| | Other Issues: previous | next | latest | archiveCorrespondence Careful with understudied phyla: The case of chaetognath Ferdinand Marlétaz and Yannick Le Parco PMCID: PMC2566580 Database A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins Xavier Bailly, Stefano Vanin, Christine Chabasse, Kenji Mizuguchi, and Serge N Vinogradov PMCID: PMC2556348 Software PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas Ahmed Moustafa and Debashish Bhattacharya PMCID: PMC2254586 PhyloFinder: An intelligent search engine for phylogenetic tree databases Duhong Chen, J Gordon Burleigh, Mukul S Bansal, and David Fernández-Baca PMCID: PMC2362120 ReXSpecies – a tool for the analysis of the evolution of gene regulation across species Stephan Struckmann, Marcos J Araúzo-Bravo, Hans R Schöler, Rolland A Reinbold, and Georg Fuellen PMCID: PMC2346469 Exploring historical trends using taxonomic name metadata Indra Neil Sarkar, Ryan Schenk, and Catherine N Norton PMCID: PMC2408592 Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs Julien Dutheil and Bastien Boussau PMCID: PMC2559849 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: PMC2613921 Research Articles Prezygotic reproductive isolation between Saccharomyces cerevisiae and Saccharomyces paradoxus Calum J Maclean and Duncan Greig PMCID: PMC2249576 Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome Jason G Mezey, Sergey V Nuzhdin, Fangfei Ye, and Corbin D Jones PMCID: PMC2266709 Environmental induction and phenotypic retention of adaptive maternal effects Alexander V Badyaev and Kevin P Oh PMCID: PMC2231342 Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea Christian P Kubicek, Scott Baker, Christian Gamauf, Charles M Kenerley, and Irina S Druzhinina PMCID: PMC2253510 Evidence for divergent selection between the molecular forms of Anopheles gambiae: role of predation Abdoulaye Diabaté, Roch K Dabiré, Kyle Heidenberger, Jacob Crawford, William O Lamp, Lauren E Culler, and Tovi Lehmann PMCID: PMC2217532 Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales Kenneth M Noll, Pascal Lapierre, J Peter Gogarten, and Dhaval M Nanavati PMCID: PMC2246101 Molecular evolution of the cytochrome c oxidase subunit 5A gene in primates Monica Uddin, Juan C Opazo, Derek E Wildman, Chet C Sherwood, Patrick R Hof, Morris Goodman, and Lawrence I Grossman PMCID: PMC2241769 The amphioxus (Branchiostoma floridae) genome contains a highly diversified set of G protein-coupled receptors Karl JV Nordström, Robert Fredriksson, and Helgi B Schiöth PMCID: PMC2246102 Inbreeding depression in Solanum carolinense (Solanaceae), a species with a plastic self-incompatibility response Jorge I Mena-Ali, Lidewij H Keser, and Andrew G Stephenson PMCID: PMC2244599 Comparisons of mutation rate variation at genome-wide microsatellites: evolutionary insights from two cultivated rice and their wild relatives Li-zhi Gao and Hongyan Xu PMCID: PMC2241587 Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes David Moreira and Céline Brochier-Armanet PMCID: PMC2263039 Ancestral feeding state of ruminants reconsidered: earliest grazing adaptation claims a mixed condition for Cervidae Daniel DeMiguel, Mikael Fortelius, Beatriz Azanza, and Jorge Morales PMCID: PMC2270802 Broadly sampled multigene trees of eukaryotes Hwan Su Yoon, Jessica Grant, Yonas I Tekle, Min Wu, Benjamin C Chaon, Jeffrey C Cole, John M Logsdon, Jr, David J Patterson, Debashish Bhattacharya, and Laura A Katz PMCID: PMC2249577 Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments Simon C Harvey, Alison Shorto, and Mark E Viney PMCID: PMC2267162 Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships Nicholas D Bland, John W Pinney, Josie E Thomas, Anthony J Turner, and R Elwyn Isaac PMCID: PMC2259306 A genome-wide screen for noncoding elements important in primate evolution Eliot C Bush and Bruce T Lahn PMCID: PMC2242780 IS4 family goes genomic Daniel De Palmenaer, Patricia Siguier, and Jacques Mahillon PMCID: PMC2266710 hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions Luciano Brocchieri, Everly Conway de Macario, and Alberto JL Macario PMCID: PMC2266713 Bird evolution: testing the Metaves clade with six new mitochondrial genomes Mary Morgan-Richards, Steve A Trewick, Anna Bartosch-Härlid, Olga Kardailsky, Matthew J Phillips, Patricia A McLenachan, and David Penny PMCID: PMC2259304 Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact Hua Zhang, Jie Yan, Guoqiang Zhang, and Kaiya Zhou PMCID: PMC2262875 The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment Wagied Davids and Zhaolei Zhang PMCID: PMC2259305 Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): Founder effects, vicariance, or both? Gert Wörheide, Laura S Epp, and Luciana Macis PMCID: PMC2267160 Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids Shao-Lun Liu and Keith Adams PMCID: PMC2258280 Evolution of a family of metazoan active-site-serine enzymes from penicillin-binding proteins: a novel facet of the bacterial legacy Nina Peitsaro, Zydrune Polianskyte, Jarno Tuimala, Isabella Pörn-Ares, Julius Liobikas, Oliver Speer, Dan Lindholm, James Thompson, and Ove Eriksson PMCID: PMC2266909 Evolution of sexual mimicry in the orchid subtribe orchidinae: the role of preadaptations in the attraction of male bees as pollinators Florian P Schiestl and Salvatore Cozzolino PMCID: PMC2267782 Assortative mating and fragmentation within dog breeds Susanne Björnerfeldt, Frank Hailer, Maria Nord, and Carles Vilà PMCID: PMC2266708 Parasitism, life history traits and immune defence in cyprinid fish from Central Europe Andrea Šimková, Thomas Lafond, Markéta Ondračková, Pavel Jurajda, Eva Ottová, and Serge Morand PMCID: PMC2270801 The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution Christoph Kneip, Christine Voβ, Peter J Lockhart, and Uwe G Maier PMCID: PMC2246100 The origin of a novel gene through overprinting in Escherichia coli Luis Delaye, Alexander DeLuna, Antonio Lazcano, and Arturo Becerra PMCID: PMC2268670 Climate-driven diversification in two widespread Galerida larks Alban Guillaumet, Pierre-André Crochet, and Jean-Marc Pons PMCID: PMC2275783 Independent Origins of New Sex-Linked Chromosomes in the melanica and robusta Species Groups of Drosophila Sergio V Flores, Amy L Evans, and Bryant F McAllister PMCID: PMC2268673 Experimental demonstration of ecological character displacement Jabus G Tyerman, Melanie Bertrand, Christine C Spencer, and Michael Doebeli PMCID: PMC2267161 Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora Jeremy R Dettman, James B Anderson, and Linda M Kohn PMCID: PMC2270261 Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots Rui-Jiang Wang, Chiao-Lei Cheng, Ching-Chun Chang, Chun-Lin Wu, Tian-Mu Su, and Shu-Miaw Chaw PMCID: PMC2275221 