@article {46016,
	title = {Dramatically elevated rate of mitochondrial substitution in lice (Insecta: Phthiraptera)},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {26},
	year = {2003},
	month = {2003},
	pages = {231 - 242},
	abstract = {<p>Few estimates of relative substitution rates, and the underlying mutation rates, exist between mitochondrial and nuclear genes in insects. Previous estimates for insects indicate a 2-9 times faster substitution rate in mitochondrial genes relative to nuclear genes. Here we use novel methods for estimating relative rates of substitution, which incorporate multiple substitutions, and apply these methods to a group of insects (lice, Order: Phthiraptera). First, we use a modification of copath analysis (branch length regression) to construct independent comparisons of rates, consisting of each branch in a phylogenetic tree. The branch length comparisons use maximum likelihood models to correct for multiple substitution. In addition, we estimate codon-specific rates under maximum likelihood for the different genes and compare these values. Estimates of the relative synonymous substitution rates between a mitochondrial (COI) and nuclear (EF-1alpha) gene in lice indicate a relative rate of several 100 to 1. This rapid relative mitochondrial rate (\&gt;100 times) is at least an order of magnitude faster than previous estimates for any group of organisms. Comparisons using the same methods for another group of insects (aphids) reveals that this extreme relative rate estimate is not simply attributable to the methods we used, because estimates from aphids are substantially lower. Taxon sampling affects the relative rate estimate, with comparisons involving more closely related taxa resulting in a higher estimate. Relative rate estimates also increase with model complexity, indicating that methods accounting for more multiple substitution estimate higher relative rates.</p>
},
	keywords = {animals, Bird parasites, Evolution, Molecular, Lice/classification/genetics, mammal, Mitochondria/genetics, Models, Genetic, Phylogeny, polymerase, Research Support, Non-U.S. Gov{\textquoteright}t, Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S., variation},
	url = {http://www.phthiraptera.info/sites/phthiraptera.info/files/44823.pdf},
	author = {Kevin P. Johnson and Cruickshank,Robert H. and Richard J. Adams and Vincent Stuart Smith and Page,Roderic D. M. and Clayton,Dale H.}
}
@article {43333,
	title = {When do parasites fail to speciate in response to host speciation?},
	journal = {Systematic Biology},
	volume = {52},
	year = {2003},
	month = {2003},
	pages = {37 - 47},
	abstract = {<p>Abstract.\&mdash; Cospeciation generally increases the similarity between host and parasite phylogenies. Incongruence between host and parasite phylogenies has previously been explained in terms of host switching, sorting, and duplication events. Here, we describe an additional process, failure of the parasite to speciate in response to host speciation, that may be im- portant in some host\&ndash;parasite systems. Failure to speciate is likely to occur when gene flow among parasite populations is much higher than that of their hosts. We reconstructed trees from mitochondrial and nuclear DNA sequences for pigeons and doves (Aves: Columbiformes) and their feather lice in the genus Columbicola (Insecta: Phthiraptera). Although com- parisons of the trees from each group revealed a significant amount of cospeciation, there was also a significant degree of incongruence. Cophylogenetic analyses generally indicated that host switching may be an important process in the history of this host\&ndash;parasite association. Using terminal sister taxon comparisons, we also identified three apparent cases where the host has speciated but the associated parasite has not. In two of these cases of failure to speciate, these comparisons involve allopatric sister taxa of hosts whose lice also occur on hosts sympatric with both of the allopatric sisters. These additional hosts for generalist lice may promote gene flow with lice on the allopatric sister species. Relative rate comparisons for the mitochondrial cytochrome oxidase I gene indicate that molecular substitution occurs about 11 times faster in lice than in their avian hosts. [Coevolution; Columbiformes; cospeciation; lice; molecular phylogeny; Phthiraptera.]</p>
},
	url = {http://www.phthiraptera.info/sites/phthiraptera.info/files/41850.pdf},
	author = {Kevin P. Johnson and Richard J. Adams and Page,Roderic D. M. and Clayton,Dale H.}
}
