Publications Enabled by the CIPRES Science Gateway (2010-2011) and CIPRES Portal (2007-2009)

In addition to those listed below, as of 4/15/2011; there were 24 manuscipts in review, and a reported 103 in preparation.

2011 in the Press (2 articles)

  1. Sharma, B., and Kramer, E.M. (2011) "The MADS box gene family of the lower eudicot Aquilegia coerulea E. James." Annals of the Missouri Botanical Garden, in press.
  2. Fishbein, M., Chuba, D., Ellison, C., Mason-Gamer, R., and Lynch, S.P. (2011) "Phylogenetic relationships of Asclepias (Apocynaceae) estimated from non-coding cpDNA sequences." Systematic Botany in press.

2011 (51 articles)

  1. Munro J.B., Heraty, J.M., Burks, R.A., Hawks, D., Mottern, J., et al. (2011) "A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)." PLoS ONE 6(11):e27023.doi:10.1371/journal.pone.0027023.[pdf]
  2. Fong, J.J. and Fujita, M. K. (2011) Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Molecular Phylogenetics and Evolution 61(2):300-7. Epub 2011 Jul 1. [abstract]
  3. Sharma, B., Guo, C. Kong, H., Kramer, E. M. (2011) "Petal-specific subfunctionalization of an APETALA3 paralog in the Ranunculales and its implications for petal evolution." New Phytologist 191(3): 870–883. [abstract]
  4. Fuselier, L., Shaw, B., Engel, J., von Konrat, M., Costa, D., Devos, N., and Shaw, A.J. (2011) "The status and phylogeography of the liverwort genus Apometzgeria Kuwah (Metzgeriaceae)." The Bryologist 114(1):92-101. [abstract]
  5. Němcová, Y., Eliáš, M., Škaloud, P., Neustupa, J., Hodač, L. (2011) "Jenufa gen. nov., a new genus of coccoid green algae (Chlorophyceae, incertae sedis) previously recorded by environmental sequencing." Journal of Phycology 47(4) 928–938. [abstract]
  6. Storz, J.F., Hoffmann, F.G., and Opazo, J.C. (2011) "Phylogenetic diversification of the globin gene superfamily in chordates." IUBMB Life: Special Issue: XVIth International Conference on Dioxygen Binding and Sensing Proteins (O2BIP) – Part 2 63(5):313–322. [abstract]
  7. Zhang, G.-C. and Zhang, L.-B. (2011) "Impatiens shimianensis sp. nov (Balsaminaceae): A new species from Sichuan, China based on morphological and molecular evidence". Systematic Botany \ 36(3):721-729. [abstract]
  8. Mah, C., and Foltz, D. (2011) "Molecular Phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): Systematics & Biogeography." Zoological Journal of the Linnean Society. 162(3): 646–660. [abstract]
  9. Dawson, M.N, Barber, P.H., González-Guzmán, L.I., Toonen, R.J., Dugan, J.E. and Grosberg, R.K., (2011) "Phylogeography of Emerita analoga (Crustacea, Decapoda, Hippidae), an eastern Pacific Ocean sand crab with long-lived pelagic larvae." J. Biogeogr. 38(8) 1600–1612.[abstract]
  10. Schell, W.A., Lee, A.G., and Aime, M.C. (2011) "A new lineage in Pucciniomycotina: class Tritirachiomycetes, order Tritirachiales, family Tritirachiaceae." Mycologia10-333; Published online: June 3, 2011, doi:10.3852/10-333 [abstract]
  11. Sharanowski, B.J. Dowling, A.P.G., and Sharkey, M.J (2011) "Molecular Systematics of Braconidae (Hymenoptera: Ichneumonoidea): phylogenetic insights from a multi-gene dataset. Systematic Entomology 36(3): 549–572. [abstract]
  12. Zhou X., Xu S, Xu J, Chen B, Zhou K, Yang G.(2011). "Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals." Systematic Biology published online September 7, 2011 doi:10.1093/sysbio/syr089   [abstract]
  13. Gräfenhan, T., Schroers, H.-J., Nirenberg, H.I. and Seifert, K.A. (2011) "An overview of the taxonomy, phylogeny, and typification of nectriaceous fungi in Cosmospora, Acremonium, Fusarium, Stilbella, and Volutella" Stud Mycol 68(1): 79-113.
  14. Ovrebo, C.L., Lodge, D.J., and Aime, M.C. "A new Cantharocybe from Belize with notes on the type of Cantharocybe gruberi." Mycologia: Apr 11.
  15. Mereditha, R.W., Hekkala, E.R., Amato, G., and Gatesy, J. (2011) "A Phylogenetic Hypothesis for Crocodylus (Crocodylia) Based on Mitochondrial DNA: Evidence for a Trans-Atlantic Voyage from Africa to the New World." Molecular Phylogenetics and Evolution Apr 1. [Epub ahead of print].
  16. Lemaire, B., De Block, P., Van Oevelen, S., Verstraete, B., Smets, E., and Dessein, S (2011). "Identification of the bacterial endosymbionts in leaf nodulating Pavetta species (Rubiaceae)." Int. J. Syst. Evol. Microbiol. Mar 4. [Epub ahead of print].
  17. Andrew, D.R. (2011) "A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics." Arthropod Structure and Development Arthropod Struct Dev. Feb 21. [Epub ahead of print].
  18. Bueno-Silva, M., Boeger, W.A., and Pie, M.R. (2011) "Choice matters: Incipient speciation in Gyrodactylus corydori (Monogenoidea: Gyrodactylidae)?" International Journal for Parasitology, Feb 23. [Epub ahead of print].
  19. Aruda, A.M., Baumgartner, M.F., Reitzel, A.M., and Tarrant, A.M. (2011) "Heat shock protein expression during stress and diapause in the marine copepod Calanus finmarchicus." J Insect Phys. Mar 16. [Epub ahead of print].
  20. Silva, J.C., Egan, A., Friedman, R., Munro, J.B., Carlton, J.M., and Hughes A.L. (2011) "Genome sequences reveal divergence times of malaria parasite lineages". Parasitology 138:1–13. doi: 10.1017/S0031182010001575.
  21. Ballerini, E. and Kramer, E. M.(2011) "The control of flowering time in the lower eudicot model Aquilegia." EvoDevo, 2:4.