Genetic variation for parental effects on the propensity to gregarise in Locusta migratoria Marie-Pierre Chapuis, Arnaud Estoup, Arnaud Augé-Sabatier, Antoine Foucart, Michel Lecoq, and Yannis Michalakis PMCID: PMC2276201 From speciation to introgressive hybridization: the phylogeographic structure of an island subspecies of termite, Reticulitermes lucifugus corsicus Thomas Lefebvre, Nicolas Châline, Denis Limousin, Simon Dupont, and Anne-Geneviève Bagnères PMCID: PMC2262054 Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers Nicola J Patron, Dion G Durnford, and Stanislav Kopriva PMCID: PMC2275785 The evolutionary history of sharp- and blunt-snouted lenok (Brachymystax lenok (Pallas, 1773)) and its implications for the paleo-hydrological history of Siberia Elsa Froufe, Sergey Alekseyev, Paulo Alexandrino, and Steven Weiss PMCID: PMC2275220 Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members Inna Hughes, Jonathan Binkley, Belen Hurle, Eric D Green, NISC Comparative Sequencing Program, Arend Sidow, and David M Ornitz PMCID: PMC2268672 A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish Kerry J Laing, Maureen K Purcell, James R Winton, and John D Hansen PMCID: PMC2268669 Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization Frédéric JJ Chain, Dora Ilieva, and Ben J Evans PMCID: PMC2275784 Slipins: ancient origin, duplication and diversification of the stomatin protein family Jasper B Green and J Peter W Young PMCID: PMC2258279 Mitochondrial DNA structure in the Arabian Peninsula Khaled K Abu-Amero, José M Larruga, Vicente M Cabrera, and Ana M González PMCID: PMC2268671 Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals Christina M Laukaitis, Andreas Heger, Tyler D Blakley, Pavel Munclinger, Chris P Ponting, and Robert C Karn PMCID: PMC2291036 Phenotypic plasticity or speciation? A case from a clonal marine organism Carlos Prada, Nikolaos V Schizas, and Paul M Yoshioka PMCID: PMC2275222 Structural and functional diversification in the teleost S100 family of calcium-binding proteins Andreas M Kraemer, Luis R Saraiva, and Sigrun I Korsching PMCID: PMC2266712 Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species Christian Michel, Brendan J Hicks, Kai N Stölting, Andrew C Clarke, Mark I Stevens, Ray Tana, Axel Meyer, and Michael R van den Heuvel PMCID: PMC2270262 Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota) Martin Ryberg, R Henrik Nilsson, Erik Kristiansson, Mats Töpel, Stig Jacobsson, and Ellen Larsson PMCID: PMC2275786 The emergence of leaders and followers in foraging pairs when the qualities of individuals differ Sean A Rands, Guy Cowlishaw, Richard A Pettifor, J Marcus Rowcliffe, and Rufus A Johnstone PMCID: PMC2276478 Epigenetic inheritance based evolution of antibiotic resistance in bacteria Mike Adam, Bhuvana Murali, Nicole O Glenn, and S Steven Potter PMCID: PMC2262874 Correlates of substitution rate variation in mammalian protein-coding sequences John J Welch, Olaf RP Bininda-Emonds, and Lindell Bromham PMCID: PMC2289806 Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor Roger S Holmes, Jeannie Chan, Laura A Cox, William J Murphy, and John L VandeBerg PMCID: PMC2266714 Wolbachia transmission dynamics in Formica wood ants Lumi Viljakainen, Max Reuter, and Pekka Pamilo PMCID: PMC2277377 Post-Messinian evolutionary relationships across the Sicilian channel: Mitochondrial and nuclear markers link a new green toad from Sicily to African relatives Matthias Stöck, Alessandra Sicilia, Natalia M Belfiore, David Buckley, Sabrina Lo Brutto, Mario Lo Valvo, and Marco Arculeo PMCID: PMC2276203 From sea to land and beyond – New insights into the evolution of euthyneuran Gastropoda (Mollusca) Annette Klussmann-Kolb, Angela Dinapoli, Kerstin Kuhn, Bruno Streit, and Christian Albrecht PMCID: PMC2287175 Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups Martin Osterholz, Lutz Walter, and Christian Roos PMCID: PMC2268674 Signals of demographic expansion in Drosophila virilis Patricia M Mirol, Jarkko Routtu, Anneli Hoikkala, and Roger K Butlin PMCID: PMC2276204 Daphnia Halloween genes that encode cytochrome P450s mediating the synthesis of the arthropod molting hormone: Evolutionary implications Kim F Rewitz and Lawrence I Gilbert PMCID: PMC2276477 Evolution of gastropod mitochondrial genome arrangements Cristina Grande, José Templado, and Rafael Zardoya PMCID: PMC2291457 Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution Dana K Howe and Dee R Denver PMCID: PMC2279117 Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species Catarina Pinho, D James Harris, and Nuno Ferrand PMCID: PMC2277379 The evolution of genome size in ants Neil D Tsutsui, Andrew V Suarez, Joseph C Spagna, and J Spencer Johnston PMCID: PMC2268675 Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus) Clifton M Ramsdell, Adrienne A Lewandowski, Julie L Weston Glenn, Paul B Vrana, Rachel J O'Neill, and Michael J Dewey PMCID: PMC2266908 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: PMC2266711 Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach Kirsten A Bratke and Aoife McLysaght PMCID: PMC2268676 The evolution of body size under environmental gradients in ectotherms: why should Bergmann's rule apply to lizards? Daniel Pincheira-Donoso, David J Hodgson, and Tom Tregenza PMCID: PMC2268677 Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera Oliver Voigt, Dirk Erpenbeck, and Gert Wörheide PMCID: PMC2289807 Unusual accelerated rate of deletions and insertions in toxin genes in the venom glands of the pygmy copperhead (Austrelaps labialis) from kangaroo island Robin Doley, Nguyen Ngoc Bao Tram, Md Abu Reza, and R Manjunatha Kini PMCID: PMC2287176 Barking up the wrong tree: Modern northern European dogs fail to explain their origin Helena Malmström, Carles Vilà, M Thomas P Gilbert, Jan Storå, Eske Willerslev, Gunilla Holmlund, and Anders Götherström PMCID: PMC2288593 Molecular evolution and functional divergence of the bestrophin protein family Vladimir M Milenkovic, Thomas Langmann, Rainer Schreiber, Karl Kunzelmann, and Bernhard HF Weber PMCID: PMC2292144 Cranial bone morphometric study among mouse strains Minoru Kawakami and Ken-ichi Yamamura PMCID: PMC2287174 Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans Santos Alonso, Neskuts Izagirre, Isabel Smith-Zubiaga, Jesús Gardeazabal, José Luís Díaz-Ramón, José Luís Díaz-Pérez, Diana Zelenika, María Dolores Boyano, Nico Smit, and Concepción de la Rúa PMCID: PMC2292700 X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans) Carmen Tomas, Juan J Sanchez, Anna Barbaro, Conxita Brandt-Casadevall, Alexis Hernandez, Mohamed Ben Dhiab, Misericordia Ramon, and Niels Morling PMCID: PMC2315647 The evolutionary costs of immunological maintenance and deployment