@article {94426, title = {Phylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera: Columbicola)}, journal = {Systematic Biology}, volume = {66}, year = {2017}, month = {Jul-01-2018}, pages = {896-911}, abstract = {

Parasitic \“wing lice\” (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90\% of all relationships receiving 100\% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice.

}, keywords = {aTRAM, coalescent, coevolution, concatenation, species tree.}, issn = {1063-5157}, doi = {10.1093/sysbio/syx027}, url = {https://academic.oup.com/sysbio/article/66/6/896/2929402}, author = {Boyd, Bret M. and Julie M. Allen and Nam-phuong Nguyen and Andrew D. Sweet and Tandy Warnow and Michael D. Shapiro and Villa, Scott M. and Sarah E. Bush and Clayton,Dale H. and Kevin P. Johnson} } @article {47800, title = {Mitochondrial and Nuclear DNA Sequences Support a Cretaceous Origin of Columbiformes and a Dispersal-Driven Radiation in the Paleogene}, journal = {Systematic Biology}, volume = {56}, year = {2007}, month = {2007}, pages = {656 - 672}, abstract = {

Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies.We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.

}, url = {http://www.phthiraptera.info/sites/phthiraptera.info/files/46934.pdf}, author = {Pereira,Sergio L. and Kevin P. Johnson and Clayton,Dale H. and Baker,Allan J.} } @article {43343, title = {Untangling coevolutionary history}, journal = {Systematic Biology}, volume = {53}, year = {2004}, month = {2004}, pages = {92 - 94}, url = {http://www.phthiraptera.info/sites/phthiraptera.info/files/41861.pdf}, author = {Kevin P. Johnson 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 = {

Abstract.\— 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\–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\–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.]

}, 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.} } @article {43306, title = {Ecology of Congruence: Past Meets Present}, journal = {Systematic Biology}, volume = {53}, year = {2004}, month = {2004}, pages = {165 - 173}, abstract = {

Phylogenetic congruence is governed by various macroevolutionary events, including cospeciation, host switching, sorting, duplication, and failure to speciate. The relative frequency of these events may be influenced by factors that govern the distribution and abundance of the interacting groups; i.e., ecological factors. If so, it may be possible to predict the degree of phylogenetic congruence between two groups from information about their ecology. Unfortunately, adequate comparative ecological data are not available for many of the systems that have been subjected to cophylogenetic analysis. An exception is provided by chewing lice (Insecta: Phthiraptera), which parasitize birds and mammals. For a few genera of these lice, enough data have now been published to begin exploring the relationship between ecology and congruence. In general, there is a correspondence between important ecological factors and the degree of phylogenetic congruence. Careful comparison of these genera suggests that dispersal is a more fundamental barrier to host switching among related hosts than is establishment. Transfer experiments show that host-specific lice can survive and reproduce on novel hosts that are similar in size to the native host as long as the lice can disperse to these hosts. To date, studies of parasite dispersal have been mainly inferential. A better understanding of the role of dispersal will require more direct data on dispersal frequency and distances.

}, keywords = {cospeciation, Host specificity, host switching, lice, parasite, Phthiraptera, Phylogeny}, url = {https://phthiraptera.myspecies.info/sites/phthiraptera.info/files/43306.pdf}, author = {Clayton,Dale H. and Sarah E. Bush and Kevin P. Johnson} }