Animal phylogenomics: multiple interspecific genome comparisons.
The utility of DNA sequence information for phylogenetics and phylogeography is now well known. Rather than attempt to summarize studies addressing this well-demonstrated utility, this chapter focuses on fundamental approaches and techniques that implement the collection of DNA sequence data for comparative phylogenetic purposes in a genomic context (phylogenomics). Whole genome sequencing approaches have changed the way we think about phylogenetics and have opened the way for new perspectives on "old" phylogenetics concerns. Some of these concerns are which gene regions to use and how much sequence information is needed for robust phylogenetic inference. Whole genome sequences of a few animal model organisms have gone a long way to implement approaches to better understand these important phylogenetic concerns. This chapter also addresses how genomics has made it more important for a clear understanding of orthology of gene regions in comparative biology. Finally, genome-enabled technologies that are affecting comparative biology are also discussed.
DeSalle
Rob
R
Department of Interbrate Zoology, American Museum of Natural History, New York, New York 10024, USA.
D000818:Animals; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data / Q000639:trends; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
D017931:DNA Primers; D004272:DNA, Mitochondrial