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Commentary Sleeping to fuel the immune system: mammalian sleep and resistance to parasites Mark R Opp PMCID: PMC2633283 Correspondence Sexual selection does not influence minisatellite mutation rate William Amos PMCID: PMC2636768 Evolution of C2H2-zinc finger genes revisited James H Thomas and Ryan O Emerson PMCID: PMC2667407 Minisatellite mutation rates increase with extra-pair paternity among birds Anders P Møller and José J Cuervo PMCID: PMC2693433 Database Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment Nadia Anwar and Ela Hunt PMCID: PMC2685121 SNP@Evolution: a hierarchical database of positive selection on the human genome Feng Cheng, Wei Chen, Elliott Richards, Libin Deng, and Changqing Zeng PMCID: PMC2755008 Editorial Evolving e-taxonomy Hans Zauner PMCID: PMC2714837 Research article An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals Tokiharu Takahashi, Carmel McDougall, Jolyon Troscianko, Wei-Chung Chen, Ahamarshan Jayaraman-Nagarajan, Sebastian M Shimeld, and David EK Ferrier PMCID: PMC2762978 Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes? Michael E Alfaro, Chad D Brock, Barbara L Banbury, and Peter C Wainwright PMCID: PMC2779191 Asymmetric introgression between sympatric molestus and pipiens forms of Culex pipiens (Diptera: Culicidae) in the Comporta region, Portugal Bruno Gomes, Carla A Sousa, Maria T Novo, Ferdinando B Freitas, Ricardo Alves, Ana R Côrte-Real, Patrícia Salgueiro, Martin J Donnelly, António PG Almeida, and João Pinto PMCID: PMC2778655 Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae Jeffrey P Mower and Linda Bonen PMCID: PMC2780418 Software PhyloExplorer: a web server to validate, explore and query phylogenetic trees Vincent Ranwez, Nicolas Clairon, Frédéric Delsuc, Saeed Pourali, Nicolas Auberval, Sorel Diser, and Vincent Berry PMCID: PMC2695458 PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis Huai-Chun Wang, Edward Susko, and Andrew J Roger PMCID: PMC2758850 Research Articles Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences Sigisfredo Garnica, Michael Weiß, Bernhard Oertel, Joseph Ammirati, and Franz Oberwinkler PMCID: PMC2653478 Evolution and differential expression of a vertebrate vitellogenin gene cluster Roderick Nigel Finn, Jelena Kolarevic, Heidi Kongshaug, and Frank Nilsen PMCID: PMC2632621 Parallel shifts in ecology and natural selection in an island lizard Ryan Calsbeek, Wolfgang Buermann, and Thomas B Smith PMCID: PMC2630972 Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis David A Hughes, Martin Jastroch, Mark Stoneking, and Martin Klingenspor PMCID: PMC2627829 Multiple mating and a low incidence of cuckoldry for nest-holding males in the two-spotted goby, Gobiusculus flavescens Kenyon B Mobley, Trond Amundsen, Elisabet Forsgren, Per A Svensson, and Adam G Jones PMCID: PMC2631507 Parasite resistance and the adaptive significance of sleep Brian T Preston, Isabella Capellini, Patrick McNamara, Robert A Barton, and Charles L Nunn PMCID: PMC2631508 Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes Aditi Kanhere and Martin Vingron PMCID: PMC2651853 Evolution of prokaryotic SPFH proteins Markus Hinderhofer, Christina A Walker, Anke Friemel, Claudia AO Stuermer, Heiko M Möller, and Alexander Reuter PMCID: PMC2636767 Comparative mitochondrial genomics within and among species of killifish Andrew Whitehead PMCID: PMC2631509 Dynamic evolution of bitter taste receptor genes in vertebrates Dong Dong, Gareth Jones, and Shuyi Zhang PMCID: PMC2646699 Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus Daniel Croll and Ian R Sanders PMCID: PMC2630297 Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi Samantha C Lewis, Leslie A Dyal, Caroline F Hilburn, Stephanie Weitz, Wei-Siang Liau, Craig W LaMunyon, and Dee R Denver PMCID: PMC2632994 Sex-specific dispersal and evolutionary rescue in metapopulations infected by male killing endosymbionts Dries Bonte, Thomas Hovestadt, and Hans-Joachim Poethke PMCID: PMC2633281 A P2X receptor from the tardigrade species Hypsibius dujardini with fast kinetics and sensitivity to zinc and copper Selvan Bavan, Volko A Straub, Mark L Blaxter, and Steven J Ennion PMCID: PMC2633282 Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers John R Finnerty, Maureen E Mazza, and Peter A Jezewski PMCID: PMC2655272 Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi Nickias Kienle, Tobias H Kloepper, and Dirk Fasshauer PMCID: PMC2639358 Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales Ye Xiong, Matthew C Brandley, Shixia Xu, Kaiya Zhou, and Guang Yang PMCID: PMC2656474 Eumalacostracan phylogeny and total evidence: limitations of the usual suspects Ronald A Jenner, Ciara Ní Dhubhghaill, Matteo P Ferla, and Matthew A Wills PMCID: PMC2640363 Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance Zhengyuan Wang, John Martin, Sahar Abubucker, Yong Yin, Robin B Gasser, and Makedonka Mitreva PMCID: PMC2644674 Form and function of damselfish skulls: rapid and repeated evolution into a limited number of trophic niches W James Cooper and Mark W Westneat PMCID: PMC2654721 Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: Evidence from population genetic, phylogeographic, and paleoclimatic data Matt J Walker, Amy K Stockman, Paul E Marek, and Jason E Bond PMCID: PMC2652443 