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Commentary There's something afoot in the evolution of ontogenies Christian Peter Klingenberg PMCID: PMC2927922 Correspondence Nomenclature and placental mammal phylogeny Robert J Asher and Kristofer M Helgen PMCID: PMC2865478 Research articles Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta) Julie A Koester, Jarred E Swalwell, Peter von Dassow, and E Virginia Armbrust PMCID: PMC2821323 Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds Eléonore Durand, Maud I Tenaillon, Céline Ridel, Denis Coubriche, Philippe Jamin, Sophie Jouanne, Adrienne Ressayre, Alain Charcosset, and Christine Dillmann PMCID: PMC2837650 Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae) Lene Martinsen, Arild Johnsen, Federica Venanzetti, and Lutz Bachmann PMCID: PMC2837043 Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes R Craig Albertson, Yi-Lin Yan, Tom A Titus, Eva Pisano, Marino Vacchi, Pamela C Yelick, H William Detrich, III, and John H Postlethwait PMCID: PMC2824663 Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks Rachel S Schwartz and Rachel L Mueller PMCID: PMC2827399 Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop Shi Wang, Lingling Zhang, Jingjie Hu, Zhenmin Bao, and Zhanjiang Liu PMCID: PMC2818637 Biogeography and evolution of the Carassius auratus-complex in East Asia Mikumi Takada, Katsunori Tachihara, Takeshi Kon, Gunji Yamamoto, Kei'ichiro Iguchi, Masaki Miya, and Mutsumi Nishida PMCID: PMC2820001 Molecular evolution of the three short PGRPs of the malaria vectors Anopheles gambiae and Anopheles arabiensis in East Africa Cristina Mendes, Rute Felix, Ana-Margarida Sousa, Joana Lamego, Derek Charlwood, Virgílio E do Rosário, João Pinto, and Henrique Silveira PMCID: PMC2820002 The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata Steven Lockton and Brandon S Gaut PMCID: PMC2837042 Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations Tim F Cooper and Richard E Lenski PMCID: PMC2827396 Population genetics at three spatial scales of a rare sponge living in fragmented habitats Andrea Blanquer and Maria J Uriz PMCID: PMC2818636 Concerted evolution of duplicated mitochondrial control regions in three related seabird species James A Morris-Pocock, Scott A Taylor, Tim P Birt, and Vicki L Friesen PMCID: PMC2820450 The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history Yi Peng, Hong Shi, Xue-bin Qi, Chun-jie Xiao, Hua Zhong, Run-lin Z Ma, and Bing Su PMCID: PMC2823730 Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life Heroen Verbruggen, Christine A Maggs, Gary W Saunders, Line Le Gall, Hwan Su Yoon, and Olivier De Clerck PMCID: PMC2826327 Phylogeography and sexual macrocyst formation in the social amoeba Dictyostelium giganteum Natasha J Mehdiabadi, Marcus R Kronforst, David C Queller, and Joan E Strassmann PMCID: PMC2824659 Historical biogeography of the land snail Cornu aspersum: a new scenario inferred from haplotype distribution in the Western Mediterranean basin Annie Guiller and Luc Madec PMCID: PMC2826328 Altruistic defence behaviours in aphids Gi-Mick Wu, Guy Boivin, Jacques Brodeur, Luc-Alain Giraldeau, and Yannick Outreman PMCID: PMC2823731 Genetic and potential non-genetic benefits increase offspring fitness of polyandrous females in non-resource based mating system Jukka Kekäläinen, Geir Rudolfsen, Matti Janhunen, Lars Figenschou, Nina Peuhkuri, Niina Tamper, and Raine Kortet PMCID: PMC2827397 The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes Dai Suzuki, Matthew C Brandley, and Masayoshi Tokita PMCID: PMC2825197 The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms Juan P Jaramillo-Correa, Miguel Verdú, and Santiago C González-Martínez PMCID: PMC2826329 Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas Paulina Schmitt, Yannick Gueguen, Erick Desmarais, Evelyne Bachère, and Julien de Lorgeril PMCID: PMC2823732 Signature proteins for the major clades of Cyanobacteria Radhey S Gupta and Divya W Mathews PMCID: PMC2823733 Human evolution in Siberia: from frozen bodies to ancient DNA Eric Crubézy, Sylvain Amory, Christine Keyser, Caroline Bouakaze, Martin Bodner, Morgane Gibert, Alexander Röck, Walther Parson, Anatoly Alexeev, and Bertrand Ludes PMCID: PMC2829035 Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships Kathryn E Bushley and B Gillian Turgeon PMCID: PMC2823734 Lineage-specific co-evolution of the Egf receptor/ligand signaling system Juliette AGC Laisney, Ingo Braasch, Ronald B Walter, Svenja Meierjohann, and Manfred Schartl PMCID: PMC2834686 Epigenetic effects on the mouse mandible: common features and discrepancies in remodeling due to muscular dystrophy and response to food consistency Sabrina Renaud, Jean-Christophe Auffray, and Sabine de la Porte PMCID: PMC2827398 Ancient origin of a Western Mediterranean radiation of subterranean beetles Ignacio Ribera, Javier Fresneda, Ruxandra Bucur, Ana Izquierdo, Alfried P Vogler, Jose M Salgado, and Alexandra Cieslak PMCID: PMC2834687 Periostin shows increased evolutionary plasticity in its alternatively spliced region Sebastian Hoersch and Miguel A Andrade-Navarro PMCID: PMC2824660 Evolution of trappin genes in mammals Akira Kato, Alejandro P Rooney, Yutaka Furutani, and Shigehisa Hirose PMCID: PMC2831891 The synapsin gene family in basal chordates: evolutionary perspectives in metazoans Simona Candiani, Luca Moronti, Roberta Pennati, Fiorenza De Bernardi, Fabio Benfenati, and Mario Pestarino PMCID: PMC2825198 Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population Donald Blomqvist, Angela Pauliny, Mikael Larsson, and Lars-Åke Flodin PMCID: PMC2824661 The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans Alexandre Alié and Michaël Manuel PMCID: PMC2824662 Old divergences in a boreal bird supports long-term survival through the Ice Ages Takema Saitoh, Per Alström, Isao Nishiumi, Yoshimitsu Shigeta, Dawn Williams, Urban Olsson, and Keisuke Ueda PMCID: PMC2848155 A worldwide correlation of lactase persistence phenotype and genotypes Yuval Itan, Bryony L Jones, Catherine JE Ingram, Dallas M Swallow, and Mark G Thomas PMCID: PMC2834688 Discovery and identification of a male-killing agent in the Japanese ladybird Propylea japonica (Coleoptera: Coccinellidae) Tamsin MO Majerus and Michael EN Majerus PMCID: PMC2833154 The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals Angèle Tingaud-Sequeira, Magdalena Calusinska, Roderick N Finn, François Chauvigné, Juanjo Lozano, and Joan Cerdà PMCID: PMC2829555 Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins Claire C Morgan, Noeleen B Loughran, Thomas A Walsh, Alan J Harrison, and Mary J O'Connell PMCID: PMC2830953 Structural diversity and evolution of the N-terminal isoform-specific region of ecdysone receptor-A and -B1 isoforms in insects Takayuki Watanabe, Hideaki Takeuchi, and Takeo Kubo PMCID: PMC2829036 Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana Haining Lin, Gaurav Moghe, Shu Ouyang, Amy Iezzoni, Shin-Han Shiu, Xun Gu, and C Robin Buell PMCID: PMC2829037 Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants Ayumu Konno, Shintarou Yonemaru, Atsushi Kitagawa, Koji Muramoto, Tsuyoshi Shirai, and Tomohisa Ogawa PMCID: PMC2843614 The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis Runchun Jing, Alexander Vershinin, Jacek Grzebyta, Paul Shaw, Petr Smýkal, David Marshall, Michael J Ambrose, TH Noel Ellis, and Andrew J Flavell PMCID: PMC2834689 Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae) Thomas Marcussen, Bengt Oxelman, Anna Skog, and Kjetill S Jakobsen PMCID: PMC2834690 Phenotypic effect of mutations in evolving populations of RNA molecules Michael Stich, Ester Lázaro, and Susanna C Manrubia PMCID: PMC2841169 Evolutionary dynamics of U12-type spliceosomal introns Chiao-Feng Lin, Stephen M Mount, Artur Jarmołowski, and Wojciech Makałowski PMCID: PMC2831892 Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia Laura Baldo, Christopher A Desjardins, Jacob A Russell, Julie K Stahlhut, and John H Werren PMCID: PMC2843615 Gene duplication in the genome of parasitic