and one rare variant in the gene's 3'UTR. When genotypes were grouped assuming dominance of the minor alleles, no significant genotype or compound genotype effects were observed on tinnitus severity. The newly identified V47I substitution argues in favor of an enlarged spectrum of mutations in hearing disorders. However, with regard to allele frequencies in healthy control populations from earlier studies, more common KCNE1 variants are unlikely to play a major role in chronic tinnitus. Further investigations are invited to address variation in additional channel subunits as possible risk factors in tinnitus. Full article

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Open AccessReview

Asymmetric Introgressive Hybridization Among Louisiana Iris Species

by Michael L. Arnold, Shunxue Tang, Steven J. Knapp and Noland H. Martin

Genes 2010, 1(1), 9-22; https://doi.org/10.3390/genes1010009 - 15 Mar 2010

Cited by 47 | Viewed by 10791

Abstract

In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes from [...] Read more.

In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes from Iris fulva into both Iris brevicaulis and Iris hexagona. Furthermore, our analyses have detected certain prezygotic and postzygotic barriers to reproduction that appear to contribute to the asymmetric introgression. Finally, our studies have determined that a portion of the genes transferred apparently affects adaptive traits. Full article

(This article belongs to the Special Issue Reticulate Evolution)

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Open AccessEditorial

The Secret Lives of Pluripotent Cells: There and Back Again

by Paolo Cinelli

Genes 2010, 1(1), 4-8; https://doi.org/10.3390/genes1010004 - 09 Mar 2010

Cited by 1 | Viewed by 6725

Abstract

Embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs) hold great promise for the therapeutic treatment of human diseases, but their functional similarity, their stability and especially the mechanism underlying their derivation are not yet clearly explained. [...] Full article

(This article belongs to the Special Issue Natural and Induced Pluripotency in Stem Cells)

23 KiB

Open AccessEditorial

Genes: an Open Access Journal

by J. Peter W. Young

Genes 2010, 1(1), 1-3; https://doi.org/10.3390/genes1010001 - 02 Nov 2009

Cited by 2 | Viewed by 7321

Abstract

Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [...] Read more.

Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [1], but others were already pointing to chromosomes as the likely location of genes. The science of genetics was born at that time, and genes were rapidly connected with mutations, with patterns of inheritance, with development, with quantitative traits, with evolution and with biochemical pathways. All this was achieved without knowledge of the physical nature of genes, but this changed in mid-century with the discoveries of molecular biology. DNA was revealed as the genetic material, and the mechanisms were elucidated by which the information was encoded, and propagated, and linked to the phenotype. However, the concept of a "gene" did not become clearer. Quite the reverse, as the units of mutation, of recombination, of inheritance, of expression, of regulation, etc. did not necessarily coincide. [...] Full article

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Genes, Volume 1, Issue 1 (June 2010) – 9 articles , Pages 1-142

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