Methods In Enzymology, Volume 395

Table of Contents:
Isolation of DNA from plants with large amounts of secondary metabolites Nucleic Acid Isolation from Environmental Aqueous Samples Nucleic acid isolation from ecological samples—vertebrate gut flora Nucleic acid isolation from ecological samples — fungal associations, lichens Nucleic acid isolation from ecological samples—fungal associations, mycorrhizae Nucleic acid isolation from ecological samples—animal scat and other associated materials Isolation and analysis of DNA from archaeological, clinical and natural history specimens Isolation and characterization of proteins from archaeological and ancient specimens Animal Phylogenomics: Multiple Interspecific Genome Comparisons ISSR techniques for evolutionary biology Use of Amplified Fragment Length Polymorphism (AFLP) markers in surveys of vertebrate diversity Use of AFLP markers in surveys of arthropod diversity Use of AFLP markers in surveys of plant diversity Isolating microsatellite DNA loci Use of microsatellites for parentage and kinship analyses in animals Use of capillary array electrophoresis single strand conformational polymorphism analysis to estimate genetic diversity of candidate genes in germplasm collections Ribosomal RNA probes and microarrays: Their potential use in assessing microbial biodiversity The role of geographic analyses in locating, understanding and using plant genetic diversity In Situ Hybridization of Phytoplankton Using Fluorescently-Labelled rRNA Probes Sequencing and comparing whole mitochondrial genomes of animals Methods for obtaining and analyzing whole chloroplast genome sequences Construction of Bacterial Artificial Chromosome libraries for use in phylogenetic studies Comparative EST analyses in plant systems Isolation of genes from plant Y chromosomes Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation Experimental methods for assaying natural transformation and inferring horizontal gene transfer Use of confocal microscopy in comparative studies of vertebrate morphology PrimerSelect: A transcriptome-wide oligonucleotide primer pair design program for kinetic RT-PCR-based transcript profiling Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids genome-wide analysis of gene expression changes in polyploids Designing experiments using spotted microarrays to detect gene regulation differences within and among species Methods for studying the evolution of plant reproductive structures: Comparative gene expression techniques Developing antibodies to synthetic peptides based on comparative DNA sequencing of multigene families Application of ancestral protein reconstruction in understanding protein function: GFP-like proteins Advances in phylogeny reconstruction from gene order and content data Analytical methods for detecting paralogy in molecular datasets Analytical methods for studying the evolution of paralogs using duplicate gene data sets Supertree construction in the genomic age Maximum-likelihood methods for phylogeny estimation Context Dependence and Co-Evolution among Amino Acid Resideue in Proteins