  22. Lahr, D.J.G., Nguyen, T.B., Barbero, E. and Katz, L.B. (2011) "Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions." Mol Biol Evol 28(1): 223-236.
  23. Buerki, S., Forest, F., Salamin, N., and Alvarez, N (2011) "Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study." Systematic Biology, 60: 32-44.
  24. Arrigo, N., Buerki, S., Béguin, A., Guadagnuolu, R., and Kozlowski, G. (2011) "Phylogenetic relationships in Baldellia (Alismataceae) inferred from AFLP markers, nuclear and chloroplast DNA sequences." Molecular Phylogenetics and Evolution 58: 33-42.
  25. Seitzman, B.H., Ouimette, A., Mixon, R.L., Hobbie, E.A., and Hibbett, D.S. (2011) Conservation of biotrophy in Hygrophoraceae inferred from combined stable isotope and phylogenetic analyses. Mycologia 103 (2): 280-290. doi: 10.3852/10-195.
  26. Cognato, A. I., Hulcr, J., Dole, S., and Jordal, B. H. (2011) "Phylogeny of haplo-diploid, fungus-growing ambrosia beetles (Coleoptera: Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data." Zoologica Scripta 40 (2) 174-186.
  27. Cavallero, S., Nadler, S.A., Paggi, L., Barros, N.B., D'Amelio, S. (2011) "Molecular characterization and phylogeny of anisakid nematodes from cetaceans from southeastern Atlantic coasts of USA, Gulf of Mexico, and Caribbean Sea." Parasitol Res. 108(4):781-92. Epub 2011 Jan 7.
  28. Gold, J. R., Voelker, G., and Renshaw, M.A. (2011) "Phylogenetic relationships of tropical western Atlantic snappers in Subfamily Lutjaninae (Lutjanidae; Perciformes) inferred from mitochondrial DNA sequences." Biol. J. Linnean Society 102:915-929.
  29. Avendaño, J. E (2011) "Molecular phylogenetics, phylogeography, geographic variation, and species limits in the Chlorospingus ophthalmicus complex (Aves, Emberizidae)." Maters thesis. Universidad de los Andes, Bogotá, Colombia.
  30. Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C.L., Dalin, E., Tu, H., Huang, E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet, P., Anjard, C., Madan Babu, M., Basu, S., Bushmanova, Y., van der Wel, H., Katoh-Kurasawa, M., Dinh, C., Coutinho, P.M., Saito, T., Elias, M., Schaap, P., Kay, R.R., Henrissat, B., Eichinger, L., Rivero, F., Putnam, N.H., West, C.M., Loomis, W.F., Chisholm, R., Shaulsky, G., Strassmann, J.E., Queller, D.C., Kuspa, A., and Grigoriev, I. (2011) "Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum." Genome Biology 12:R20.
  31. Vlahou, G., Elias, M., von Kleist-Retzow, J.C., Wiesner, R.J., and Rivero, F. (2011) "Non-metazoan Ras related GTPases of the Miro family are not required for mitochondrial transport: functional analysis of the Dictyostelium discoideum ortholog." European Journal of Cell Biology 90:342–355.
  32. Neustupa, J., Eliáš, M., Škaloud, P., Němcová, Y. and Šejnohová, L. (2011) "Xylochloris irregularis gen. et sp. nov (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga." Phycologia 50: 57-66.
  33. Baker, W. J., Norup, M.V., Clarkson, J.J., Couvreur, T.L.P., Dowe, J.L., Lewis, C.E., Pintaud, J.C., Savolainen, V., Wilmot, T., and Chase, M.W.(2011) "Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)." Annals of Botany doi:10.1093/aob/mcr020.
  34. Weirauch, C., Forero, D., and Jacobs, D. H. (2011) "On the evolution of raptorial legs - an insect example (Hemiptera: Reduviidae Phymatinae)." Cladistics 27: 138-149.
  35. Martinson, V.G., Minckley, R., Danforth, B., Rueppell, O., Tingek, S., and Moran, N.A. (2011) "A simple and distinct microbiota associated with honey bees and bumble bees." Molecular Ecology, 20, 619-628.
  36. Lapoint, R.T., Gidaya, A., and O’Grady, P.M. (2011) "Phylogenetic relationships in the spoon tarsus subgroup of Hawaiian Drosophila; Conflict and concordance between gene trees." Molecular Phylogenetics and Evolution. 58:492-501.
  37. Mah, C., and Foltz, D. (2011) Molecular phylogeny of the Valvatacea (Asteroidea: Echinodermata). Zoological Journal of the Linnean Society. 161(4) 769-788.
  38. O’Grady, P.M., Lapoint, R.T., Bonacum, J., Lasola, J., Owen, E., Wu, Y., and DeSalle, R. (2011) “Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis.” Molecular Phylogenetics and Evolution 58:244-256.
  39. Lowenstein, J.H., Osmundson, T.W., Becker, S., Hanner, R., and Stiassny, M.L. (2011) “Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study.” Mitochondrial DNA. Feb 8. [Epub ahead of print].
  40. Townsend, T.M., Tolley, K.A., Glaw, F., Böhme, W., and Vences, M (2011) “Eastward from Africa: Palaeocurrent-mediated chameleon dispersal to the Seychelles Islands.” Biology Letters 7, 225-228.
  41. Townsend, T.M., Leavitt, D.H.,and Reeder, T.W. (2011)”Intercontinental dispersal by a microendemic burrowing reptile (Dibamidae)”. Proceedings of the Royal Society of London Series B-Biological Sciences.
  42. Moreno-Letelier, A., Olmedo, G., Eguiarte, L.E., Martinez-Castilla, L., and Souza, V. (2011) “Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments,” International Journal of Evolutionary Biology, vol. 2011, Article ID 781642, 10 pages, (2011) doi:10.4061/2011/781642
  43. Mitchell, M. N., Ocamb, C. M., Grunwald, N. J., Mancino, L. E., and Gent, D. H. (2011) "Genetic and Pathogenic Relatedness of Pseudoperonospora cubensis and P. humuli." Phytopathology, 0:ja.
  44. Wong, M.K.S. and Takei, Y.(2011) "Characterization of a native angiotensin from an anciently diverged serine protease inhibitor in lamprey." J Endocrinol 209:127-137.