Giardia lamblia Jun Sun, Huifeng Jiang, Roberto Flores, and Jianfan Wen PMCID: PMC2829556 Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA Hélène Doucet-Beaupré, Sophie Breton, Eric G Chapman, Pierre U Blier, Arthur E Bogan, Donald T Stewart, and Walter R Hoeh PMCID: PMC2834691 Functional evolution of the trace amine associated receptors in mammals and the loss of TAAR1 in dogs Eric J Vallender, Zhihua Xie, Susan V Westmoreland, and Gregory M Miller PMCID: PMC2838891 Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites Hiromi Sawai, Hiroto Otani, Nobuko Arisue, Nirianne Palacpac, Leonardo de Oliveira Martins, Sisira Pathirana, Shiroma Handunnetti, Satoru Kawai, Hirohisa Kishino, Toshihiro Horii, and Kazuyuki Tanabe PMCID: PMC2832629 Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions Minoru Hatayama and Jun Aruga PMCID: PMC2837044 Two Frequenins in Drosophila: unveiling the evolutionary history of an unusual Neuronal Calcium Sensor (NCS) duplication Alejandro Sánchez-Gracia, Jesús Romero-Pozuelo, and Alberto Ferrús PMCID: PMC2837045 Retrotransposition and mutation events yield Rap1 GTPases with differential signalling capacity Tomasz Zemojtel, Marlena Duchniewicz, Zhongchun Zhang, Taisa Paluch, Hannes Luz, Tobias Penzkofer, Jürgen S Scheele, and Fried JT Zwartkruis PMCID: PMC2831893 Animal HECT ubiquitin ligases: evolution and functional implications Ignacio Marín PMCID: PMC2837046 Evolution of spliceosomal introns following endosymbiotic gene transfer Nahal Ahmadinejad, Tal Dagan, Nicole Gruenheit, William Martin, and Toni Gabaldón PMCID: PMC2834692 Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective Masaki Miya, Theodore W Pietsch, James W Orr, Rachel J Arnold, Takashi P Satoh, Andrew M Shedlock, Hsuan-Ching Ho, Mitsuomi Shimazaki, Mamoru Yabe, and Mutsumi Nishida PMCID: PMC2836326 Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome Marco Fondi, Giovanni Bacci, Matteo Brilli, Maria Cristiana Papaleo, Alessio Mengoni, Mario Vaneechoutte, Lenie Dijkshoorn, and Renato Fani PMCID: PMC2848654 Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore Hanna M Heidel-Fischer, Heiko Vogel, David G Heckel, and Christopher W Wheat PMCID: PMC2841170 Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels Jill M Duarte, P Kerr Wall, Patrick P Edger, Lena L Landherr, Hong Ma, J Chris Pires, Jim Leebens-Mack, and Claude W dePamphilis PMCID: PMC2848037 Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans Nicolas Montagné, Yves Desdevises, Daniel Soyez, and Jean-Yves Toullec PMCID: PMC2841656 Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.) Kathrin Pascher, Susanne Macalka, Domenico Rau, Günter Gollmann, Helmut Reiner, Josef Glössl, and Georg Grabherr PMCID: PMC2848156 Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes Krishanu Mukherjee, Everly Conway de Macario, Alberto JL Macario, and Luciano Brocchieri PMCID: PMC2846930 The role of phenotypic plasticity on the proteome differences between two sympatric marine snail ecotypes adapted to distinct micro-habitats Mónica Martínez-Fernández, María Páez de la Cadena, and Emilio Rolán-Alvarez PMCID: PMC2841171 Sex-specific population structure, natural selection, and linkage disequilibrium in a wild bird population as revealed by genome-wide microsatellite analyses Meng-Hua Li and Juha Merilä PMCID: PMC2846931 Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus Tyler S Zemlak, Evelyn M Habit, Sandra J Walde, Cecilia Carrea, and Daniel E Ruzzante PMCID: PMC2838892 New insights into the evolution of subtilisin-like serine protease genes in Pezizomycotina Juan Li, Li Yu, Jinkui Yang, Linqian Dong, Baoyu Tian, Zefen Yu, Lianming Liang, Ying Zhang, Xu Wang, and Keqin Zhang PMCID: PMC2848655 A phylogenetic estimate for golden moles (Mammalia, Afrotheria, Chrysochloridae) Robert J Asher, Sarita Maree, Gary Bronner, Nigel C Bennett, Paulette Bloomer, Paul Czechowski, Matthias Meyer, and Michael Hofreiter PMCID: PMC2850353 Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity Achim Meyer, Christiane