Kurt A McKean, Christopher P Yourth, Brian P Lazzaro, and Andrew G Clark PMCID: PMC2292698 Birth-death prior on phylogeny and speed dating Örjan Åkerborg, Bengt Sennblad, and Jens Lagergren PMCID: PMC2270800 Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences Caroline Deshayes, Emmanuel Perrodou, Daniel Euphrasie, Eric Frapy, Olivier Poch, Pablo Bifani, Odile Lecompte, and Jean-Marc Reyrat PMCID: PMC2277376 The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex Aristeidis Parmakelis, Michel A Slotman, Jonathon C Marshall, Parfait H Awono-Ambene, Christophe Antonio-Nkondjio, Frederic Simard, Adalgisa Caccone, and Jeffrey R Powell PMCID: PMC2288592 Parasite-mediated disruptive selection in a natural Daphnia population Meghan A Duffy, Chad E Brassil, Spencer R Hall, Alan J Tessier, Carla E Cáceres, and Jeffrey K Conner PMCID: PMC2276202 Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds Erika S Tavares and Allan J Baker PMCID: PMC2279116 Gene expression analysis of the ovary of hybrid females of Xenopus laevis and X. muelleri John H Malone and Pawel Michalak PMCID: PMC2330042 Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers MJTN Timmermans, D Roelofs, J Mariën, and NM van Straalen PMCID: PMC2315649 Gene flow rise with habitat fragmentation in the bog fritillary butterfly (Lepidoptera: Nymphalidae) Gabriel Nève, Bernard Barascud, Henri Descimon, and Michel Baguette PMCID: PMC2329611 Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) X174 Kim M Pepin and Holly A Wichman PMCID: PMC2292699 General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability Markus Göker and Guido W Grimm PMCID: PMC2291458 Intergeneric transfer of ribosomal genes between two fungi Jiatao Xie, Yanping Fu, Daohong Jiang, Guoqing Li, Junbin Huang, Bo Li, Tom Hsiang, and Youliang Peng PMCID: PMC2277378 Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa) Laurence Loewe and Dunja K Lamatsch PMCID: PMC2292145 Selection against tandem splice sites affecting structured protein regions Michael Hiller, Karol Szafranski, Klaus Huse, Rolf Backofen, and Matthias Platzer PMCID: PMC2279118 Molecular evolution of dimeric α-amylase inhibitor genes in wild emmer wheat and its ecological association Ji-Rui Wang, Yu-Ming Wei, Xiang-Yu Long, Ze-Hong Yan, Eviatar Nevo, Bernard R Baum, and You-Liang Zheng PMCID: PMC2324104 The evolution of core proteins involved in microRNA biogenesis Dennis Murphy, Barry Dancis, and James R Brown PMCID: PMC2287173 Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus Pai-Chung Gwee, Chris T Amemiya, Sydney Brenner, and Byrappa Venkatesh PMCID: PMC2315648 Differences in the selection response of serially repeated color pattern characters: Standing variation, development, and evolution Cerisse E Allen, Patrícia Beldade, Bas J Zwaan, and Paul M Brakefield PMCID: PMC2322975 Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? Stefanie Hartmann and Todd J Vision PMCID: PMC2359737 Evolution of the DAZ gene and the AZFc region on primate Y chromosomes Yueh-Hsiang Yu, Yi-Wen Lin, Jane-Fang Yu, Werner Schempp, and Pauline H Yen PMCID: PMC2322974 Influence of continental history on the ecological specialization and macroevolutionary processes in the mammalian assemblage of South America: Differences between small and large mammals Ana Moreno Bofarull, Antón Arias Royo, Manuel Hernández Fernández, Edgardo Ortiz-Jaureguizar, and Jorge Morales PMCID: PMC2330041 Gene flow persists millions of years after speciation in Heliconius butterflies Marcus R Kronforst PMCID: PMC2322973 Both selective and neutral processes drive GC content evolution in the human genome Uberto Pozzoli, Giorgia Menozzi, Matteo Fumagalli, Matteo Cereda, Giacomo P Comi, Rachele Cagliani, Nereo Bresolin, and Manuela Sironi PMCID: PMC2292697 Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation Guislaine Refrégier, Mickaël Le Gac, Florian Jabbour, Alex Widmer, Jacqui A Shykoff, Roxana Yockteng, Michael E Hood, and Tatiana Giraud PMCID: PMC2324105 The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions Noeleen B Loughran, Brendan O'Connor, Ciarán Ó'Fágáin, and Mary J O'Connell PMCID: PMC2315650 Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses Céline Poux, Ole Madsen, Julian Glos, Wilfried W de Jong, and Miguel Vences PMCID: PMC2330147 Evolution of pharmacologic specificity in the pregnane X receptor Sean Ekins, Erica J Reschly, Lee R Hagey, and Matthew D Krasowski PMCID: PMC2358886 Costs and benefits of multiple resistance to insecticides for Culex quinquefasciatus mosquitoes Claire Berticat, Julien Bonnet, Stéphane Duchon, Philip Agnew, Mylène Weill, and Vincent Corbel PMCID: PMC2359736 GPR50 is the mammalian ortholog of Mel1c: Evidence of rapid evolution in mammals Laurence Dufourny, Anthony Levasseur, Martine Migaud, Isabelle Callebaut, Pierre Pontarotti, Benoit Malpaux, and Philippe Monget PMCID: PMC2323367 Reducing the false positive rate in the non-parametric analysis of molecular coevolution Francisco M Codoñer, Shirley O'Dea, and Mario A Fares PMCID: PMC2362121 Phylogenetic distribution of large-scale genome patchiness José L Oliver, Pedro Bernaola-Galván, Michael Hackenberg, and Pedro Carpena PMCID: PMC2397391 Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria Chih-Horng Kuo and Jessica C Kissinger PMCID: PMC2330040 The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa Lotta Wik, Magnus Karlsson, and Hanna Johannesson PMCID: PMC2335104 The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses Nicolas Delaroque and Wilhelm Boland PMCID: PMC2373305 The evolution of protostome GATA factors: Molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships William Q Gillis, Bruce A Bowerman, and Stephan Q Schneider PMCID: PMC2383905 Directional and balancing selection in human beta-defensins Edward J Hollox and John AL Armour PMCID: PMC2373304 Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae) Hinrich Schulenburg and Claudia Boehnisch PMCID: PMC2383907 Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins Michal Grunt, Viktor Žárský, and Fatima Cvrčková PMCID: PMC2386819 Evidence of a chimeric genome in the cyanobacterial ancestor of plastids Jeferson Gross, Jörg Meurer, and Debashish Bhattacharya PMCID: PMC2412073 A theoretical quantitative genetic study of negative ecological interactions and extinction times in changing environments Adam G Jones PMCID: PMC2386129 Evolution of the insect Sox genes Megan J Wilson and Peter K Dearden PMCID: PMC2386450 DNA from extinct giant lemurs links archaeolemurids to extant indriids Ludovic Orlando, Sébastien Calvignac, Céline Schnebelen, Christophe J Douady, Laurie R Godfrey, and Catherine Hänni PMCID: PMC2386821 Hybridization produces novelty when the mapping of form to function is many