  45. Komoto, N., Yukuhiro, K., Ueda, K., and Tomita, S (2011) "Exploring the molecular phylogeny of phasmids with whole mitochondrial genome sequences." Mol. Phylogenet. Evol. 58: 43-52.
  46. Funaro, C.F., Kronauer, D.J.C., Moreau, C.S., Goldman-Huertas, B., Pierce, N.E., and Russell, J.A. (2011) "Army ants harbor a host-specific clade of Entomoplasmatales bacteria." Applied and Environmental Microbiology 77: 346-350.
  47. Levy, A., Wirtz, P., Floeter, S.R., Almada, V.C. (2011) "The Lusitania Province as a center of diversification: The phylogeny of the genus Microlipophrys (Pisces: Blenniidae)." Molecular Phylogenetics and Evolution 58: 409–413.
  48. Jackson, K. (2011) "The diversity and activity of sulfate-reducing bacteria in relationship to soil salinity in a drained salt marsh." California State University, Long Beach.
  49. Griffiths, K.E., Trueman, J.W.H., Brown, G.R., and Peakall, R. (2011) "Molecular genetic analysis and ecological evidence reveals multiple cryptic species among thynnine wasp pollinators of sexually deceptive orchids." Molecular Phylogenetics and Evolution 59:195-205.
  50. Bourland, W.A., Vdacny, P., Davis, M.C., and Hampikian, G. (2011) "Morphology, Morphometrics, and Molecular Characterization of Bryophrya gemmea n. sp (Ciliophora, Colpodea): Implications for the Phylogeny and Evolutionary Scenario for the Formation of Oral Ciliature in the Order Colpodida." The Journal of Eukaryotic Microbiology 58: 22-36. 47.
  51. Huhndorf, S. M. and Miller, A.N. (2011) "A molecular re-appraisal of Sordariomycetidae taxa and a new species of Rimaconus from New Zealand." Stud Mycol 68(1): 203-210.

2010 (77 articles)

  1. Fong, J. J. and Chen, T. H. (2010). DNA evidence for the hybridization of wild turtles in Taiwan: possible genetic pollution from trade animals. Conservation Genetics 11: 2061-2066.
  2. Espíndola, A.; Buerki, S.; Bedalov, M.; Küpfer, P. and Alvarez, N. (2010) "New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history." Botanical Journal of the Linnean Society. 163 (1):14-32.
  3. Xu S, W. Ren, X. Zhou, K. Zhou, G. Yang (2010) "Sequence polymorphism and geographical variation at a positively selected MHC-DRB gene in the finless porpoise (Neophocaena phocaenoides): implication for recent differentiation of the Yangtze finless porpoise?" Journal of Molecular Evolution 71: 6-22. 
  4. Sass, C., and Specht, C.D. (2010) "Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae)."Molecular Phylogenetics and Evolution 55(2) 559-571.
  5. Gryganskyi, A.P., Lee, S.C., Litvintseva, A.P., Smith, M.E., Bonito, G., Porter, T.M., Anishchenko, I.M., Heitman, J., and Vilgalys, R. (2010) "Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex". PLoS ONE 5,12:1-12.
  6. Soza, V.L. and Olmstead, R.G. (2010) "Evolution of breeding systems and fruits in New World Galium and relatives (Rubiaceae)." American Journal of Botany 97(10): 1630-1646.
  7. Bayha, K.M., and Dawson, M.N. (2010) "A new family of allomorphic jellyfish, Drymonematidae (Scyphozoa, Discomedusae), emphasizes evolution in the functional morphology and trophic ecology of gelatinous zooplankton." Biological Bulletin 219:249-267.
  8. Bayha, K.M., Dawson, M.N., Collins, A.G., Barbeitos, M.S., and Haddock, S.H.D. (2010) "Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA." Integrative & Comparative Biology doi: 10.1093/icb/icq074.
  9. Dawson, M.N, Grosberg, R.K., Sanford, E., and Stuart, Y.E. (2010) "Population genetic analysis of a recent range expansion: mechanisms regulating the poleward range limit in the volcano barnacle Tetraclita rubescens." Molecular Ecology 19:1585-1605.
  10. Herrera S., Baco, A., and Sánchez, J.A. (2010) "Molecular systematics of the bubblegum coral genera (Paragorgiidae, Octocorallia) and description of a new deep-sea species." Molecular Phylogenetics and Evolution, 55: 123–135.
  11. Buerki, S., Phillipson, P.B., Lowry II, P.P., and Callmander, M.W. (2010) "Molecular phylogenetics and morphological evidence support recognition of Gereaua, a new endemic genus of Sapindaceae from Madagascar." Systematic Botany 35: 172-180.
  12. Buerki, S., Lowry II, P.P., Alvarez, N., Razafimandimbison, S.G., Küpfer, P., and Callmander, M.W. (2010) "Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae." Plant Ecology and Evolution, 143: 148-161.
  13. Tedersoo, L., Nilsson, R.H., Abarenkov, K., Jairus, T., Sadam, A., Saar, I., Bahram, M., Bechem, E., Chuyong, G., and Kõljalg, U. (2010) "454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases." New Phytol. 188: 291-301.
  14. Qiu, Y.-L., Li, L., Wang, B., Xue, J.-Y., Hendry, T. A., Li, R.-Q., Brown, J.W., Liu, Y., Hudson, G.T., and Chen, Z. (2010) "Angiosperm phylogeny inferred from sequences of four mitochondrial genes." Journal of Systematics and Evolution 48: 391-425.
  15. Wang, B., Yeun, L.H., Xue, J.-Y., Liu, Y., Ané, J.M., and Qiu, Y.-L.(2010) "Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants." New Phytologist 186: 514-525.
  16. Crews, S.C. and Gillespie, R.G. (2010) "Molecular systematics of Selenops spiders (Araneae: Selenopidae) from North and Central America: implications for Caribbean biogeography." Biological Journal of the Linnean Society 101: 288-322.
  17. Spagna, J.C., Crews, S.C., and Gillespie, R.G. (2010) "Patterns of habitat affinity and Austral/Holarctic parallelism in dictynoid spiders (Araneae: Entelegynae)." Invertebrate Systematics 24: 238-257.