Todt, Nina T Mikkelsen, and Bernhard Lieb PMCID: PMC2841657 Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii) Bailey D McKay, Herman L Mays, Jr, Yi-Wen Peng, Kenneth H Kozak, Cheng-Te Yao, and Hsiao-Wei Yuan PMCID: PMC2848157 Parallel evolution of character displacement driven by competitive selection in terrestrial salamanders Dean C Adams PMCID: PMC2841172 A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution Morgane Thomas-Chollier, Valérie Ledent, Luc Leyns, and Michel Vervoort PMCID: PMC2842273 Mitochondrial evidence for multiple radiations in the evolutionary history of small apes Van Ngoc Thinh, Alan R Mootnick, Thomas Geissmann, Ming Li, Thomas Ziegler, Muhammad Agil, Pierre Moisson, Tilo Nadler, Lutz Walter, and Christian Roos PMCID: PMC2841658 Adaptive evolution and inherent tolerance to extreme thermal environments Jennifer Cox, Alyxandria M Schubert, Michael Travisano, and Catherine Putonti PMCID: PMC2850354 Cheating does not explain selective differences at high and low relatedness in a social amoeba Gerda Saxer, Debra A Brock, David C Queller, and Joan E Strassmann PMCID: PMC2848656 Genome wide exploration of the origin and evolution of amino acids Xiaoxia Liu, Jingxian Zhang, Feng Ni, Xu Dong, Bucong Han, Daxiong Han, Zhiliang Ji, and Yufen Zhao PMCID: PMC2853539 Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis Sylvain Marcellini, Carola Bruna, Juan P Henríquez, Miguel Albistur, Ariel E Reyes, Elias H Barriga, Berta Henríquez, and Martín Montecino PMCID: PMC2848158 Evolutionary history and stress regulation of the lectin superfamily in higher plants Shu-Ye Jiang, Zhigang Ma, and Srinivasan Ramachandran PMCID: PMC2846932 Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube Carolina Díaz Arenas and Niles Lehman PMCID: PMC2850355 Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes Dong Li, Yiran Guo, Haojing Shao, Laurent C Tellier, Jun Wang, Zhonghuai Xiang, and Qingyou Xia PMCID: PMC2856562 Evolution of female carotenoid coloration by sexual constraint in Carduelis finches Gonçalo C Cardoso and Paulo Gama Mota PMCID: PMC2865479 Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion Stefano Mona, Giulio Catalano, Martina Lari, Greger Larson, Paolo Boscato, Antonella Casoli, Luca Sineo, Carolina Di Patti, Elena Pecchioli, David Caramelli, and Giorgio Bertorelle PMCID: PMC2858146 The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions Georgios Athanasiadis, Emili González-Pérez, Esther Esteban, Jean-Michel Dugoujon, Mark Stoneking, and Pedro Moral PMCID: PMC2853540 Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae) Thomas Mehner, Kirsten Pohlmann, Che Elkin, Michael T Monaghan, Barbara Nitz, and Jörg Freyhof PMCID: PMC2853541 Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae) Milla Suutari, Markus Majaneva, David P Fewer, Bryson Voirin, Annette Aiello, Thomas Friedl, Adriano G Chiarello, and Jaanika Blomster PMCID: PMC2858742 High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe Helena Malmström, Anna Linderholm, Kerstin Lidén, Jan Storå, Petra Molnar, Gunilla Holmlund, Mattias Jakobsson, and Anders Götherström PMCID: PMC2862036 Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria Krishna R Veeramah, Bruce A Connell, Naser Ansari Pour, Adam Powell, Christopher A Plaster, David Zeitlyn, Nancy R Mendell, Michael E Weale, Neil Bradman, and Mark G Thomas PMCID: PMC2867817 Evolution of the MAGUK protein gene family in premetazoan lineages Alex de Mendoza, Hiroshi Suga, and Iñaki Ruiz-Trillo PMCID: PMC2859873 The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages Irina S Druzhinina, Christian P Kubicek, Monika Komoń-Zelazowska, Temesgen Belayneh Mulaw, and John Bissett PMCID: PMC2858147 Discrimination of different species from the genus Drosophila by intact protein profiling using matrix-assisted laser desorption ionization mass spectrometry Ralph Feltens, Renate Görner, Stefan Kalkhof, Helke Gröger-Arndt, and Martin von Bergen PMCID: PMC2858148 A female signal reflects MHC genotype in a social primate