Tracking costs of virulence in natural populations of the wheat pathogen, Puccinia striiformis f.sp.tritici Bochra Bahri, Oliver Kaltz, Marc Leconte, Claude de Vallavieille-Pope, and Jérôme Enjalbert PMCID: PMC2660305 Convergent and divergent patterns of morphological differentiation provide more evidence for reproductive character displacement in a wood cricket Gryllus fultoni (Orthoptera: Gryllidae) Yikweon Jang, Yong-Jin Won, and Jae Chun Choe PMCID: PMC2640364 Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom Lukasz Huminiecki, Leon Goldovsky, Shiri Freilich, Aristidis Moustakas, Christos Ouzounis, and Carl-Henrik Heldin PMCID: PMC2657120 The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data Roberto V Vilela, Taís Machado, Karen Ventura, Valéria Fagundes, Maria José de J Silva, and Yatiyo Yonenaga-Yassuda PMCID: PMC2646700 Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus Linn F Groeneveld, David W Weisrock, Rodin M Rasoloarison, Anne D Yoder, and Peter M Kappeler PMCID: PMC2652444 The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues José M Eirín-López, Rodrigo González-Romero, Deanna Dryhurst, Toyotaka Ishibashi, and Juan Ausió PMCID: PMC2644675 Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs Jennifer Pastorini, Alphonse Zaramody, Deborah J Curtis, Caroline M Nievergelt, and Nicholas I Mundy PMCID: PMC2657121 Sex differences in the genetic architecture of lifespan in a seed beetle: extreme inbreeding extends male lifespan Trine Bilde, Alexei A Maklakov, Katrine Meisner, Lucia la Guardia, and Urban Friberg PMCID: PMC2657122 Evolution of the multifaceted eukaryotic akirin gene family Daniel J Macqueen and Ian A Johnston PMCID: PMC2660306 Evolutionary morphology of the rattlesnake style Jesse M Meik and André Pires-daSilva PMCID: PMC2645363 Recurring cluster and operon assembly for Phenylacetate degradation genes Fergal J Martin and James O McInerney PMCID: PMC2653477 Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay Iñigo Martínez-Solano and Robin Lawson PMCID: PMC2656473 Gain and loss of elongation factor genes in green algae Ellen Cocquyt, Heroen Verbruggen, Frederik Leliaert, Frederick W Zechman, Koen Sabbe, and Olivier De Clerck PMCID: PMC2652445 The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago Jenny R Ovenden, Tom Kashiwagi, Damien Broderick, Jenny Giles, and John Salini PMCID: PMC2660307 Evolution of the sugar receptors in insects Lauren B Kent and Hugh M Robertson PMCID: PMC2667405 The effect of three environmental conditions on the fitness of cytochrome P450 monooxygenase-mediated permethrin resistance in Culex pipiens quinquefasciatus Melissa C Hardstone, Brian P Lazzaro, and Jeffrey G Scott PMCID: PMC2661048 Expression and evolutionary divergence of the non-conventional olfactory receptor in four species of fig wasp associated with one species of fig Bin Lu, Nina Wang, Jinhua Xiao, Yongyu Xu, Robert W Murphy, and Dawei Huang PMCID: PMC2661049 Phylogenetic diversity of stress signalling pathways in fungi Elissavet Nikolaou, Ino Agrafioti, Michael Stumpf, Janet Quinn, Ian Stansfield, and Alistair JP Brown PMCID: PMC2666651 Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites Zac H Forsman, Daniel J Barshis, Cynthia L Hunter, and Robert J Toonen PMCID: PMC2656472 Allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of Rhipicephalus (Boophilus) microplus Marcelo B Labruna, Victoria Naranjo, Atilio J Mangold, Carolina Thompson, Agustín Estrada-Peña, Alberto A Guglielmone, Frans Jongejan, and José de la Fuente PMCID: PMC2656471 Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes Pai-Chung Gwee, Boon-Hui Tay, Sydney Brenner, and Byrappa Venkatesh PMCID: PMC2656470 Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation Don Hayward, Paul D van Helden, and Ian JF Wiid PMCID: PMC2667176 Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest Ana M Delgado and James M Cook PMCID: PMC2671496 A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera) as a test case Steffen Roth, Bastian Fromm, Gerd Gäde, and Reinhard Predel PMCID: PMC2667406 Differential stepwise evolution of SARS coronavirus functional proteins in different host species Xianchun Tang, Gang Li, Nikos Vasilakis, Yuan Zhang, Zhengli Shi, Yang Zhong, Lin-Fa Wang, and Shuyi Zhang PMCID: PMC2676248 Assortative mating among Lake Malawi cichlid fish populations is not simply predictable from male nuptial colour Jonatan Blais, Martin Plenderleith, Ciro Rico, Martin I Taylor, Ole Seehausen, Cock van Oosterhout, and George F Turner PMCID: PMC2667177 The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals Benoit Nabholz, Sylvain Glémin, and Nicolas Galtier PMCID: PMC2660308 A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes Liang Yang and Jun Yu PMCID: PMC2670823 Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles Phillip Q Spinks, Robert C Thomson, Geoff A Lovely, and H Bradley Shaffer PMCID: PMC2660309 Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae Anne Roulin, Benoit Piegu, Philippe M Fortune, François Sabot, Angélique D'Hont, Domenica Manicacci, and Olivier Panaud PMCID: PMC2664808 Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation Arne W Nolte, Sébastien Renaut, and Louis Bernatchez PMCID: PMC2662803 Ancient diversification of eukaryotic MCM DNA replication proteins Yuan Liu, Thomas A