  18. Crisp, M. D., Isagi, Y. Kato, Y., Cook, L.G., and Bowman, D.M.S. (2010) "Livistona palms in Australia: ancient relics or opportunistic immigrants?" Molecular Phylogenetics and Evolution 54:512-523.
  19. Claramunt, S. (2010) "Discovering exceptional diversifications at continental scales: the case of the endemic families of Neotropical suboscine passerines." Evolution 64(7):2004–2019.
  20. Claramunt, S., Derryberry, E.P., Chesser, R.T., Aleixo, A., and Brumfield, R.T. (2010) "Polyphyly of Campylorhamphus, and description of a new genus for C. pucherani (Dendrocolaptinae)." Auk 127(2):430-439.
  21. Derryberry, E. P., Claramunt, S., O'Quin, K.E., Aleixo, A., Chesser, R.T., Remsen Jr., J.V., and Brumfield, R.T. (2010) "Pseudasthenes, a new genus of ovenbird (Aves: Passeriformes: Furnariidae)." Zootaxa 2416:61-68.
  22. Derryberry, E. P., Claramunt, S., Chesser, R.T., Aleixo, A., Cracraft, J., Moyle, R.G., and Brumfield, R.T. (2010) "Certhiasomus, a new genus of woodcreeper (Aves: Passeriformes: Dendrocolaptidae)." Zootaxa 2416:44-50.
  23. Hulcr, J., and Cognato, A. (2010) "Repeated evolution of theft in fungus farming ambrosia beetles." Evolution 64 (11): 3205–3212.
  24. Espíndola, A., Buerki, S., Bedalov, M., Kupfer, P., Alvarez, N. (2010) "New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history." Botanical Journal of the Linnean Society 163, 14-32.
  25. Schreiber, L. (2010). "Assessing the genetic potential of uncultivated sulfate reducing bacteria." PhD thesis. University of Bremen, Germany. URN: urn:nbn:de:gbv:46-diss000120197
  26. Smith, S., Belov, K. and Hughes, J (2010) "MHC screening for marsupial conservation: extremely low levels of class II diversity indicate population vulnerability for an endangered Australian marsupial." Conservation Genetics. 11 (1): 269-278.
  27. Smith, S., Turbill, C. and Suchentrunk, F (2010) "Introducing mother’s curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares." Molecular Ecology. 19 (1): 36-43.
  28. Chaves, J.C., Cuervo, A.M., Miller, M.J., and Cadena, C.D. (2010) "Revising species limits in a group of Myrmeciza antbirds reveals a cryptic species within M. laemosticta (Thamnophilidae)." The Condor 112: 718-730
  29. Elias, M (2010) "Patterns and processes in the evolution of the eukaryotic endomembrane system." Molecular Membrane Biology 27:469-489.
  30. Eliáš, M., Němcová, Y., Škaloud, P., Neustupa, J., Kaufnerová, V., and Šejnohová, L. (2010) "Hylodesmus singaporensis gen. et sp. nov., a new autosporine subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore." International Journal of Systematic and Evolutionary Microbiology 60:1224-1235.
  31. Rai, H.S. and Graham, S.W. (2010) "Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes)." American Journal of Botany. 97(9): 1-13.
  32. Wiens, J.J., Kuczynski, C.A., Townsend, T.M., Reeder, T.W., Mulcahy, D.G., and Sites, J.W., Jr., (2010) "Combining phylogenomics and fossils in higher-level squamate phylogeny: Molecular data change the placement of fossil taxa." Systematic Biology 59, 674-688.
  33. Ye, W., and Zhu, R-L. (2010) Leucolejeunea, a new synonym of Cheilolejeunea (Lejeuneaceae), with special reference to new combinations and nomenclature. Journal of Bryology 32 (4): 279-282.
  34. He, M., Feng, J., and Zhao, E. (2010) The complete mitochondrial genome of the Sichuan hot spring keel-back (Thermophis zhaoermii; Serpentes: Colubridae) and a mitogenomic phylogeny of the snakes. Mitochondrial DNA, 21: 8-18.
  35. Bartlett, M.E., and Specht, C.D. (2010) "Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales." New Phytologist 187:521-541.
  36. Bart, H.L. Jr., Reneau, P.C., Doosey, M.H., and Bell, C.D. (2010) "Evolutionary divergence of duplicate copies of the growth hormone gene in suckers (Actinopterygii: Catostomidae)." International Journal of Molecular Sciences 11, 1090-1102.
  37. Doosey, M.H., Bart, H.L. Jr., Saitoh, K., and Miya, M. (2010) "Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences." Molecular Phylogenetics and Evolution 54, 1028-1034.
  38. Liu, N., Sliwinski M.K., Correa, R. and Baum, D. A (2010) "Possible contributions of TERMINAL FLOWER 1 to the evolution of rosette flowering in Leavenworthia (Brassicaceae)." New Phytologist (published online: 3 NOV 2010 | DOI: 10.1111/j.1469-8137.2010.03511.x).
  39. Koopman, M. and Baum, D.A. (2010) "Isolating nuclear genes and identifying lineages without monophyly: An example of closely related species from Southern Madagascar." International Journal of Plant Sciences. 171: 761-771.
  40. Sharanowski, B.J., Robbertse, B., Walker, J., Voss, S.R., Yoder, S.R., Spatafora, J., and Sharkey, M.J. (2010) "Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta)." Molecular Phylogenetics and Evolution 57: 101-112.
  41. Gardner, J.L., Trueman, J.W.H., Ebert, D., Joseph, L., and Magrath, R.D. (2010) "Phylogeny and evolution of the Meliphagoidea, the largest radiation of Australasian songbirds." Molecular Phylogenetics and Evolution 55:1087-1102.
  42. Gusmão, L.C. and Daly, M. (2010) "Evolution of sea anemones (Cnidaria: Actiniaria: Hormathiidae) symbiotic with hermit crabs." Mol. Phylo. Evol. 56:868-877.
  43. Rosell, J.A., Olson, M.E., Weeks, A., De-Nova, A., Medina-Lemos,R., Pérez-Camacho,J., Feria, T.P., Gómez-Bermejo,R., Montero, J.C., Eguiarte, L. (2010) "Diversification in species complexes: tests of species origin and delimitation in the Bursera simaruba clade of tropical trees (Burseraceae)." Molecular Phylogenetics and Evol. 57(2):798-811. Epub 2010 Aug 17.