Elise Huchard, Michel Raymond, Julio Benavides, Harry Marshall, Leslie A Knapp, and Guy Cowlishaw PMCID: PMC2858743 Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses Rob W Briddon, Basavaprabhu L Patil, Basavaraj Bagewadi, Muhammad Shah Nawaz-ul-Rehman, and Claude M Fauquet PMCID: PMC2858149 The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier Roswitha Schmickl, Marte H Jørgensen, Anne K Brysting, and Marcus A Koch PMCID: PMC2858744 FLU, an amino acid substitution model for influenza proteins Cuong Cao Dang, Quang Si Le, Olivier Gascuel, and Vinh Sy Le PMCID: PMC2873421 Allopolyploid speciation and ongoing backcrossing between diploid progenitor and tetraploid progeny lineages in the Achillea millefolium species complex: analyses of single-copy nuclear genes and genomic AFLP Jin-Xiu Ma, Yan-Nan Li, Claus Vogl, Friedrich Ehrendorfer, and Yan-Ping Guo PMCID: PMC2873412 The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages Nikki Traylor-Knowles, Ulla Hansen, Timothy Q Dubuc, Mark Q Martindale, Les Kaufman, and John R Finnerty PMCID: PMC2873413 Hybrid floral scent novelty drives pollinator shift in sexually deceptive orchids Nicolas J Vereecken, Salvatore Cozzolino, and Florian P Schiestl PMCID: PMC2875231 Phylogeographic history of grey wolves in Europe Małgorzata Pilot, Wojciech Branicki, Włodzimierz Jędrzejewski, Jacek Goszczyński, Bogumiła Jędrzejewska, Ihor Dykyy, Maryna Shkvyrya, and Elena Tsingarska PMCID: PMC2873414 Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus) Nicole Schneider, Lounès Chikhi, Mathias Currat, and Ute Radespiel PMCID: PMC2875232 Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio Pim van Hooft, Herbert HT Prins, Wayne M Getz, Anna E Jolles, Sipke E van Wieren, Barend J Greyling, Paul D van Helden, and Armanda DS Bastos PMCID: PMC2875233 Sexual conflict predicts morphology and behavior in two species of penduline tits René E van Dijk, Ákos Pogány, Jan Komdeur, Penn Lloyd, and Tamás Székely PMCID: PMC2873415 Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication Ertao Wang, Xun Xu, Lin Zhang, Hong Zhang, Lin Lin, Qin Wang, Qun Li, Song Ge, Bao-Rong Lu, Wen Wang, and Zuhua He PMCID: PMC2873416 The origins of species richness in the Hymenoptera: insights from a family-level supertree Robert B Davis, Sandra L Baldauf, and Peter J Mayhew PMCID: PMC2873417 Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton Bill Wickstead, Keith Gull, and Thomas A Richards PMCID: PMC2867816 Phylogeography of the Italian vairone (Telestes muticellus, Bonaparte 1837) inferred by microsatellite markers: evolutionary history of a freshwater fish species with a restricted and fragmented distribution Flavio Marchetto, Serena Zaccara, Frauke M Muenzel, and Walter Salzburger PMCID: PMC2868840 A Δ11 desaturase gene genealogy reveals two divergent allelic classes within the European corn borer (Ostrinia nubilalis) Kerry A Geiler and Richard G Harrison PMCID: PMC2877688 Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family Mark G Nielsen, Sudhindra R Gadagkar, and Lisa Gutzwiller PMCID: PMC2880298 Non-random genomic integration - an intrinsic property of retrogenes in Drosophila? Muralidhar Metta and Christian Schlötterer PMCID: PMC2879276 Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE Chaobo Tong, Xiaoni Gan, and Shunping He PMCID: PMC2873951 Divergence of imprinted genes during mammalian evolution Barbara Hutter, Matthias Bieg, Volkhard Helms, and Martina Paulsen PMCID: PMC2875234 Phylogenetic analysis of the vertebrate Excitatory/Neutral Amino Acid Transporter (SLC1/EAAT) family reveals lineage specific subfamilies Matthias Gesemann, Annegret Lesslauer, Colette M Maurer, Helia B Schönthaler, and Stephan CF Neuhauss PMCID: PMC2873418 Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation Ryan C Garrick, Paul Sunnucks, and Rodney J Dyer PMCID: PMC2880299 Sequence variation and selection of small RNAs in domesticated rice Yu Wang, Dan Shen, Shiping Bo, Huan Chen, Jian Zheng, Qian-Hao Zhu, Daguang Cai, Chris Helliwell, and