Richards, and Stephen J Aves PMCID: PMC2667178 Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms J Gordon Burleigh, Khidir W Hilu, and Douglas E Soltis PMCID: PMC2674047 Evolution of MIR168 paralogs in Brassicaceae Silvia Gazzani, Mingai Li, Silvia Maistri, Eliana Scarponi, Michele Graziola, Enrico Barbaro, Jörg Wunder, Antonella Furini, Heinz Saedler, and Claudio Varotto PMCID: PMC2664809 Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup Viktor Černý, Verónica Fernandes, Marta D Costa, Martin Hájek, Connie J Mulligan, and Luísa Pereira PMCID: PMC2680838 The joint evolutionary histories of Wolbachia and mitochondria in Hypolimnas bolina Sylvain Charlat, Anne Duplouy, Emily A Hornett, Emily A Dyson, Neil Davies, George K Roderick, Nina Wedell, and Gregory DD Hurst PMCID: PMC2669805 Effects of shortened host life span on the evolution of parasite life history and virulence in a microbial host-parasite system Thibault Nidelet, Jacob C Koella, and Oliver Kaltz PMCID: PMC2666652 Evolution based on domain combinations: the case of glutaredoxins Rui Alves, Ester Vilaprinyo, Albert Sorribas, and Enrique Herrero PMCID: PMC2679010 Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence Jianhua Cao, Siluo Huang, Ji Qian, Jinlin Huang, Li Jin, Zhixi Su, Ji Yang, and Jianfeng Liu PMCID: PMC2670285 Influence of ancient glacial periods on the Andean fauna: the case of the pampas cat (Leopardus colocolo) Daniel Cossíos, Mauro Lucherini, Manuel Ruiz-García, and Bernard Angers PMCID: PMC2669060 Genetic clusters and sex-biased gene flow in a unicolonial Formica ant Barbara Holzer, Laurent Keller, and Michel Chapuisat PMCID: PMC2670286 Rapid speciation in a newly opened postglacial marine environment, the Baltic Sea Ricardo T Pereyra, Lena Bergström, Lena Kautsky, and Kerstin Johannesson PMCID: PMC2674422 Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades Shani Blanga-Kanfi, Hector Miranda, Osnat Penn, Tal Pupko, Ronald W DeBry, and Dorothée Huchon PMCID: PMC2674048 Modular evolution of glutathione peroxidase genes in association with different biochemical properties of their encoded proteins in invertebrate animals Young-An Bae, Guo-Bin Cai, Seon-Hee Kim, Young-Gun Zo, and Yoon Kong PMCID: PMC2679728 Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates László Z Garamszegi, Natasja G de Groot, and Ronald E Bontrop PMCID: PMC2674423 Evolutionary history of the iroquois/Irx genes in metazoans Pierre Kerner, Aissam Ikmi, Dario Coen, and Michel Vervoort PMCID: PMC2674049 Natural variation of outcrossing in the hermaphroditic nematode Pristionchus pacificus Arielle Click, Chandni H Savaliya, Simone Kienle, Matthias Herrmann, and Andre Pires-daSilva PMCID: PMC2676249 Rodent malaria-resistant strains of the mosquito, Anopheles gambiae, have slower population growth than -susceptible strains Maarten J Voordouw, Bradley R Anholt, Pam J Taylor, and Hilary Hurd PMCID: PMC2675531 Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes Erin K Bomati, Gerard Manning, and Dimitri D Deheyn PMCID: PMC2679011 Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution Andrew M Schurko, John M Logsdon, Jr, and Brian D Eads PMCID: PMC2680839 The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors D Carolina Peñalva-Arana, Michael Lynch, and Hugh M Robertson PMCID: PMC2680840 On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola Margarida Coelho, Fernando Sequeira, Donata Luiselli, Sandra Beleza, and Jorge Rocha PMCID: PMC2682489 Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses Mariana Mondragón-Palomino, Luisa Hiese, Andrea Härter, Marcus A Koch, and Günter Theißen PMCID: PMC2680841 Timing of organogenesis support basal position of turtles in the amniote tree of life Ingmar Werneburg and Marcelo R Sánchez-Villagra PMCID: PMC2679012 Mitochondrial phylogeography of baboons (Papio spp.) – Indication for introgressive hybridization? Dietmar Zinner, Linn F Groeneveld, Christina Keller, and Christian Roos PMCID: PMC2681462 Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution Claus Kemkemer, Matthias Kohn, David N Cooper, Lutz Froenicke, Josef Högel, Horst Hameister, and Hildegard Kehrer-Sawatzki PMCID: PMC2681463 Origin and evolution of the RIG-I like RNA helicase gene family Jun Zou, Mingxian Chang, Pin Nie, and Chris J Secombes PMCID: PMC2686710 DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms Mathieu Piednoël and Eric Bonnivard PMCID: PMC2685390 Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences Guy Baele, Yves Van de Peer, and Stijn Vansteelandt PMCID: PMC2695821 Geographic distribution of suitable hosts explains the evolution of specialized gentes in the European cuckoo Cuculus canorus Juan J Soler, Manuel Martín Vivaldi, and Anders Pape Møller PMCID: PMC2683792 Weak preservation of local neutral substitution rates across mammalian genomes Hideo Imamura, John E Karro, and Jeffrey H Chuang PMCID: PMC2689173 Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants Wenyan Li, Bing Liu, Lujun Yu, Dongru Feng, Hongbin Wang, and Jinfa Wang PMCID: PMC2688005 Common peptides shed light on evolution of Olfactory Receptors Assaf Gottlieb, Tsviya Olender, Doron Lancet, and David Horn PMCID: PMC2681464 Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini) Niklas Wahlberg, Elisabet Weingartner, Andrew D Warren, and Sören Nylin PMCID: PMC2688511 Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids Pierre Kerner, Johanne Hung, Julien Béhague, Martine Le Gouar, Guillaume Balavoine, and Michel Vervoort PMCID: PMC2688512 Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution Eske Willerslev, M Thomas P Gilbert, Jonas Binladen, Simon YW Ho, Paula F Campos, Aakrosh Ratan, Lynn P Tomsho, Rute R da Fonseca, Andrei Sher, Tatanya V Kuznetsova, Malgosia Nowak-Kemp, Terri L Roth, Webb Miller, and Stephan C Schuster PMCID: PMC2694787 Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa Bert Breugelmans, Gert Simonet, Vincent van Hoef, Sofie Van Soest, and Jozef Vanden Broeck PMCID: PMC2689174 A single origin of the photosynthetic organelle in different Paulinella lineages Hwan Su Yoon, Takuro Nakayama, Adrian Reyes-Prieto, Robert A Andersen, Sung Min Boo, Ken-ichiro Ishida, and Debashish Bhattacharya PMCID: PMC2685391 Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies Nélida Pohl, Marilou P Sison-Mangus, Emily N Yee, Saif W Liswi, and Adriana D Briscoe PMCID: PMC2689175 Phylogeny and evolution of Rab7 and Rab9 proteins Paweł Mackiewicz and Elżbieta Wyroba PMCID: PMC2693434 Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons Pamela Styles and John FY Brookfield PMCID: PMC2686708 Phylogeographical patterns of a generalist acorn weevil: insight into the biogeographical history of broadleaved deciduous and evergreen forests Kyoko Aoki, Makoto Kato, and Noriaki Murakami PMCID: PMC2691738 Females prefer the scent of outbred males: good-genes-as-heterozygosity? Petteri Ilmonen, Gloria Stundner, Michaela Thoß, and Dustin J Penn PMCID: PMC2698884 Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences Yudai Okuyama and Makoto Kato PMCID: PMC2695457 Compensatory evolution for a gene deletion is not limited to its immediate functional network WR Harcombe, R Springman, and JJ Bull PMCID: PMC2696425 The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes Sarah J Bourlat, Omar Rota-Stabelli, Robert Lanfear, and Maximilian J Telford PMCID: PMC2697986 Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata) Emiliano Trucchi and Valerio Sbordoni PMCID: PMC2686709 Evolution of sexual dimorphism of wing shape in the Drosophila melanogaster subgroup Nelly A Gidaszewski, Michel Baylac, and Christian Peter Klingenberg PMCID: PMC2691407 Species delimitation and phylogeny of a New Zealand plant species radiation Heidi M Meudt, Peter J Lockhart, and David Bryant PMCID: PMC2700801 Geminiviruses: a tale of a plasmid becoming a virus Mart Krupovic, Janne J Ravantti, and Dennis H Bamford PMCID: PMC2702318 Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments Diana L Huestis, Brenda Oppert, and Jeremy L Marshall PMCID: PMC2688510 Historic hybridization and persistence of a novel mito-nuclear combination in red-backed voles (genus Myodes) Amy M Runck, Marjorie D Matocq, and Joseph A Cook PMCID: PMC2697987 Recombination, cryptic clades and neutral molecular divergence of the microcystin synthetase (mcy) genes of toxic cyanobacterium Microcystis aeruginosa Yuuhiko Tanabe, Tomoharu Sano, Fumie Kasai, and Makoto M Watanabe PMCID: PMC2693435 Molecular phylogeny of ocelloid-bearing dinoflagellates (Warnowiaceae) as inferred from SSU and LSU rDNA sequences Mona Hoppenrath, Tsvetan R Bachvaroff, Sara M Handy, Charles F Delwiche, and Brian S Leander PMCID: PMC2694157 Evidence for increased olfactory receptor gene repertoire size in two nocturnal bird species with well-developed olfactory ability Silke S Steiger, Andrew E Fidler, and Bart Kempenaers PMCID: PMC2701422 Insights into the evolution of sialic acid catabolism among bacteria Salvador Almagro-Moreno and E Fidelma Boyd PMCID: PMC2693436 Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships Björn M von Reumont, Karen Meusemann, Nikolaus U Szucsich, Emiliano Dell'Ampio, Vivek Gowri-Shankar, Daniela Bartel, Sabrina Simon, Harald O Letsch, Roman R Stocsits, Yun-xia Luan, Johann Wolfgang Wägele, Günther Pass, Heike Hadrys, and Bernhard Misof PMCID: PMC2695459 Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis David Roy Smith and Robert W Lee PMCID: PMC2698885 Evolution of the leukotoxin promoter in genus Mannheimia Jesper Larsen, Anders G Pedersen, Robert L Davies, Peter Kuhnert, Joachim Frey, Henrik Christensen, Magne Bisgaard, and John E Olsen PMCID: PMC2697988 Evolution of resource cycling in ecosystems and individuals Anton Crombach and Paulien Hogeweg PMCID: PMC2698886 A complex selection signature at the human AVPR1B gene Rachele Cagliani, Matteo Fumagalli, Uberto Pozzoli, Stefania Riva, Matteo Cereda, Giacomo P Comi, Linda Pattini, Nereo Bresolin, and Manuela Sironi PMCID: PMC2700802 Parasites may help stabilize cooperative relationships Ainslie EF Little and Cameron R Currie PMCID: PMC2701933 Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family: strategies for functional analysis in Paramecium tetraurelia Raghida Damaj, Sébastien Pomel, Geneviève Bricheux, Gérard Coffe, Bernard Viguès, Viviane Ravet, and Philippe Bouchard PMCID: PMC2709106 The evolution of nuclear auxin signalling Ivan A Paponov, William Teale, Daniel Lang, Martina Paponov, Ralf Reski, Stefan A Rensing, and Klaus Palme PMCID: PMC2708152 Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication Yukuto Sato, Yasuyuki Hashiguchi, and Mutsumi Nishida