  44. Unmack, P.J. and Dowling, T.E. (2010) "Biogeography of the genus Craterocephalus (Teleostei: Atherinidae) in Australia." Molecular Phylogenetics and Evolution. 55:968-984. [abstract].
  45. Foltz, D. W. and Mah, C. L. (2010) "Difference in larval type explains patterns of nonsynonymous substitutions in two ancient paralogs of the histone H3 gene in sea stars." Evolution & Development 12:222–230. [abstract]
  46. Alexander, P.J., Windham, M.D., Al-Shehbaz, I. A. and Bailey C.D. (2010) Molecular phylogenetics and taxonomy of the genus Thysanocarpus (Brassicaceae). Systematic Botany 35(3):559-577. [abstract].
  47. Promputtha, I. and Miller, A.N. (2010) "Three new species of Acanthostigma (Tubeufiaceae, Pleosporales) from the Great Smoky Mountains National Park." Mycologia 102(3):574-587. [abstract].
  48. Hirayama, K., Tanaka, K., Raja, H.A. Miller, A.N. and Shearer, C.A. (2010) "A molecular phylogenetic assessment of Massarina ingoldiana sensu lato." Mycologia 102(3):729-746. [abstract]
  49. Raja, H.A., Ferrer, A., Shearer, C.A., and Miller, A.N. (2010) Freshwater Ascomycetes: Wicklowia aquatica, a new genus and species in the Pleosporales from Florida and Costa Rica. Mycoscience: 51:208–214. [abstract]
  50. Edgcomb, V., Beaudoin, D., Gast, R., Biddle, J.F. and Teske, A. (2010) "Marine subsurface eukaryotes: the fungal majority." Environ. Microbiol. Epub. [abstract]
  51. Schreeg L.A., D.L. Erickson, W.J. Kress and Swenson, N.G. (2010) "Phylogenetic analysis of local-scale tree soil associations in a lowland moist tropical forest" PLoS ONE 5(10): e13685. doi:10.1371/journal.pone.0013685.
  52. Tanga, K. L., Agnewa, M.K., Hirt, M.V., Sado, T., Schneider, L.M., Freyhofd, J., Sulaiman, Z., Swartz, E., Vidthayanon, C., Miya, M., Saitoh, K., Simons, A.M., Wood, R.M., and Richard L. Mayden (2010) "Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae)" Molecular Phylogenetics and Evolution 57(1):189-214. [abstract]
  53. Miller, T.L., Adlard, R.D., Bray, R.A., Justine, J-L. and Cribb, T.H. (2010). "Cryptic species of Euryakaina n. g. (Digenea: Cryptogonimidae) from sympatric lutjanids in the Indo-West Pacific." Systematic Parasitology 77(3) 185-204, DOI: 10.1007/s11230-010-9266-7.
  54. Miller, T.L., Bray, R.A., Justine, J-L. and Cribb, T.H. (2010) "Varialvus gen. nov. (Digenea, Cryptogonimidae), from species of Lutjanidae (Perciformes) off the Great Barrier Reef, New Caledonia and the Maldives." Acta Parasitologica. 55(4) 327-339.
  55. Draisma, S.G.A., Prud’homme van Reine, W.F. and Kawai, H. (2010) "A revised classification of the Sphacelariales (Phaeophyceae) inferred from a psbC and rbcL based phylogeny." European Journal of Phycology 45(3):308-326. [abstract]
  56. Unterseher, M. and Schnittler, M. (2010) "Species richness analysis and ITS rDNA phylogeny revealed the majority of cultivable foliar endophytes from beech (Fagus sylvatica L.)." Fungal Ecology 3(4) 366-378 [abstract].
  57. Lara, E., Mitchell, E.A.D., Moreira, D., and López García, P. (2010) "Highly diverse and seasonally dynamic protist community in a pristine peat bog." Protist Aug 6. [Epub ahead of print] [abstract]
  58. Heger, T.J., Pawlowski, J., Lara, E., Leander, B.S., Todorov, M., Golemansky, V., and Mitchell, E.A.D. (2010) "Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)" Protist 2010 Aug 9. [Epub ahead of print] [abstract]
  59. Heger, T.J., Mitchell, E.A.D, Todorov, M., Golemansky, V., Lara, E., Leander, B.S., and Pawlowski, J. (2010) "Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent." Mol Phyl Evol 55: 113–122. [abstract]
  60. Dunthorn, M., Foissner, W., and Katz, L.A. (2010). "Expanding character sampling in ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker." Protist Aug 12. [Epub ahead of print] [abstract]
  61. Yi, Z., M. Dunthorn, W. Song, and Stoeck, T. (2010) "Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea)." Mol Phylogenet Evol. Aug 10. [Epub ahead of print] [abstract]
  62. Schulte II, J. A., and Moreno-Roark, F. (2010) "Live birth among iguanian lizards predates Pliocene-Pleistocene glaciations." Proceedings of the Royal Society of London, Biological Sciences, Biology Letters 6:216-218. [abstract]
  63. Taylor D. J., Leach, R. W., and Bruenn, J. (2010) "Filoviruses are ancient and integrated into mammalian genomes." BMC Evolutionary Biology 10:193.[pdf]
  64. Kotov, A. A. and Taylor, D. J. (2010) "A new African lineage of the Daphnia obtusa group (Cladocera: Daphniidae) disrupts continental vicariance patterns." J. Plankton Res. 32:937-949. [abstract]
  65. Sangster, G., Alstrom, P., Forsmark, E. & Olsson, U. (2010) "Multi-locus phylogenetic analysis of Old World chats and flycatchers reveals extensive paraphyly at family, subfamily and genus level (Aves: Muscicapidae)." Molecular Phylogenetics and Evolution 57(1):380-92. [abstract]
  66. Naumann, M., Schüßler, A., Bonfante, P. (2010) "The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes." The ISME Journal 4:862-871. [abstract]
  67. Olsen, K.M., Gross, B.L., Reagon, M, Hsu, S.C., Caicedo, A.L., and Jia, Y. (2010) "Seeing red: the origin of grain pigmentation in US weedy rice." Molecular Ecology 19(16):3380-3393. [abstract]
  68. Barley AJ, Spinks PQ, Thomson RC, Shaffer HB. (2010) "Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life." Mol Phylogenet Evol. 55(3):1189-94. [abstract]
  69. Toon, A., Pérez-Losada, M., Schweitzer, C. E., Feldmann, R. M., Carlson, M. and Crandall, K. A. (2010) Gondwanan radiation of the southern hemisphere crayfish (Decapoda: Parastacidae): Evidence from fossils and molecules. Journal of Biogeography, Epub, Aug 3, 2010. [abstract]
  70. Toon, A., Hughes, J. M. and Joseph, L. (2010) Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Molecular Ecology, 19: 2980-2994. [abstract]
  71. Parfrey, L.W., Grant, J., Tekle, Y.I., Lasek-Nesselquist, E., Morrison, H.G., Sogin, M.L., Patterson, D.J., Katz, L.A (2010) "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life." Systematic Biology. Epub July 23, 2010. [abstract]
  72. San Mauro, D., and Agorreta, A. (2010) "Molecular systematics: A synthesis of the common methods and the state of knowledge." Cell Mol Biol Lett.15(2):311-41. Epub 2010 Mar 5. [abstract]
  73. Regier, J.C., Shultz, J.W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J. W., and Cunningham, C. W. (2010) "Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences." Nature 463, 1079-1083.