Longjiang Fan PMCID: PMC2887405 The transcription factor Krüppel homolog 1 is linked to hormone mediated social organization in bees Hagai Shpigler, Harland M Patch, Mira Cohen, Yongliang Fan, Christina M Grozinger, and Guy Bloch PMCID: PMC2876159 Cryptic diversity of the bent-wing bat, Miniopterus schreibersii (Chiroptera: Vespertilionidae), in Asia Minor Andrzej Furman, Tomasz Postawa, Tunç Öztunç, and Emrah Çoraman PMCID: PMC2873419 A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing Makoto K Shimada, Yosuke Hayakawa, Jun-ichi Takeda, Takashi Gojobori, and Tadashi Imanishi PMCID: PMC2882926 Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach Ajna S Rivera, M Sabrina Pankey, David C Plachetzki, Carlos Villacorta, Anna E Syme, Jeanne M Serb, Angela R Omilian, and Todd H Oakley PMCID: PMC2888819 Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes Pei-Chun Liao, Dai-Chang Kuo, Chia-Chia Lin, Kuo-Chieh Ho, Tsan-Piao Lin, and Shih-Ying Hwang PMCID: PMC2880300 Functional bias in molecular evolution rate of Arabidopsis thaliana Andrew S Warren, Ramu Anandakrishnan, and Liqing Zhang PMCID: PMC2876160 Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators Naoki Takata, Shigeru Saito, Claire Tanaka Saito, and Matsuo Uemura PMCID: PMC2887406 The molecular evolution of PL10 homologs Ti-Cheng Chang and Wan-Sheng Liu PMCID: PMC2874800 Molecular evolution of the duplicated TFIIAγ genes in Oryzeae and its relatives Hong-Zheng Sun and Song Ge PMCID: PMC2887407 Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium Francesco Catania and Michael Lynch PMCID: PMC2874801 Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans Jeffrey SC Chu, David L Baillie, and Nansheng Chen PMCID: PMC2873420 A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae Yong-Yi Shen, Lu Liang, Yan-Bo Sun, Bi-Song Yue, Xiao-Jun Yang, Robert W Murphy, and Ya-Ping Zhang PMCID: PMC2880301 Evolutionary diversity of bile salts in reptiles and mammals, including analysis of ancient human and extinct giant ground sloth coprolites Lee R Hagey, Nicolas Vidal, Alan F Hofmann, and Matthew D Krasowski PMCID: PMC2886068 WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family Damien Chevanne, Sven J Saupe, Corinne Clavé, and Mathieu Paoletti PMCID: PMC2873952 The serendipitous origin of chordate secretin peptide family members João CR Cardoso, Florbela A Vieira, Ana S Gomes, and Deborah M Power PMCID: PMC2880984 Mortality affects adaptive allocation to growth and reproduction: field evidence from a guild of body snatchers Ryan F Hechinger PMCID: PMC2887408 Viral quasispecies profiles as the result of the interplay of competition and cooperation Juan Arbiza, Santiago Mirazo, and Hugo Fort PMCID: PMC2885392 The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages Nourdin Harich, Marta D Costa, Verónica Fernandes, Mostafa Kandil, Joana B Pereira, Nuno M Silva, and Luísa Pereira PMCID: PMC2875235 Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins Kelsey J Metzger and Michael A Thomas PMCID: PMC2880985 The gene transformer-2 of Anastrepha fruit flies (Diptera, Tephritidae) and its evolution in insects Francesca Sarno, María F Ruiz, José M Eirín-López, André LP Perondini, Denise Selivon, and Lucas Sánchez PMCID: PMC2885393 Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications Yasuhisa Okajima and Yoshinori Kumazawa PMCID: PMC2889956 Duplication, concerted evolution and purifying selection drive the evolution of mosquito vitellogenin genes Song Chen, Jennifer S Armistead, Katie N Provost-Javier, Joyce M Sakamoto, and Jason L Rasgon PMCID: PMC2875236 Two behavioural traits promote fine-scale species segregation and moderate hybridisation in a recovering sympatric fur seal population Melanie L Lancaster, Simon D Goldsworthy, and Paul Sunnucks PMCID: PMC2885394 Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes Wee Tek Tay, Gajanan T Behere, Philip Batterham, and David G Heckel PMCID: PMC2887409 Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication Xudong Wu and Xiaoquan Qi