to one Nicholas F Parnell, C Darrin Hulsey, and J Todd Streelman PMCID: PMC2386449 Polymorphism at the apical membrane antigen 1 locus reflects the world population history of Plasmodium vivax Priscila Grynberg, Cor Jesus F Fontes, Austin L Hughes, and Érika M Braga PMCID: PMC2394524 Mortality selection during the 2003 European heat wave in three-spined sticklebacks: effects of parasites and MHC genotype K Mathias Wegner, Martin Kalbe, Manfred Milinski, and Thorsten BH Reusch PMCID: PMC2386451 On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans Laurence Loewe and Asher D Cutter PMCID: PMC2408595 Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny Keren-Or Amar, Nanette E Chadwick, and Baruch Rinkevich PMCID: PMC2391163 Gene Structure Evolution of the Na+-Ca2+ Exchanger (NCX) Family Caly On, Christian R Marshall, Nansheng Chen, Christopher D Moyes, and Glen F Tibbits PMCID: PMC2408596 Experimental manipulation of immune-mediated disease and its fitness costs for rodent malaria parasites Gráinne H Long, Brian HK Chan, Judith E Allen, Andrew F Read, and Andrea L Graham PMCID: PMC2391164 The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis N Kamesh, Gopala K Aradhyam, and Narayanan Manoj PMCID: PMC2396169 The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates Skip R McCoy, Jennifer V Kuehl, Jeffrey L Boore, and Linda A Raubeson PMCID: PMC2386820 The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates Virginie Daburon, Sébastien Mella, Jean-Louis Plouhinec, Sylvie Mazan, Michèle Crozatier, and Alain Vincent PMCID: PMC2394523 Gene flow and the genealogical history of Heliconius heurippa Camilo Salazar, Chris D Jiggins, Jesse E Taylor, Marcus R Kronforst, and Mauricio Linares PMCID: PMC2391162 Selection dramatically reduces effective population size in HIV-1 infection Yi Liu and John E Mittler PMCID: PMC2396635 The spread of incompatibility-inducing parasites in sub-divided host populations Max Reuter, Laurent Lehmann, and Frédéric Guillaume PMCID: PMC2396168 Oldest record of Trimeniaceae from the Early Cretaceous of northern Japan Toshihiro Yamada, Harufumi Nishida, Masayoshi Umebayashi, Kazuhiko Uemura, and Masahiro Kato PMCID: PMC2390519 Unexpected diversity of cnidarian integrins: expression during coral gastrulation Brent A Knack, Akira Iguchi, Chuya Shinzato, David C Hayward, Eldon E Ball, and David J Miller PMCID: PMC2397394 Reproductive isolation, evolutionary distinctiveness and setting conservation priorities: The case of European lake whitefish and the endangered North Sea houting (Coregonus spp.) Michael M Hansen, Dylan J Fraser, Thomas D Als, and Karen-Lise D Mensberg PMCID: PMC2396634 Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10 Jarl A Anmarkrud, Oddmund Kleven, Lutz Bachmann, and Jan T Lifjeld PMCID: PMC2396632 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: PMC2396633 The relative nature of fertilization success: Implications for the study of post-copulatory sexual selection Francisco García-González PMCID: PMC2408597 Multilocus analysis of introgression between two sand fly vectors of leishmaniasis Camila J Mazzoni, Alejandra S Araki, Gabriel EM Ferreira, Renata VDM Azevedo, Guido Barbujani, and Alexandre A Peixoto PMCID: PMC2413237 RPS4Y gene family evolution in primates Olga Andrés, Thomas Kellermann, Francesc López-Giráldez, Julio Rozas, Xavier Domingo-Roura, and Montserrat Bosch PMCID: PMC2397393 Evolution of testicular architecture in the Drosophilidae: A role for sperm length Lukas Schärer, Jean-Luc Da Lage, and Dominique Joly PMCID: PMC2396631 AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota Mirjam MJ Jacobs, Ronald G van den Berg, Vivianne GAA Vleeshouwers, Marcel Visser, Rolf Mank, Mariëlle Sengers, Roel Hoekstra, and Ben Vosman PMCID: PMC2413236 Paternal genetic affinity between western Austronesians and Daic populations Hui Li, Bo Wen, Shu-Juo Chen, Bing Su, Patcharin Pramoonjago, Yangfan Liu, Shangling Pan, Zhendong Qin, Wenhong Liu, Xu Cheng, Ningning Yang, Xin Li, Dinhbinh Tran, Daru Lu, Mu-Tsu Hsu, Ranjan Deka, Sangkot Marzuki, Chia-Chen Tan, and Li Jin PMCID: PMC2408594 Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context Iñaki Comas, Fernando González-Candelas, and Manuel Zúñiga PMCID: PMC2405797 The Xenopus FcR family demonstrates continually high diversification of paired receptors in vertebrate evolution Sergey V Guselnikov, Thaminda Ramanayake, Aleksandra Y Erilova, Ludmila V Mechetina, Alexander M Najakshin, Jacques Robert, and Alexander V Taranin PMCID: PMC2413239 Testing a hypothesis of unidirectional hybridization in plants: Observations on Sonneratia, Bruguiera and Ligularia Renchao Zhou, Xun Gong, David Boufford, Chung-I Wu, and Suhua Shi PMCID: PMC2409324 Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations Jochen BW Wolf, Chris Harrod, Sylvia Brunner, Sandie Salazar, Fritz Trillmich, and Diethard Tautz PMCID: PMC2408593 Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes Shinichiro Maruyama, Kazuharu Misawa, Mineo Iseki, Masakatsu Watanabe, and Hisayoshi Nozaki PMCID: PMC2416651 Landforms predict phylogenetic structure on one of the world's most ancient surfaces Mitzy Pepper, Paul Doughty, Richard Arculus, and J Scott Keogh PMCID: PMC2397392 Origins of asexuality in Bryobia mites (Acari: Tetranychidae) Vera ID Ros, Johannes AJ Breeuwer, and Steph BJ Menken PMCID: PMC2426695 Evidence against the energetic cost hypothesis for the short introns in highly expressed genes Yi-Fei Huang and Deng-Ke Niu PMCID: PMC2424036 Bending for love: losses and gains of sexual dimorphisms are strictly correlated with changes in the mounting position of sepsid flies (Sepsidae: Diptera) Nalini Puniamoorthy, Kathy Feng-Yi Su, and Rudolf Meier PMCID: PMC2409323 Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture David Roy Smith and Robert W Lee PMCID: PMC2412866 Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean Luiz A Rocha, Claudia R Rocha, D Ross Robertson, and Brian W Bowen PMCID: PMC2423375 The prevalence of genome replacement in unisexual salamanders of the genus Ambystoma (Amphibia, Caudata) revealed by nuclear gene genealogy Ke Bi, James P Bogart, and Jinzhong Fu PMCID: PMC2413238 Molecular evolution of Cide family proteins: Novel domain formation in early vertebrates and the subsequent divergence Congyang Wu, Yinxin Zhang, Zhirong Sun, and Peng Li PMCID: PMC2426694 Integration, heterochrony, and adaptation in pedal digits of syndactylous marsupials Vera Weisbecker and Maria Nilsson PMCID: PMC2430710 Evolutionary history of the endangered fish Zoogoneticus quitzeoensis (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data Omar Domínguez-Domínguez, Fernando Alda, Gerardo Pérez-Ponce de León, José Luis García-Garitagoitia, and Ignacio