遗传学实验技术

DNA barcoding, a new method for the quick identification of any species based on extracting a DNA sequence from a tiny tissue sample of any organism, is now being applied to taxa across the tree of life. As a research tool for taxonomists, DNA barcoding assists in identification by expanding the ability to ...

DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breed ...

DNA barcoding provides an operational framework for mammalian taxonomic identification and cryptic species discovery. Focused effort to build a reference library of genetic data has resulted in the assembly of over 35 K mammalian cytochrome c oxidase subunit I sequences and outlined ...

Conventional DNA barcoding uses an approximately 650 bp DNA barcode of the mitochondrial gene COI for species identification in animal groups. Similar size fragments from chloroplast genes have been proposed as barcode markers for plants. While PCR amplification and sequencing of a 650 ...

Metagenetic analysis using second-generation sequencing offers a novel methodology for measuring the diversity of metazoan communities. Among commercially available second-generation sequencers, the 454 GS FLX Titanium (Roche Diagnostics) offers by far the longest read ...

This chapter describes a workflow for measuring the efficacy of a barcode in identifying species. First, assemble individual sequence databases corresponding to each barcode marker. A controlled collection of taxonomic data is preferable to GenBank data, because GenBank data can be p ...

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and g ...

The evolutionary processes of mutation, migration, genetic drift, and natural selection shape patterns of genetic variation among individuals, populations, and species, and they can do so differentially across genomes. The field of population genomics provides a comprehensive ...

Next-generation sequencing systems allow high-throughput production of DNA sequence data. But this technology is more adapted for analyzing a small number of samples needing a huge amount of sequences rather than a large number of samples needing a small number of sequences. One solution to ...

Landscape genomics, based on the sampling of individuals genotyped for a large number of markers, may lead to the identification of regions of the genome correlated to selection pressures caused by the environment. In this chapter, we discuss sampling strategies to be used in a landscape genom ...

Restriction-site Associated DNA (RAD) markers are rapidly becoming a standard for SNP discovery and genotyping studies even in organisms without a sequenced reference genome. It is difficult, however, to identify genes nearby RAD markers of interest or move from SNPs identified by RAD to a h ...

Transcriptome sequencing from cDNA libraries has been extensively and efficiently used to analyze sequence variation in protein-coding genes (Expressed Sequence Tags) in eukaryote species. Rapid advances in next-generation sequencing (NGS) technology, in terms of cost, spe ...

Since the development of so-called “next generation” high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized p ...

Genome scans based on anonymous Amplified Fragment Length Polymorphism (AFLP) markers scattered throughout the genome are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation in natural populations. A shortcoming of this approach is t ...

In the last 20 years, we have observed an exponential growth of the DNA sequence data and simular increase in the volume of DNA polymorphism data generated by numerous molecular marker technologies. Most of the investment, and therefore progress, concentrated on human genome and genomes of sel ...

The Amplified fragment Length Polymorphism (AFLP) is one of the cost-effective and useful fingerprinting techniques to study non-model species. One crucial AFLP step in the AFLP procedure is the choice of restriction enzymes and selective bases providing good-quality AFLP profiles. ...

Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, the primary issues facing the development of SNPs from the transcriptome in non-model species are prese ...

Allelic variation within species provides fundamental insights into the evolution and ecology of organisms, and information about this variation is becoming increasingly available in sequence datasets of multiple and/or outbred individuals. Unfortunately, identifying ...

Recent advances in Molecular Biology and improvements in microarray and sequencing technologies have led biologists toward high-throughput genomic studies. These studies aim at finding associations between genetic markers and a phenotype and involve conducting many stati ...

METAPOP (http://webs.uvigo.es/anpefi/metapop/) is a desktop application that provides an analysis of gene and allelic diversity in subdivided populations from molecular genotype or coancestry data as well as a tool for the management of genetic diversity in conservation programs. A ...