  74. Meyer, A., and Lieb, B. (2010) "Respiratory proteins in Sipunculus nudus - Implications for phylogeny and evolution of the hemerythrin family." Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 155, 171-177. [abstract]
  75. Fritz-Laylin, L.K., Prochnik, S.E., Ginger, M.L., Dacks, J.B., Carpenter, M.L., Field, M.C., Kuo, A., Paredez, A., Chapman, J., Pham, J., Shu, S., Neupane, R., Cipriano, M., Mancuso, J., Tu,H., Salamov, A., Lindquist, E., Shapiro, H., Lucas, S., Grigoriev, I.V., Cande, W.Z., Fulton, C., Rokhsar, D.S., and Dawson, S.C. (2010) "The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility" Cell, 140(5):631-642.
  76. Penna, A., Fraga, S, Batocchi, C., Casabianca, S., Giacobbe, M.G., Riobò, P. and Vernesi, C. (2010) "A phylogeographic study of the toxic benthic dinoflagellate genus Ostreopsis Schmidt." Journal of Biogeography Volume 37(5): 830–841.
  77. Jabaily, R.S. and Sytsma, K.J. (2010) "Phylogenetics of Puya (Bromeliaceae): Placement, major lineages and evolution of Chilean species." Am. J. Botany 97: 337-356.

2009 (58 articles)

  1. Xu, S., L. Chen, K. Zhou, G. Yang. (2009) "Sequence polymorphism and evolution of three cetacean MHC genes." Journal of Molecular Evolution 69: 260-275.
  2. Xiong Y., M. C. Brandley, S. Xu, K. Zhou, and G. Yang. (2009) "Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales." BMC Evolutionary Biology, 9: 20.
  3. Fuselier, L., Davison, P.G., Clements, M., Shaw, B., Devos, N., Heinrichs, J., Hentschel, J., Sabovljevic, M., Szövényi, P., Schuette, S., Hofbaurer, W., and Shaw., A. J. (2009) "Phylogeographic analyses reveal distinct lineages of Metzgeria furcata (L.) Dumort. and M. conjugata Lindb. (Metzgeriaceae) in Europe and North America." Biological Journal of the Linnean Society 98:745-756.
  4. Buerki, S., Forest, F., Acevedo-Rodríguez, P., Callmander, M.W., Nylander, J.A.A., Harrington, M., Sanmartín, I., Küpfer, P., Alvarez, N. (2009) "Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae)." Molecular Phylogenetics and Evolution 51: 238-258.
  5. Chesser, R. T., Claramunt, S., Derryberry, E.P. and Brumfield, R.T. (2009) "Geocerthia, a new genus of terrestrial ovenbird (Aves: Passeriformes: Furnariidae)." Zootaxa 2213: 64–68.
  6. Eliáš, M., and Neustupa, J. (2009) "Pseudomarvania gen. nov. (Chlorophyta, Trebouxiophyceae), a new genus for the “budding” subaerial green algae Marvania aerophytica Neustupa & Šejnohová and Stichococcus ampulliformis Handa." Fottea 9:169-177.
  7. Ali, F. and Meier, R. (2009) "Primate home range and GRIN2A, a receptor gene involved in neuronal plasticity: implications for the evolution of spatial memory." Genes, Brain and Behavior, 8: 435-441.
  8. Pie, M.R., Baggio, R.A., Boeger, W.A., Patella, L. A., Ostrensky, A., Vitule, J. R. S., and Abilhoa, V. (2009) "Molecular data reveal a diverse species complex in the upper Iguaçu River." Journal of Fish Biology 75:2357-2362.
  9. Townsend, T.M., Vieites, D.R., Glaw, F., Vences, M. (2009) "Testing species-level diversification hypotheses in Madagascar: The case of microendemic Brookesia leaf chameleons." Systematic Biology 58, 641-656.
  10. Zhang, Y., Schoch, C.L., Fournier, J., Crous, P.W., de Gruyter, J., Woudenberg, J.H., Hirayama, K., Tanaka, K., Pointing, S.B., Spatafora, J.W. and Hyde, K.D. (2009) "Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation." Stud Mycol. 64: 85-102S5.
  11. Hea, M., Fengb, J-C., Liuc, S.-Y., Guod, P., Zhao, E-M. (2009) "The phylogenetic position of Thermophis (Serpentes: Colubridae), an endemic snake from the Qinghai-Xizang Plateau." China.Journal of Natural History 43: 479-488.
  12. Hayes, K.A., Cowie, R.H., and Thiengo, S.C. (2009) "A global phylogeny of apple snails: Gondwanan origin, generic relationships and the influence of outgroup choice (Caenogastropoda: Ampullariidae)." Biological Journal of the Linnean Society 98:61-76.
  13. Hayes, K.A. (2009) "Evolution, molecular systematics and invasion biology of Ampullariidae." Ph.d. Dissertation. University of Hawaii, Department of Zoology. Honolulu, HI.