Doadrio PMCID: PMC2435552 Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations Björn M Hallström and Axel Janke PMCID: PMC2435553 Evolution of the CDKN1C-KCNQ1 imprinted domain Eleanor I Ager, Andrew J Pask, Helen M Gehring, Geoff Shaw, and Marilyn B Renfree PMCID: PMC2427030 Genetic hitchhiking in a subdivided population of Mytilus edulis Matthieu F Faure, Patrice David, François Bonhomme, and Nicolas Bierne PMCID: PMC2459173 Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection Eric G Chapman, Helen Piontkivska, Jennifer M Walker, Donald T Stewart, Jason P Curole, and Walter R Hoeh PMCID: PMC2430956 Developmental expression of the alpha-skeletal actin gene Laura D Bertola, Elisabeth B Ott, Sander Griepsma, Freek J Vonk, and Christoph P Bagowski PMCID: PMC2443135 Mutation patterns of mtDNA: Empirical inferences for the coding region Cristina Santos, Rafael Montiel, Adriana Arruda, Luis Alvarez, Maria Pilar Aluja, and Manuela Lima PMCID: PMC2438339 Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family Nupur Oswal, Narinder Singh Sahni, Alok Bhattacharya, Sneha Sudha Komath, and Rohini Muthuswami PMCID: PMC2446393 Phylogenetic studies of the genus Cebus (Cebidae-Primates) using chromosome painting and G-banding PJS Amaral, LFM Finotelo, EHC De Oliveira, A Pissinatti, CY Nagamachi, and JC Pieczarka PMCID: PMC2435554 atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-Helix-Loop-Helix genes Elena Simionato, Pierre Kerner, Nicolas Dray, Martine Le Gouar, Valérie Ledent, Detlev Arendt, and Michel Vervoort PMCID: PMC2435551 Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates Karl R Wotton, Frida K Weierud, Susanne Dietrich, and Katharine E Lewis PMCID: PMC2446394 Dopamine receptor genetic polymorphisms and body composition in undernourished pastoralists: An exploration of nutrition indices among nomadic and recently settled Ariaal men of northern Kenya Dan TA Eisenberg, Benjamin Campbell, Peter B Gray, and Michael D Sorenson PMCID: PMC2440754 Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken Sriramana Kanginakudru, Muralidhar Metta, RD Jakati, and J Nagaraju PMCID: PMC2474866 The tiny Hairless protein from Apis mellifera: a potent antagonist of Notch signaling in Drosophila melanogaster Dieter Maier, Anna X Chen, Anette Preiss, and Manuela Ketelhut PMCID: PMC2440387 Evolution of C2H2-zinc finger genes and subfamilies in mammals: Species-specific duplication and loss of clusters, genes and effector domains Hamsa D Tadepally, Gertraud Burger, and Muriel Aubry PMCID: PMC2443715 The medaka novel immune-type receptor (NITR) gene clusters reveal an extraordinary degree of divergence in variable domains Salil Desai, Amy K Heffelfinger, Timothy M Orcutt, Gary W Litman, and Jeffrey A Yoder PMCID: PMC2442602 Diversification of myco-heterotrophic angiosperms: Evidence from Burmanniaceae Vincent Merckx, Lars W Chatrou, Benny Lemaire, Moses N Sainge, Suzy Huysmans, and Erik F Smets PMCID: PMC2492876 Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene Zoe R Donaldson, Fyodor A Kondrashov, Andrea Putnam, Yaohui Bai, Tara L Stoinski, Elizabeth AD Hammock, and Larry J Young PMCID: PMC2483724 Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis David A Fitzpatrick, Mary E Logue, and Geraldine Butler PMCID: PMC2459174 Male-biased genes are overrepresented among novel Drosophila pseudoobscura sex-biased genes Muralidhar Metta and Christian Schlötterer PMCID: PMC2443716 Identification of geographically distributed sub-populations of Leishmania (Leishmania) major by microsatellite analysis Amer Al-Jawabreh, Stephanie Diezmann, Michaela Müller, Thierry Wirth, Lionel F Schnur, Margarita V Strelkova, Dmitri A Kovalenko, Shavkat A Razakov, Jan Schwenkenbecher, Katrin Kuhls, and Gabriele Schönian PMCID: PMC2447845 Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions Tomas A Larsson, Frida Olsson, Gorel Sundstrom, Lars-Gustav Lundin, Sydney Brenner, Byrappa Venkatesh, and Dan Larhammar PMCID: PMC2453138 On the nature of fur evolution: A phylogenetic approach in Actinobacteria Catarina L Santos, João Vieira, Fernando Tavares, David R Benson, Louis S Tisa, Alison M Berry, Pedro Moradas-Ferreira, and Philippe Normand PMCID: PMC2464607 Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects Aleah K Fox, Brian B Tuch, and Jeffrey H Chuang PMCID: PMC2447844 The genetic architecture of susceptibility to parasites Lena Wilfert and Paul Schmid-Hempel PMCID: PMC2446395 Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations Heather A Jackson and Eric A Accili PMCID: PMC2483723 Color signaling in conspicuous red sticklebacks: do ultraviolet signals surpass others? Ingolf P Rick and Theo CM Bakker PMCID: PMC2453139 Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi Chendhore S Veerappan, Zoya Avramova, and Etsuko N Moriyama PMCID: PMC2474616 Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East Anita Brandstätter, Bettina Zimmermann, Janine Wagner, Tanja Göbel, Alexander W Röck, Antonio Salas, Angel Carracedo, and Walther Parson PMCID: PMC2491632 Adaptive evolution of SCML1 in primates, a gene involved in male reproduction Hai-hui Wu and Bing Su PMCID: PMC2459175 Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes Frank E Rheindt, Les Christidis, and Janette A Norman PMCID: PMC2467406 Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins David H Lunt PMCID: PMC2478646 High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Beta genes Pille Hallast, Janna Saarela, Aarno Palotie, and Maris Laan PMCID: PMC2478647 Accelerated exchange of exon segments in Viperid three-finger toxin genes (Sistrurus catenatus edwardsii; Desert Massasauga) Robin Doley, Susanta Pahari, Stephen P Mackessy, and R Manjunatha Kini PMCID: PMC2474615 Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna Jérôme Fuchs, Jean-Marc Pons, Steven M Goodman, Vincent Bretagnolle, Martim Melo, Rauri CK Bowie, David Currie, Roger Safford, Munir Z Virani, Simon Thomsett, Alawi Hija, Corinne Cruaud, and Eric Pasquet PMCID: PMC2483963 The origin and evolution of plant cystatins and their target cysteine proteinases indicate a complex functional relationship Manuel Martinez and Isabel Diaz PMCID: PMC2474614 Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily Emilie Lecompte, Ken Aplin, Christiane Denys, François Catzeflis, Marion Chades, and Pascale Chevret PMCID: PMC2490707 Protein evolution of ANTP and PRD homeobox genes Nuno A Fonseca, Cristina P Vieira, Peter WH Holland, and Jorge Vieira PMCID: PMC2491631 Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences Liang Zhao, Jie Zhang, Zhijin Liu, Stephan M Funk, Fuwen Wei, Muqi Xu, and Ming Li PMCID: PMC2483725 Using supernetworks to distinguish hybridization from lineage-sorting Barbara R Holland, Steffi