PMCID: PMC2702319 Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao Xuanyang Li, Jennifer Slife, Neil Patel, and Shaying Zhao PMCID: PMC2700803 You can't always get what you want: size assortative mating by mutual mate choice as a resolution of sexual conflict Sebastian A Baldauf, Harald Kullmann, Stefanie H Schroth, Timo Thünken, and Theo CM Bakker PMCID: PMC2719620 Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes Lei Gao, Xuan Yi, Yong-Xia Yang, Ying-Juan Su, and Ting Wang PMCID: PMC2706227 Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot Ines Van Bocxlaer, SD Biju, Simon P Loader, and Franky Bossuyt PMCID: PMC2706228 Sexual conflict over the duration of copulation in Drosophila montana: why is longer better? Dominique Mazzi, Jenni Kesäniemi, Anneli Hoikkala, and Kirsten Klappert PMCID: PMC2704186 Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes Jimeng Hua, Ming Li, Pengzhi Dong, Ying Cui, Qiang Xie, and Wenjun Bu PMCID: PMC2711072 Gamete types, sex determination and stable equilibria of all-hybrid populations of diploid and triploid edible frogs (Pelophylax esculentus) Ditte G Christiansen PMCID: PMC2709657 The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis Yu-Juan Zhang, Hai-Feng Tian, and Jian-Fan Wen PMCID: PMC2706819 Conservation of the glucan phosphatase laforin is linked to rates of molecular evolution and the glucan metabolism of the organism Matthew S Gentry and Rachel M Pace PMCID: PMC2714694 Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence Christopher S Willett and Jason T Ladner PMCID: PMC2708153 Diversity and evolution of the small multidrug resistance protein family Denice C Bay and Raymond J Turner PMCID: PMC2716321 Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs Ramil N Nurtdinov, Andrey A Mironov, and Mikhail S Gelfand PMCID: PMC2711938 Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations Gang Song, Yanhua Qu, Zuohua Yin, Shouhsien Li, Naifa Liu, and Fumin Lei PMCID: PMC2714695 Unexpected relationships of substructured populations in Chinese Locusta migratoria De-Xing Zhang, Lu-Na Yan, Ya-Jie Ji, Godfrey M Hewitt, and Zu-Shi Huang PMCID: PMC2718889 Adaptive radiation of gobies in the interstitial habitats of gravel beaches accompanied by body elongation and excessive vertebral segmentation Tomohiko Yamada, Tomoshige Sugiyama, Nana Tamaki, Atsushi Kawakita, and Makoto Kato PMCID: PMC2709658 Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins Robin Doley, Stephen P Mackessy, and R Manjunatha Kini PMCID: PMC2711939 Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird Hervé Mulard, Etienne Danchin, Sandra L Talbot, Andrew M Ramey, Scott A Hatch, Joël F White, Fabrice Helfenstein, and Richard H Wagner PMCID: PMC2709659 Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses Jeri Lynn Parrent, Timothy Y James, Rimvydas Vasaitis, and Andrew FS Taylor PMCID: PMC2728104 Phylogenetic analysis of the SAP30 family of transcriptional regulators reveals functional divergence in the domain that binds the nuclear matrix Keijo M Viiri, Taisto YK Heinonen, Markku Mäki, and Olli Lohi PMCID: PMC2711940 On the phylogenetic position of Myzostomida: can 77 genes get it wrong? Christoph Bleidorn, Lars Podsiadlowski, Min Zhong, Igor Eeckhaut, Stefanie Hartmann, Kenneth M Halanych, and Ralph Tiedemann PMCID: PMC2716322 Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards Christy A Hipsley, Lin Himmelmann, Dirk Metzler, and Johannes Müller PMCID: PMC2719621 Impacts of inbreeding on bumblebee colony fitness under field conditions Penelope R Whitehorn, Matthew C Tinsley, Mark JF Brown, Ben Darvill, and Dave Goulson PMCID: PMC2712462 Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea Yvonne CF Su and Richard MK Saunders PMCID: PMC2722625 Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation Simona Fornarino, Maria Pala, Vincenza Battaglia, Ramona Maranta, Alessandro Achilli, Guido Modiano, Antonio Torroni, Ornella Semino, and Silvana A Santachiara-Benerecetti PMCID: PMC2720951 Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years Andrew R Carson and Stephen W Scherer PMCID: PMC2720389 Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites Satoko Noda, Yuichi Hongoh, Tomoyuki Sato, and Moriya Ohkuma PMCID: PMC2717939 Genetic specificity and potential for local adaptation between dengue viruses and mosquito vectors Louis Lambrechts, Christine Chevillon, Rebecca G Albright, Butsaya Thaisomboonsuk, Jason H Richardson, Richard G Jarman, and Thomas W Scott PMCID: PMC2714696 Sexual selection on cuticular hydrocarbons in the Australian field cricket, Teleogryllus oceanicus Melissa L Thomas and Leigh W Simmons PMCID: PMC2728729 Evolution of plant senescence Howard Thomas, Lin Huang, Mike Young, and Helen Ougham PMCID: PMC2716323 Rooting human parechovirus evolution in time Nuno R Faria, Michel de Vries, Formijn J van Hemert, Kimberley Benschop, and Lia van der Hoek PMCID: PMC2723090 Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains Teresa N Giles, Derek J Fisher, and David E Graham PMCID: PMC2720952 Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities Céline Gomez, Stéphane Dussert, Perla Hamon, Serge Hamon, Alexandre de Kochko, and Valérie Poncet PMCID: PMC2717059 Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloë festucae Michelle K Bryant, Christopher L