  14. Crews, S.C., Puente-Rolon, A.R., Rutstein, E., Gillespie, R.G. (2009) "A comparison of populations of island and adjacent mainland species of Caribbean Selenops (Araneae: Selenopidae) spiders." Molecular Phylogenetics and Evolution 54: 970-983.
  15. Rosauer, D., Laffan, S.W., Crisp, M.D., Donnellan, S.C., and Cook, L.G. (2009) "Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history." Molecular Ecology 18:4061-4072.
  16. Kuzmina, M., Johnson, K., Barron, H., and Hebert, P. (2009) "A DNA Barcode Reference Library for the Vascular Plants of Churchill, Manitoba." Oral presentation at CBA ABC meeting in Ottawa.
  17. Bracken, H.D., Toon, A., Felder, D., Martin, J., Finley, M., Rasmussen, J., Palero, F., and Crandall, K.A. (2009) "The Decapod Tree of Life: Compiling the data and moving toward a consensus of decapod evolution." Arthropod Phylogenetics and Systematics 67 (1) 99-116.
  18. Bracken, H.D., De Grave, S., and Felder, D.L. (2009) "Phylogeny of the infraorder Caridea based on mitochondrial and nuclear genes (Crustacea: Decapoda)." In: J. MARTIN, K.A. CRANDALL, D.L. FELDER (eds.). Decapod Crustacean Phylogenetics (Crustacean Issues), Taylor and Francis/CRC Press, Bocan Raton. Pp. 281-305.
  19. Wong, M.K.S., and Takei, Y. (2009) "Cyclostome and chondrichthyan adrenomedullins reveal ancestral features of the adrenomedullin family." Comp Biochem Physiol B 154:317-325.
  20. Foltz, D. W. and Mah, C. L. (2009) "Recent relaxation of purifying selection on the tandem-repetitive early-stage histone H3 gene in brooding sea stars" Marine Genomics 2:113-118. [abstract]
  21. Schoch, C. L., Crous, P.W., Groenewald, J.Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., de Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, S., Hosoya, T., Hyde, K.D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Lücking, R., Lumbsch, H.T., Lutzoni, F., Marvanová, L., McVay, A.H., Mbatchou, J.S., Miller, A.N. , Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C A., Li, Y.M.,. Phillips, A.J.L, Phongpaichit, S., Pointing, S.B., Pujade-Renaud, V., Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y., Spatafora, J.W. (2009) "A class-wide phylogenetic assessment of Dothideomycetes." Studies in Mycology 64:1–15. [abstract]
  22. Shearer, C.A., Raja, H.A., Miller, A.N., Nelson, P., Tanaka, K. Hirayama, K., Marvanová, L., Hyde, K. D. and Zhang Y. (2009) "The molecular phylogeny of freshwater Dothideomycetes". Studies in Mycology: 64:145–153. [abstract]
  23. Boehm, E.W.A., Mugambi, G.K., Miller, A.N. Huhndorf, S.M., Marincowitz, S., Spatafora, J.W., and Schoch, C.L. (2009) "A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species." Studies in Mycology 64:49–83. [pdf]
  24. Kress W.J., D.L. Erickson, N. A. Swensen, F.A. Jones, O. Sanjur, and E. Bermingham. (2009) "Plant DNA Barcodes and a Community Phylogeny of a Tropical Forest Dynamics Plot in Panama." Proceedings of the National Academy of Sciences, 106: 18621-18626. {article]
  25. Taylor, D. J. and Bruenn, J. (2009) "The evolution of novel fungal genes from non-retroviral RNA viruses." BMC Biology 7:88 [pdf]
  26. Stockinger H, Walker C, Schüßler A (2009) "Glomus intraradices DAOM197198', a model fungus in arbuscular mycorrhiza research, is not Glomus intraradices."
    New Phytologist 183:1176-1187. [pdf]
  27. Parks, M., Cronn, R., and Liston, A. (2009) "Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes." BMC Biology 7:84 [pdf]
  28. Ruibal, C., Gueidan, C., Selbmann, L., Gorbushina, A.A., Crous, P.W., Groenewald, J.Z., Muggia, L., Grube, M., Isola, D., Schoch, C.L., Staley, J.T., Lutzoni, F., De Hoog, G.S. (2009) Phylogeny of rock-inhabiting fungi related to Dothideomycetes. Studies in Mycology 64:123-133. [pdf]
  29. Pang, P.S., Planet, P.J., and Glenn, J.S. (2009) "The Evolution of the Major Hepatitis C Genotypes Correlates with Clinical Response to Interferon Therapy" PLoS ONE 4(8): e6579. [citation] [pdf]
  30. McKenna, D.D., Sequeira, A.S., Marvaldi, A.E., and Farrell, B.D. (2009). "Temporal lags and overlap in the diversification of weevils and flowering plants." PNAS. 106(17):7083-7088. [citation] [abstract]
  31. Van der Merwe, M.M., Kinnear, M.W., Barrett, L.G., Dodds, P.N., Ericson, L., Thrall, P.H., and Burdon, J.J., "Positive selection in AvrP4 avirulence gene homologues across the genus Melampsora" Proc. R. Soc. B 276:2913-2922. [citation] [abstract]
  32. Zimkus, B.M. (2009) "Patterns of speciation and diversity among African frogs (genus Phrynobatrachus)." Ph.D. dissertation, Harvard University.
  33. Toon, A., Finley, M., Staples, J., and Crandall, K.A. (2009) "Decapod phylogenetics and molecular evolution" in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton. pp.15-30.
  34. Felder DL, Robles R. (2009) "Molecular Phylogeny of Callianassidae." in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton. pp. 327-342.
  35. Robles R, Tudge CC, Dworschak PC, Poore GCB, Felder DL. "Molecular phylogeny of the Thalassinidea based on nuclear and mitochondrial genes." in Decapod Crustacean Phylogenetics (Crustacean Issues) (J. Martin, D. L. Felder, and K. A. Crandall, eds.). CRC Press, Bocan Raton. pp. 309-326.
  36. Dolapsakis, N. and Economou-Amilli, A. (2009) "A new marine species of Amphidinium (Dinophyceae) from Thermaikos Gulf, Greece." Acta Protozoologica 48(2):91-190. [abstract]
  37. Klassen, J.L. (2009) "Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis." PhD thesis, University of Alberta, Edmonton, Canada.