Benthin, Peter J Lockhart, Vincent Moulton, and Katharina T Huber PMCID: PMC2500029 Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes Burkhard Becker, Kerstin Hoef-Emden, and Michael Melkonian PMCID: PMC2490706 Nuptial gifts fail to resolve a sexual conflict in an insect Nina Wedell, Tom Tregenza, and Leigh W Simmons PMCID: PMC2491630 Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads Martin Kolisko, Ivan Cepicka, Vladimir Hampl, Jessica Leigh, Andrew J Roger, Jaroslav Kulda, Alastair GB Simpson, and Jaroslav Flegr PMCID: PMC2496913 Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes Simon Duval, Anne-Lise Ducluzeau, Wolfgang Nitschke, and Barbara Schoepp-Cothenet PMCID: PMC2500031 Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection Samuel Ojosnegros, Rubén Agudo, Macarena Sierra, Carlos Briones, Saleta Sierra, Claudia González- López, Esteban Domingo, and Juan Cristina PMCID: PMC2515104 Differences in evolutionary pressure acting within highly conserved ortholog groups Teresa M Przytycka, Raja Jothi, L Aravind, and David J Lipman PMCID: PMC2488352 Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, Miniopterus schreibersii (Chiroptera: Vespertilionidae) Raşit Bilgin, Ahmet Karataş, Emrah Çoraman, Todd Disotell, and Juan Carlos Morales PMCID: PMC2483726 The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites Matthew N Ward, Allison M Churcher, Kevin J Dick, Chris RJ Laver, Greg L Owens, Megan D Polack, Pam R Ward, Felix Breden, and John S Taylor PMCID: PMC2527612 The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses Xuhua Xia PMCID: PMC2488353 A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification? Yusuke Yamanoue, Masaki Miya, Keiichi Matsuura, Masaya Katoh, Harumi Sakai, and Mutsumi Nishida PMCID: PMC2500030 Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba Isabel Mendizabal, Karla Sandoval, Gemma Berniell-Lee, Francesc Calafell, Antonio Salas, Antonio Martínez-Fuentes, and David Comas PMCID: PMC2492877 Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family Jari Intra, Giulio Pavesi, and David S Horner PMCID: PMC2492878 Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences Yoichiro Azuma, Yoshinori Kumazawa, Masaki Miya, Kohji Mabuchi, and Mutsumi Nishida PMCID: PMC2496912 Genetic evidence links invasive monk parakeet populations in the United States to the international pet trade Michael A Russello, Michael L Avery, and Timothy F Wright PMCID: PMC2517076 ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales) Alexander Keller, Tina Schleicher, Frank Förster, Benjamin Ruderisch, Thomas Dandekar, Tobias Müller, and Matthias Wolf PMCID: PMC2519086 An amphioxus orthologue of the estrogen receptor that does not bind estradiol: Insights into estrogen receptor evolution Mathilde Paris, Katarina Pettersson, Michael Schubert, Stephanie Bertrand, Ingemar Pongratz, Hector Escriva, and Vincent Laudet PMCID: PMC2529310 Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary Johannes Krause, Tina Unger, Aline Noçon, Anna-Sapfo Malaspinas, Sergios-Orestis Kolokotronis, Mathias Stiller, Leopoldo Soibelzon, Helen Spriggs, Paul H Dear, Adrian W Briggs, Sarah CE Bray, Stephen J O'Brien, Gernot Rabeder, Paul Matheus, Alan Cooper, Montgomery Slatkin, Svante Pääbo, and Michael Hofreiter PMCID: PMC2518930 Tracing the first steps of American sturgeon pioneers in Europe Arne Ludwig, Ursula Arndt, Sebastian Lippold, Norbert Benecke, Lutz Debus, Timothy L King, and Shuichi Matsumura PMCID: PMC2527320 On the origins of arrestin and rhodopsin Carlos E Alvarez PMCID: PMC2515105 Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents Franck Prugnolle, Kate McGee, Jon Keebler, and Philip Awadalla PMCID: PMC2529309 Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures Nina Stoletzki PMCID: PMC2533328 Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties Marco Sardiello, Stefano Cairo, Bianca Fontanella, Andrea Ballabio, and Germana Meroni PMCID: PMC2533329 Identification and characterization of novel human tissue-specific RFX transcription factors Syed Aftab, Lucie Semenec, Jeffrey Shih-Chieh Chu, and Nansheng Chen PMCID: PMC2533330 Phylogeography of mtDNA haplogroup R7 in the Indian peninsula Gyaneshwer Chaubey, Monika Karmin, Ene Metspalu, Mait Metspalu, Deepa Selvi-Rani, Vijay Kumar Singh, Jüri Parik, Anu Solnik, B Prathap Naidu, Ajay Kumar, Niharika Adarsh, Chandana Basu Mallick, Bhargav Trivedi, Swami Prakash, Ramesh Reddy, Parul Shukla, Sanjana Bhagat, Swati Verma, Samiksha Vasnik, Imran Khan, Anshu Barwa, Dipti Sahoo, Archana Sharma, Mamoon Rashid, Vishal Chandra, Alla G Reddy, Antonio Torroni, Robert A Foley, Kumarasamy Thangaraj, Lalji Singh, Toomas Kivisild, and Richard Villems PMCID: PMC2529308 The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans James C Sullivan, Daniel Sher, Miriam Eisenstein, Katsuya Shigesada, Adam M Reitzel, Heather Marlow, Ditsa Levanon, Yoram Groner, John R Finnerty, and Uri Gat PMCID: PMC2527000 Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni Eduardo N Taboada, Joanne M MacKinnon, Christian C Luebbert, Victor PJ Gannon, John HE Nash, and Kris Rahn PMCID: PMC2527321 The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage Satish Kumar, PBSV Padmanabham, Rajasekhara R Ravuri, Kiran Uttaravalli, Padmaja Koneru, P Aditi Mukherjee, B Das, M Kotal, D Xaviour, SY Saheb, and VR Rao PMCID: PMC2528015 Robustness promotes evolvability of thermotolerance in an RNA virus Robert C McBride, C Brandon Ogbunugafor, and Paul E Turner PMCID: PMC2518931 Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants Nikolaos Georgelis, Edward L Braun, and L Curtis Hannah PMCID: PMC2529307 Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes Renato H Orsi, Qi Sun, and Martin Wiedmann PMCID: PMC2532693 Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura María Pilar García Guerreiro, Blanca E Chávez-Sandoval, Joan Balanyà, Lluís Serra, and Antonio Fontdevila PMCID: PMC2533020 Drift by drift: effective population size is limited by advection John P Wares and James M Pringle PMCID: PMC2536672 Male sexual ornament size is positively associated with reproductive morphology and enhanced fertility in the stalk-eyed fly Teleopsis dalmanni David W Rogers, Matthew Denniff, Tracey Chapman, Kevin Fowler, and Andrew Pomiankowski PMCID: PMC2562384 A DNA and morphology based phylogenetic framework of the ant genus Lasius with hypotheses for the evolution of social parasitism and fungiculture Munetoshi Maruyama, Florian M Steiner, Christian Stauffer, Toshiharu Akino, Ross H Crozier, and Birgit C Schlick-Steiner PMCID: PMC2542377 The coevolution of cooperation and dispersal in social groups and its implications for the emergence of multicellularity Michael E Hochberg, Daniel J