Schardl, Uljana Hesse, and Barry Scott PMCID: PMC2717940 Bats that walk: a new evolutionary hypothesis for the terrestrial behaviour of New Zealand's endemic mystacinids Suzanne J Hand, Vera Weisbecker, Robin MD Beck, Michael Archer, Henk Godthelp, Alan JD Tennyson, and Trevor H Worthy PMCID: PMC2729772 Zebrafish RNase T2 genes and the evolution of secretory ribonucleases in animals Melissa S Hillwig, Ludmila Rizhsky, Ying Wang, Alisa Umanskaya, Jeffrey J Essner, and Gustavo C MacIntosh PMCID: PMC2720953 A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone Aline Dépraz, Jacques Hausser, and Markus Pfenninger PMCID: PMC2724411 Divergent evolution in the cytoplasmic domains of PRLR and GHR genes in Artiodactyla Terhi Iso-Touru, Juha Kantanen, Meng-Hua Li, Zygmunt Gizejewski, and Johanna Vilkki PMCID: PMC2720954 Reconstructing Indian-Australian phylogenetic link Satish Kumar, Rajasekhara Reddy Ravuri, Padmaja Koneru, BP Urade, BN Sarkar, A Chandrasekar, and VR Rao PMCID: PMC2720955 Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling Ricardo Betancur-R PMCID: PMC2726142 Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders Benjamin M Fitzpatrick, Jarrett R Johnson, D Kevin Kump, H Bradley Shaffer, Jeramiah J Smith, and S Randal Voss PMCID: PMC2724412 Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure Jérôme Duminil, Olivier J Hardy, and Rémy J Petit PMCID: PMC2728730 Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora Alejandro Reyes-Bermudez, Zhiyi Lin, David C Hayward, David J Miller, and Eldon E Ball PMCID: PMC2726143 The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage Scot Libants, Kevin Carr, Hong Wu, John H Teeter, Yu-Wen Chung-Davidson, Ziping Zhang, Curt Wilkerson, and Weiming Li PMCID: PMC2728731 Demographic history of Canary Islands male gene-pool: replacement of native lineages by European Rosa Fregel, Verónica Gomes, Leonor Gusmão, Ana M González, Vicente M Cabrera, António Amorim, and Jose M Larruga PMCID: PMC2728732 Are adaptation costs necessary to build up a local adaptation pattern? Sara Magalhães, Elodie Blanchet, Martijn Egas, and Isabelle Olivieri PMCID: PMC2728733 Evolutionary genomics of LysM genes in land plants Xue-Cheng Zhang, Steven B Cannon, and Gary Stacey PMCID: PMC2728734 Maintenance of adaptive differentiation by Wolbachia induced bidirectional cytoplasmic incompatibility: the importance of sib-mating and genetic systems Antoine Branca, Fabrice Vavre, Jean-François Silvain, and Stéphane Dupas PMCID: PMC2738673 The root of the East African cichlid radiations Julia Schwarzer, Bernhard Misof, Diethard Tautz, and Ulrich K Schliewen PMCID: PMC2739198 An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models Georgia Tsagkogeorga, Xavier Turon, Russell R Hopcroft, Marie-Ka Tilak, Tamar Feldstein, Noa Shenkar, Yossi Loya, Dorothée Huchon, Emmanuel JP Douzery, and Frédéric Delsuc PMCID: PMC2739199 Positive selection at codon 38 of the human KCNE1 (= minK) gene and sporadic absence of 38Ser-coding mRNAs in Gly38Ser heterozygotes Holger Herlyn, Ulrich Zechner, Franz Oswald, Arne Pfeufer, Hans Zischler, and Thomas Haaf PMCID: PMC2743666 Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes Jan Zrzavý, Pavel Říha, Lubomír Piálek, and Jan Janouškovec PMCID: PMC2732625 How to be an attractive male: floral dimorphism and attractiveness to pollinators in a dioecious plant Marc O Waelti, Paul A Page, Alex Widmer, and Florian P Schiestl PMCID: PMC2738674 Intronization, de-intronization and intron sliding are rare in Cryptococcus Scott W Roy PMCID: PMC2740785 Does negative auto-regulation increase gene duplicability? Tobias Warnecke, Guang-Zhong Wang, Martin J Lercher, and Laurence D Hurst PMCID: PMC2739200 Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes Francesco Santini, Luke J Harmon, Giorgio Carnevale, and Michael E Alfaro PMCID: PMC2743667 Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene Shin-ichi Yokobori, Takashi Itoh, Shigeo Yoshinari, Norimichi Nomura, Yoshihiko Sako, Akihiko Yamagishi, Tairo Oshima, Kiyoshi Kita, and Yoh-ichi Watanabe PMCID: PMC2738675 Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea Aaron D Goldman, John A Leigh, and Ram Samudrala PMCID: PMC2739858 Loss of matK RNA editing in seed plant chloroplasts Michael Tillich, Vinh Le Sy, Katrin Schulerowitz, Arndt von Haeseler, Uwe G Maier, and Christian Schmitz-Linneweber PMCID: PMC2744683 Evolution and functional divergence of NLRP genes in mammalian reproductive systems Xin Tian, Géraldine Pascal, and Philippe Monget PMCID: PMC2735741 Long-range regulation is a major driving force in maintaining genome integrity Emmanuel Mongin, Ken Dewar, and Mathieu Blanchette PMCID: PMC2741452 Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes Hermann Ragg, Abhishek Kumar, Katharina Köster, Caterina Bentele, Yunjie Wang, Marc-André Frese, Natalie Prib, and Olaf Krüger PMCID: PMC2746811 Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice Thomas Thiel, Andreas Graner, Robbie Waugh, Ivo Grosse, Timothy J Close, and Nils Stein PMCID: PMC2746218 Neogastropod phylogenetic relationships based on entire mitochondrial genomes Regina L Cunha, Cristina Grande, and Rafael Zardoya PMCID: PMC2741453 Phylogenetic inference under varying proportions of indel-induced alignment gaps Bhakti Dwivedi and Sudhindra R Gadagkar PMCID: PMC2746219 Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution Werner E Mayer, Matthias Herrmann, and Ralf J Sommer PMCID: PMC2737313 Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam Aya Takahashi PMCID: PMC2741454 The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes Zi-Wen Li, Xue Li, Quan-You Yu, Zhong-Huai Xiang, Hirohisa Kishino, and Ze Zhang PMCID: PMC2745388 Inferring polyploid phylogenies from multiply-labeled gene trees Martin Lott, Andreas Spillner, Katharina T Huber, Anna Petri, Bengt Oxelman, and Vincent Moulton PMCID: PMC2748082 Comparative genomics of chondrichthyan Hoxa clusters John F Mulley, Ying-Fu Zhong, and Peter WH Holland PMCID: PMC2746220 Differential transcriptional modulation of duplicated fatty acid-binding protein genes by dietary fatty acids in zebrafish (Danio rerio): evidence for subfunctionalization or neofunctionalization of duplicated genes Santhosh Karanth, Santosh P Lall, Eileen M Denovan-Wright, and Jonathan M Wright PMCID: PMC2754478 Quaternary history and contemporary patterns in a currently expanding species Carole Kerdelhué, Lorenzo Zane, Mauro Simonato, Paola Salvato, Jérôme Rousselet, Alain Roques, and Andrea Battisti PMCID: PMC2753568 FoxO gene family evolution in vertebrates Minghui Wang, Xiangzhe Zhang, Hongbo Zhao, Qishan Wang, and Yuchun Pan PMCID: PMC2746812 Phylogenetic relationships and biogeography of the genus Algansea Girard (Cypriniformes: Cyprinidae) of central Mexico inferred from molecular data Rodolfo Pérez-Rodríguez, Omar Domínguez-Domínguez, Gerardo Pérez Ponce de León, and Ignacio Doadrio PMCID: PMC2759940 The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family Hiroki Goto, Kazunori Watanabe, Naozumi Araragi, Rui Kageyama, Kunika Tanaka, Yoko Kuroki, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki, Asao Fujiyama, Yasuyuki Fukumaki, and Hiroki Shibata PMCID: PMC2753569 FGFRL1 is a neglected putative actor of the FGF signalling pathway present in all major metazoan phyla Stephanie Bertrand, Ildiko Somorjai, Jordi Garcia-Fernandez, Thomas Lamonerie, and Hector Escriva PMCID: PMC2754479 Evolutionary conservation and changes in insect TRP channels Hironori Matsuura, Takaaki Sokabe, Keigo Kohno, Makoto Tominaga, and Tatsuhiko Kadowaki PMCID: PMC2753570 Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins Jesse Donovan and Paul R Copeland PMCID: PMC2746813 Nuclear receptor complement of the cnidarian Nematostella vectensis: phylogenetic relationships and developmental expression patterns Adam M Reitzel and Ann M Tarrant PMCID: PMC2749838 Evolutionary constraints permeate large metabolic networks Andreas Wagner PMCID: PMC2753571 Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth Alfred L Roca, Yasuko Ishida, Nikolas Nikolaidis, Sergios-Orestis Kolokotronis, Stephen Fratpietro, Kristin Stewardson, Shannon Hensley, Michele Tisdale, Gennady Boeskorov, and Alex D Greenwood PMCID: PMC2754481 Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species Hiromi Ohara, Masato Nikaido, Atsuko Date-Ito, Kazutaka Mogi, Hiroaki Okamura, Norihiro Okada, Yukari Takeuchi, Yuji Mori, and Kimiko Hagino-Yamagishi PMCID: PMC2758851 Inferring speciation modes in a clade of Iberian chafers from rates of morphological evolution in different character systems Dirk Ahrens and Ignacio Ribera PMCID: PMC2753572 An unexpectedly long history of sexual selection in birds-of-paradise Martin Irestedt, Knud A Jønsson, Jon Fjeldså, Les Christidis, and Per GP Ericson PMCID: PMC2755009 The impact of population size on the evolution of asexual microbes on smooth versus rugged fitness landscapes Andreas Handel and Daniel E Rozen PMCID: PMC2753573 Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region Christopher RE McEvoy, Paul D van Helden, Robin M Warren, and Nicolaas C Gey van Pittius PMCID: PMC2758852 Brain structure evolution in a basal vertebrate clade: evidence from phylogenetic comparative analysis of cichlid fishes Alejandro Gonzalez-Voyer, Svante Winberg, and Niclas Kolm PMCID: PMC2755010 Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise Judith Fehrer, Karol Krak, and Jindřich Chrtek, Jr PMCID: PMC2759941 High adsorption rate is detrimental to bacteriophage fitness in a biofilm-like environment Romain Gallet, Yongping Shao, and Ing-Nang Wang PMCID: PMC2762979 Amphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptors Allison M Churcher and John S Taylor PMCID: PMC2764704 The genome sequence of the protostome Daphnia pulex encodes respective orthologues of a neurotrophin, a Trk and a p75NTR: Evolution of neurotrophin signaling components and related proteins in the bilateria Karen HS Wilson PMCID: PMC2772990 Expressions of ECE-CYC2 clade genes relating to abortion of both dorsal and ventral stamens in Opithandra (Gesneriaceae) Chun-Feng Song, Qi-Bing Lin, Rong-Hua Liang, and Yin-Zheng Wang PMCID: PMC2763874 Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae) Sarah E Kingston, Lara D Adams, and Patricia E Rosel PMCID: PMC2770059 Poly-paraphyly of Hirudinidae: many lineages of medicinal leeches Anna J Phillips and Mark E Siddall PMCID: PMC2768714 Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase Xing Fan, Li-Na Sha, Rui-Wu Yang, Hai-Qin Zhang, Hou-Yang Kang, Cun-Bang Ding, Li Zhang, You-Liang Zheng, and Yong-Hong Zhou PMCID: PMC2770499 Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations Julien P Renoult, Finn Kjellberg, Cinderella Grout, Sylvain Santoni, and Bouchaïb Khadari PMCID: PMC2771017 Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes Eve Gazave, Pascal Lapébie, Gemma S Richards, Frédéric Brunet, Alexander V Ereskovsky, Bernard M Degnan, Carole Borchiellini, Michel Vervoort, and Emmanuelle Renard PMCID: PMC2770060 Polyploid evolution in Oryza officinalis complex of the genus Oryza Baosheng Wang, Zhuoya Ding, Wei Liu, Jin Pan, Changbao Li, Song Ge, and Daming Zhang PMCID: PMC2770061 Cooperative social clusters are not destroyed by dispersal in a ciliate Nicolas Schtickzelle, Else J Fjerdingstad, Alexis Chaine, and Jean Clobert PMCID: PMC2768715 Positive selection for the male functionality of a co-retroposed gene in the hominoids Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, and Liping Wei PMCID: PMC2773790 Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids Gildas Le Corguillé, Gareth Pearson, Marta Valente, Carla Viegas, Bernhard Gschloessl, Erwan Corre, Xavier Bailly, Akira F Peters, Claire Jubin, Benoit Vacherie, J Mark Cock, and Catherine Leblanc PMCID: PMC2765969 Hsp-90 and the biology of nematodes Nik AIIN Him, Victoria Gillan, Richard D Emes, Kirsty Maitland, and Eileen Devaney PMCID: PMC2771018 Nme protein family evolutionary history, a vertebrate perspective Thomas Desvignes, Pierre Pontarotti, Christian Fauvel, and Julien Bobe PMCID: PMC2777172 Relatedness facilitates cooperation in the subsocial spider, Stegodyphus tentoriicola Jasmin Ruch, Lisa Heinrich, Trine Bilde, and Jutta M Schneider PMCID: PMC2774699 Genomic taxonomy of vibrios Cristiane C Thompson, Ana Carolina P Vicente, Rangel C Souza, Ana Tereza R Vasconcelos, Tammi Vesth, Nelson Alves, Jr, David W Ussery, Tetsuya Iida, and Fabiano L Thompson PMCID: PMC2777879 Estimating the phylogeny and divergence times of primates using a supermatrix approach Helen J Chatterjee, Simon YW Ho, Ian Barnes, and Colin Groves PMCID: PMC2774700 Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae Daniel B Sloan, Bengt Oxelman, Anja Rautenberg, and Douglas R Taylor PMCID: PMC2777880 Plant chemical defence: a partner control mechanism stabilising plant - seed-eating pollinator mutualisms Sébastien Ibanez, Christiane Gallet, Fanny Dommanget, and Laurence Després PMCID: PMC2777173 Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data Ferran Palero, Joao Lopes, Pere Abelló, Enrique Macpherson, Marta Pascual, and Mark A Beaumont PMCID: PMC2777881 Methodology Articles Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches Stephen A Smith, Jeremy M Beaulieu, and Michael J Donoghue PMCID: PMC2645364 RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus Tobias L Lenz, Christophe Eizaguirre, Sven Becker, and Thorsten BH Reusch PMCID: PMC2662802 HaMStR: Profile hidden markov model based search for orthologs in ESTs Ingo Ebersberger, Sascha Strauss, and Arndt von Haeseler PMCID: PMC2723089 BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC Rahul Satija, Ádám Novák, István Miklós, Rune Lyngsø, and Jotun Hein PMCID: PMC2744684 Fast optimization of statistical potentials for structurally constrained phylogenetic models Cécile Bonnard, Claudia L Kleinman, Nicolas Rodrigue, and Nicolas Lartillot PMCID: PMC2754480 Corrections Chromosomal evolution of the PKD1 gene family in primates Stefan Kirsch, Juanjo Pasantes, Andreas Wolf, Nadia Bogdanova, Claudia Münch, Arseni Markoff, Petra Pennekamp, Michael Krawczak, Bernd Dworniczak, and Werner Schempp PMCID: PMC2649905 Corrects: Stefan Kirsch, et al. Chromosomal evolution of the PKD1 gene family in primates. BMC Evol Biol. 2008; 8: 263. Evolution of prokaryotic SPFH proteins Markus Hinderhofer, Christina A Walker, Anke Friemel, Claudia AO Stuermer, Heiko M Möller, and Alexander Reuter PMCID: PMC2644673 Corrects: Markus Hinderhofer, et al. Evolution of prokaryotic SPFH proteins. BMC Evol Biol. 2009; 9: 10. Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments Simon C Harvey, Alison Shorto, and Mark E Viney PMCID: PMC2694158 Corrects: Simon C Harvey, et al. Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments. BMC Evol Biol. 2008; 8: 15. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura Pedro Simões, Marta Pascual, Josiane Santos, Michael R Rose, and Margarida Matos PMCID: PMC2703621 Corrects: Pedro Simões, et al. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura. BMC Evol Biol. 2008; 8: 66. Correction: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria Nathaniel M Evans, Alberto Lindner, Ekaterina V Raikova, Allen G Collins, and Paulyn Cartwright PMCID: PMC2714838 Corrects: Nathaniel M Evans, et al. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria. BMC Evol Biol. 2008; 8: 139. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites Liat Shavit Grievink, David Penny, Mike D Hendy, and Barbara R Holland PMCID: PMC2731753 Corrects: Liat Shavit Grievink, et al. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol. 2008; 8: 317. Correction: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair Dong-Dong Wu, David M Irwin, and Ya-Ping Zhang PMCID: PMC2745387 Corrects: Dong-Dong Wu, et al. Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evol Biol. 2008; 8: 241. Other Issues: Journal List
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