  38. Klassen, J.L. (2009) "Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis." J. Bacteriol. 191: 7500-7508 . [citation] [abstract]
  39. Spinks, P.Q. and Shaffer, H.B. (2009). "Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization." Syst. Biol. 58(1):1–20. [citation] [abstract]
  40. Spinks, P.Q., Thomson, R.C., Lovely, G.A. and Shaffer, H.B. (2009) "Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles." BMC Evolutionary Biology 9:56. doi:10.1186/1471-2148-9-56. [citation] [abstract] [pdf]
  41. Hibbett, D.S. and Matheny, P.B. (2009) "The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses." BMC Biology 7:13 doi:10.1186/1741-7007-7-13. [citation] [abstract] [pdf]
  42. Elias M. and Archibald J. M. (2009) "The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus." Gene 442(1-2):63-72. Epub 2009 Apr 22. doi:10.1016/j.gene.2009.04.011 [abstract] [publication]
  43. Gile, G.H., Novis, P.M., Cragg D.S., Zuccarello G.C., Keeling P.J. (2009) "The distribution of EF-1alpha, EFL, and a non-canonical genetic code in the Ulvophyceae: Discrete genetic characters support a consistent phylogenetic framework." J. Eukaryot. Microbiol. 56(4):367-372. [citation] [abstract]
  44. Weirauch, C. and Munro, J. (2009) "Molecular phylogeny of the assassin bugs (Hemiptera: Reduviidae), based on mitochondrial and nuclear ribosomal genes." Molecular Phylogenetics & Evolution 53:287-299. doi:10.1016/j.ympev.2009.05.039 [abstract]
  45. Wilson, N. G., Rouse, G. W., and Giribet, G. (2009) "Assessing the molluscan hypothesis Serialia (Monoplacophora + Polyplacophora) using novel molecular data." Mol Phylogenet Evol. Jul 30. [Epub ahead of print]. doi:10.1016/j.ympev.2009.07.028 [abstract]
  46. Segade, F. (2009) "Functional evolution of the microfibril-associated glycoproteins." Gene 439:43–54. [abstract]
  47. Welsh, A.K., Dawson, J.O., Gottfried, G.J., and Hahn, D. "Diversity of Frankia in root nodules of geographically isolated Arizona alder in central Arizona (USA)." Appl. Env. Microbiol.. 75(21): 6913-6918. [citation] [abstract]
  48. Mirza, B.S., Welsh, A.K., and Hahn, D. (2009) "Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant." FEMS Microbiology Ecology 70:132-141 Epub 2009 Jul 21. [citation] [abstract]
  49. Welsh, A.K, B.S. Mirza, J.P. Rieder, M.W. Paschke, D. Hahn. (2009) "Diversity of frankiae in nodules of Morella pensylvanica grown in soils from five continents." Systematic and Applied Microbiology 32: 201-210. doi:10.1016/j.syapm.2009.01.002  [abstract]
  50. Mirza, B.S., A.K. Welsh, G. Rasul, J.P. Rieder, M.W. Paschke, D. Hahn. (2009) "Variation in Frankia populations of the Elaeagnus host infection group in nodules of six host plant species after inoculation with soil." Microbial Ecology 58:384-393. doi:10.1007/s00248-009-9513-0 [abstract]
  51. Li, J-t., Che, J., Murphy, R.W., Zhao, H., Zhao, E.-m., Rao, D.-q., and Zhang, Y.-p. (2009) "New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction." Molecular Phylogenetics and Evolution 53:509–522. doi:10.1016/j.ympev.2009.06.023 [abstract]
  52. Murienne, J., Karaman, I., and Giribet, G. (2009) "Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula." J. Biogeography Published online, Oct 14, 2009 [citation] [abstract]
  53. Schulte II, J.A., and Cartwright, E.M. (2009) Phylogenetic relationships among iguanian lizards using alternative partitioning methods and TSHZ1: A new phylogenetic marker for reptiles. Molecular Phylogenetics and Evolution 50:391-396. doi:10.1016/j.ympev.2008.10.018 [abstract]
  54. Armbruster, W.S., Leed,J., and Baldwind, B.G. (2009) "Macroevolutionary patterns of defense and pollination in Dalechampia vines: Adaptation, exaptation, and evolutionary novelty" Proc. Natl. Acad. Sci USA. Oct 19 e-pub ahead of publication. [abstract]
  55. Zimkus, B.M., Rödel, M.-C., and Hillers, A. (2009) Complex patterns of continental speciation: molecular phylogenetics and biogeography of sub-Saharan puddle frogs (Phrynobatrachus) manuscript submitted.
  56. Chen, W.-J., Lheknim, V. and Mayden, R. L. (2009). "Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma Vaillant resolved with six nuclear genes." Journal of Fish Biology 75(9):2197-208.
  57. Chen, W.-J. and Mayden, R. L. (2009). Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes. Molecular Phylogenetics and Evolution 52, 544-549. doi:10.1016/j.ympev.2009.01.006   
  58. Mayden, R. L., Chen, W.-J., Bart, H. L., Doosey, M. H., Simons, A. M., Tang, K. L., Wood, R. M., Agnew, M. K., Yang, L., Hirt, M. V., Clements, M. D., Saitoh, K., Sado, T., Miya, M. and Nishida, M. (2009). "Reconstructing the phylogenetic relationships of the Earth’s most diverse clade of freshwater fishes — Order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome." Molecular Phylogenetics and Evolution 51, 500-514. doi:10.1016/j.ympev.2008.12.015    

2008 (4 articles)

  1. Granados, C., Camargo, C., Zea, S., and Sanchez, J.A. (2008) "Phylogenetic relationships among zooxanthellae (Symbiodinium) associated to excavating sponges (Cliona spp.) reveal an unexpected lineage in the Caribbean." Molecular Phylogenetics and Evolution. 49: 554-560.
  2. Ali, F. and Meier, R. (2008) "Positive selection in ASPM is correlated with cerebral cortex evolution across primates but not with whole brain size." Molecular Biology & Evolution, 25(11): 2247-2250.
  3. Townsend, T.M., Alegre, R.E., Kelley, S.T., Wiens, J.J., and Reeder, T.W. (2008) "Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles." Molecular Phylogenetics and Evolution 47, 129-142.
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