Rankin, and Michael Taborsky PMCID: PMC2533331 Genetic structure and breeding system in a social wasp and its social parasite Eric A Hoffman, Jennifer L Kovacs, and Michael AD Goodisman PMCID: PMC2533669 The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis Eva Bellemain, Eldredge Bermingham, and Robert E Ricklefs PMCID: PMC2533019 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: PMC2528016 Sexual conflict and consistency of offspring desertion in Eurasian penduline tit Remiz pendulinus Ákos Pogány, István Szentirmai, Jan Komdeur, and Tamás Székely PMCID: PMC2535784 Male-killing endosymbionts: influence of environmental conditions on persistence of host metapopulation Dries Bonte, Thomas Hovestadt, and Hans-Joachim Poethke PMCID: PMC2546409 Tracking the evolution of a cold stress associated gene family in cold tolerant grasses Simen R Sandve, Heidi Rudi, Torben Asp, and Odd Arne Rognli PMCID: PMC2542378 Hen's teeth with enamel cap: from dream to impossibility Jean-Yves Sire, Sidney C Delgado, and Marc Girondot PMCID: PMC2542379 Metabolic innovations towards the human lineage Shiri Freilich, Leon Goldovsky, Christos A Ouzounis, and Janet M Thornton PMCID: PMC2553087 Meta-population structure in a coral reef fish demonstrated by genetic data on patterns of migration, extinction and re-colonisation Line K Bay, M Julian M Caley, and Ross H Crozier PMCID: PMC2553088 Testing whether macroevolution follows microevolution: Are colour differences among swans (Cygnus) attributable to variation at the MC1R locus? Marie A Pointer and Nicholas I Mundy PMCID: PMC2553801 Ancestry and evolution of a secretory pathway serpin Abhishek Kumar and Hermann Ragg PMCID: PMC2556349 Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839) Elena G Gonzalez, Peter Beerli, and Rafael Zardoya PMCID: PMC2559848 Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis Yves Bigot, Sylvie Samain, Corinne Augé-Gouillou, and Brian A Federici PMCID: PMC2567993 Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters Görel Sundström, Tomas A Larsson, and Dan Larhammar PMCID: PMC2566581 Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera Ave Tooming-Klunderud, David P Fewer, Thomas Rohrlack, Jouni Jokela, Leo Rouhiainen, Kaarina Sivonen, Tom Kristensen, and Kjetill S Jakobsen PMCID: PMC2564945 Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota) H Thorsten Lumbsch, Andrew L Hipp, Pradeep K Divakar, Oscar Blanco, and Ana Crespo PMCID: PMC2564941 Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: Tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes Anne Harduin-Lepers, Daniel Petit, Rosella Mollicone, Philippe Delannoy, Jean-Michel Petit, and Rafael Oriol PMCID: PMC2564942 Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication Angèle Tingaud-Sequeira, François Chauvigné, Mercedes Fabra, Juanjo Lozano, Demetrio Raldúa, and Joan Cerdà PMCID: PMC2564943 Ultraconserved coding regions outside the homeobox of mammalian Hox genes Zhenguo Lin, Hong Ma, and Masatoshi Nei PMCID: PMC2566984 Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies Christina D Fetterman, Bruce Rannala, and Michael A Walter PMCID: PMC2570691 A stochastic version of the Price equation reveals the interplay of deterministic and stochastic processes in evolution Sean H Rice PMCID: PMC2577117 Chromosomal evolution of the PKD1 gene family in primates Stefan Kirsch, Juanjo Pasantes, Andreas Wolf, Nadia Bogdanova, Claudia Münch, Petra Pennekamp, Michael Krawczak, Bernd Dworniczak, and Werner Schempp PMCID: PMC2564946 Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae) James B Pettengill and Maile C Neel PMCID: PMC2564944 Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution Anders L Kjeldbjerg, Palle Villesen, Lars Aagaard, and Finn Skou Pedersen PMCID: PMC2567338 Prebiotic replicase evolution in a surface-bound metabolic system: parasites as a source of adaptive evolution Balázs Könnyű, Tamás Czárán, and Eörs Szathmáry PMCID: PMC2575217 D- and L-lactate dehydrogenases during invertebrate evolution Melania E Cristescu, David J Innes, Jonathon H Stillman, and Teresa J Crease PMCID: PMC2570690 Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids Claudia Münch, Stefan Kirsch, António MG Fernandes, and Werner Schempp PMCID: PMC2566985 Key biosynthetic gene subfamily recruited for pheromone production prior to the extensive radiation of Lepidoptera Marjorie A Liénard, Maria Strandh, Erik Hedenström, Tomas Johansson, and Christer Löfstedt PMCID: PMC2584044 Genetic conflict outweighs heterogametic incompatibility in the mouse hybrid zone? Miloš Macholán, Stuart JE Baird, Pavel Munclinger, Petra Dufková, Barbora Bímová, and Jaroslav Piálek PMCID: PMC2576241 Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria Bastien Boussau, Laurent Guéguen, and Manolo Gouy PMCID: PMC2584045 The role of positive selection in determining the molecular cause of species differences in disease Jessica J Vamathevan, Samiul Hasan, Richard D Emes, Heather Amrine-Madsen, Dilip Rajagopalan, Simon D Topp, Vinod Kumar, Michael Word, Mark D Simmons, Steven M Foord, Philippe Sanseau, Ziheng Yang, and Joanna D Holbrook PMCID: PMC2576240 The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae Darren J Obbard, Deborah M Callister, Francis M Jiggins, Dinesh C Soares, Guiyun Yan, and Tom J Little PMCID: PMC2576239 Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis Carlos Llorens, Mario A Fares, and Andres Moya PMCID: PMC2577118 Lineage specific recombination rates and microevolution in Listeria monocytogenes Henk C den Bakker, Xavier Didelot, Esther D Fortes, Kendra K Nightingale, and Martin Wiedmann PMCID: PMC2576243 The IGS-ETS in Bacillus (Insecta Phasmida): molecular characterization and the relevance of sex in ribosomal DNA evolution Andrea Ricci, Valerio Scali, and Marco Passamonti PMCID: PMC2590618 The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification David Hoogewijs, Sasha De Henau, Sylvia Dewilde, Luc Moens, Marjolein Couvreur, Gaetan Borgonie, Serge N Vinogradov, Scott W Roy, and Jacques R Vanfleteren PMCID: PMC2576238 Unique genes in plants: specificities and conserved features throughout evolution David Armisén, Alain Lecharny, and Sébastien Aubourg PMCID: PMC2576244 Genetic hitchhiking can promote the initial spread of strong altruism Mauro Santos and Eörs Szathmáry PMCID: PMC2580771 Signatures of selection in natural populations adapted to chronic pollution Larissa M Williams and Marjorie F Oleksiak PMCID: PMC2570689 Intraspecific divergence in sperm morphology of the green sea urchin, Strongylocentrotus droebachiensis: implications for selection in broadcast spawners Mollie K Manier and Stephen R Palumbi PMCID: PMC2613923 The effect of genetic robustness on evolvability in digital organisms Santiago F Elena and Rafael Sanjuán PMCID: PMC2588588 Just how versatile are domains? January Weiner, 3rd, Andrew D Moore, and Erich Bornberg-Bauer PMCID: PMC2588589 The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands Christian Radauer, Peter Lackner, and Heimo Breiteneder PMCID: PMC2577659 The evolution of prompt reaction to adverse ties Sven Van Segbroeck, Francisco C Santos, Ann Nowé, Jorge M Pacheco, and Tom Lenaerts PMCID: PMC2576237 Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance Oliver C Jann, Dirk Werling, Jung-Su Chang, David Haig, and Elizabeth J Glass PMCID: PMC2588590 Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components Gemma C Atkinson, Sandra L Baldauf, and Vasili Hauryliuk PMCID: PMC2613156 Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis Yves Deveaux, Claire Toffano-Nioche, Gaelle Claisse, Vincent Thareau, Halima Morin, Patrick Laufs, Hervé Moreau, Martin Kreis, and Alain Lecharny PMCID: PMC2584047 The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination Alain Devault and Anne-Laure Bañuls PMCID: PMC2584048 Segregate or cooperate- a study of the interaction between two species of Dictyostelium Chandra N Jack, Julia G Ridgeway, Natasha J Mehdiabadi, Emily I Jones, Tracy A Edwards, David C Queller, and Joan E Strassmann PMCID: PMC2579437 Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence Xiaofan Zhou and Hong Ma PMCID: PMC2579438 The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice T Bilde, U Friberg, AA Maklakov, JD Fry, and G Arnqvist PMCID: PMC2596129 Island selection on mammalian life-histories: genetic differentiation in offspring size Tapio Mappes, Alessandro Grapputo, Harri Hakkarainen, Esa Huhta, Esa Koskela, Raimo Saunanen, and Petri Suorsa PMCID: PMC2584046 A homogenous nature of native Chinese duck matrilineal pool Da-Qian He, Qing Zhu, Shi-Yi Chen, Hui-Ying Wang, Yi-Ping Liu, and Yong-Gang Yao PMCID: PMC2586638 Factors affecting the concordance between orthologous gene trees and species tree in bacteria Santiago Castillo-Ramírez and Víctor González PMCID: PMC2614993 Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae) David J Lohman, Djunijanti Peggie, Naomi E Pierce, and Rudolf Meier PMCID: PMC2613918 Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids Jose V Llorens, Jonathan B Clark, Isabel Martínez-Garay, Sirena Soriano, Rosa de Frutos, and María J Martínez-Sebastián PMCID: PMC2585583 Sex dependent imprinting effects on complex traits in mice Reinmar Hager, James M Cheverud, Larry J Leamy, and Jason B Wolf PMCID: PMC2605465 Evolutionary conservation of dual Sec translocases in the cyanelles of Cyanophora paradoxa Fumie Yusa, Jürgen M Steiner, and Wolfgang Löffelhardt PMCID: PMC2600650 Evolutionary history of the UCP gene family: gene duplication and selection Joseph Hughes and Francois Criscuolo PMCID: PMC2584656 Molecular evolution of synonymous codon usage in Populus Pär K Ingvarsson PMCID: PMC2586637 Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America Daniela Milstein, Mariana C Oliveira, Felipe M Martins, and Sergio R Matioli PMCID: PMC2585584 Rapid and repeated limb loss in a clade of scincid lizards Adam Skinner, Michael SY Lee, and Mark N Hutchinson PMCID: PMC2596130 Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa Chuya Shinzato, Akira Iguchi, David C Hayward, Ulrich Technau, Eldon E Ball, and David J Miller PMCID: PMC2613919 The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods Angela McCann, James A Cotton, and James O McInerney PMCID: PMC2592249 Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates Stefano Campanaro, Laura Treu, and Giorgio Valle PMCID: PMC2600651 Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria Lori S Eggert, Lauren A Terwilliger, Bethany L Woodworth, Patrick J Hart, Danielle Palmer, and Robert C Fleischer PMCID: PMC2613920 Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster Andrew C Doxey, Michael DJ Lynch, Kirsten M Müller, Elizabeth M Meiering, and Brendan J McConkey PMCID: PMC2605760 Genetic diversity in two sibling species of the Anopheles punctulatus group of mosquitoes on Guadalcanal in the Solomon Islands Arif U Hasan, Setsuo Suguri, Chigusa Fujimoto, Rodney L Itaki, Masakazu Harada, Masato Kawabata, Hugo Bugoro, and Bobogare Albino PMCID: PMC2612007 Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses Jonathan Filée, Noëlle Pouget, and Mick Chandler PMCID: PMC2607284 Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments Claudine Montgelard, Ellen Forty, Véronique Arnal, and Conrad A Matthee PMCID: PMC2613922 Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae) Marlene Neethling, Conrad A Matthee, Rauri CK Bowie, and Sophie von der Heyden PMCID: PMC2613416 Female-driven mechanisms, ejaculate size and quality contribute to the lower fertility of sex-ratio distorter males in Drosophila simulans Caroline Angelard, Catherine Montchamp-Moreau, and Dominique Joly PMCID: PMC2612008 Evolution of the parasitic wasp subfamily Rogadinae (Braconidae): phylogeny and evolution of lepidopteran host ranges and mummy characteristics Alejandro Zaldívar-Riverón, Mark R Shaw, Alberto G Sáez, Miharu Mori, Sergey A Belokoblylskij, Scott R Shaw, and Donald LJ Quicke PMCID: PMC2614994 Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues Sandra Schmieder, Fleur Darré-Toulemonde, Marie-Jeanne Arguel, Audrey Delerue-Audegond, Richard Christen, and Jean-Louis Nahon PMCID: PMC2621205 Methodology Articles Drawing explicit phylogenetic networks and their integration into SplitsTree Tobias H Kloepper and Daniel H Huson PMCID: PMC2253509 Genome classification by gene distribution: An overlapping subspace clustering approach Jason Li, Saman K Halgamuge, and Sen-Lin Tang PMCID: PMC2383906 Rooted triple consensus and anomalous gene trees Gregory B Ewing, Ingo Ebersberger, Heiko A Schmidt, and Arndt von Haeseler PMCID: PMC2409437 Dating the time of viral subtype divergence John D O'Brien, Zhen-Su She, and Marc A Suchard PMCID: PMC2443812 Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise Christophe Dessimoz and Manuel Gil PMCID: PMC2443136 Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals Daniel J Gaffney and Peter D Keightley PMCID: PMC2576242 Patterns of evolutionary constraints on genes in humans Subhajyoti De, Nuria Lopez-Bigas, and Sarah A Teichmann PMCID: PMC2587479 Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach Michael J Hickerson and Christopher P Meyer PMCID: PMC2614435 Correction Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset Jeff W Higdon, Olaf RP Bininda-Emonds, Robin MD Beck, and Steven H Ferguson PMCID: PMC2518141 Corrects: Jeff W Higdon, et al. Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset. BMC Evol Biol. 2007; 7: 216. |