PMCID: PMC2880986 Ecological and genetic divergence between two lineages of Middle American túngara frogs Physalaemus (= Engystomops) pustulosus Heike Pröhl, Santiago R Ron, and Michael J Ryan PMCID: PMC2882927 Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders Jarrett R Johnson, Benjamin M Fitzpatrick, and H Bradley Shaffer PMCID: PMC2889957 Genomic organization and molecular phylogenies of the beta (β) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution Matthew J Greenwold and Roger H Sawyer PMCID: PMC2894828 Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids Jeffrey A Markert, Robert C Schelly, and Melanie LJ Stiassny PMCID: PMC2886069 High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2) Marshall L Hayes, Ron I Eytan, and Michael E Hellberg PMCID: PMC2880987 Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon Claudia Voelckel, Mehdi Mirzaei, Michael Reichelt, Zhiwei Luo, Dana Pascovici, Peter B Heenan, Silvia Schmidt, Bart Janssen, Paul A Haynes, and Peter J Lockhart PMCID: PMC2886070 Evolutionary ancestry and novel functions of the mammalian glucose transporter (GLUT) family Amy L Wilson-O'Brien, Nicola Patron, and Suzanne Rogers PMCID: PMC2890515 Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus Jiri Pavlicek, Sandrine Sauzet, Laurence Besseau, Steven L Coon, Joan L Weller, Gilles Boeuf, Pascaline Gaildrat, Marina V Omelchenko, Eugene V Koonin, Jack Falcón, and David C Klein PMCID: PMC2897805 Phylogenomics with incomplete taxon coverage: the limits to inference Michael J Sanderson, Michelle M McMahon, and Mike Steel PMCID: PMC2897806 Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication Jörg Lehmann, Carina Eisenhardt, Peter F Stadler, and Veiko Krauss PMCID: PMC2891723 Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and mice Ryan B MacDonald, Mélanie Debiais-Thibaud, Kyle Martin, Luc Poitras, Boon-Hui Tay, Byrappa Venkatesh, and Marc Ekker PMCID: PMC2891724 The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus) Borja Milá, Ben H Warren, Philipp Heeb, and Christophe Thébaud PMCID: PMC2894829 Experimental evolution of specialization by a microsporidian parasite Mathieu Legros and Jacob C Koella PMCID: PMC2891725 Duplicability of self-interacting human genes Åsa Pérez-Bercoff, Takashi Makino, and Aoife McLysaght PMCID: PMC2894830 On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture Catherine L Worth and Tom L Blundell PMCID: PMC2892493 Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages Lesley T Lancaster PMCID: PMC2901258 Evolutionary diversification of cryophilic Grylloblatta species (Grylloblattodea: Grylloblattidae) in alpine habitats of California Sean D Schoville and George K Roderick PMCID: PMC2898686 Exploring the HME and HAE1 efflux systems in the genus Burkholderia Elena Perrin, Marco Fondi, Maria Cristiana Papaleo, Isabel Maida, Silvia Buroni, Maria Rosalia Pasca, Giovanna Riccardi, and Renato Fani PMCID: PMC2891726 Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia) Thomas Datzmann, Otto von Helversen, and Frieder Mayer PMCID: PMC2901259 Rapid ecological isolation and intermediate genetic divergence in lacustrine cyclic parthenogens Katie S Costanzo and Derek J Taylor PMCID: PMC2895610 Capitellid connections: contributions from neuromuscular development of the maldanid polychaete Axiothella rubrocincta (Annelida) Nora Brinkmann and Andreas Wanninger PMCID: PMC2897808 Hybridisation between two cyprinid fishes in a novel habitat: genetics, morphology and life-history traits Brian Hayden, Domitilla Pulcini, Mary Kelly-Quinn, Martin O'Grady, Joe Caffrey, Aisling McGrath, and Stefano Mariani PMCID: PMC2896959 The impact of single nucleotide polymorphism in monomeric alpha-amylase inhibitor genes from wild emmer wheat, primarily from Israel and Golan Ji-Rui Wang, Yu-Ming Wei, Mei Deng, Eviatar Nevo, Ze-Hong Yan, and You-Liang Zheng PMCID: PMC2898687 Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy Jean-François Flot, Gert Wörheide, and Sharmishtha Dattagupta PMCID: PMC2896373 Phylogenetics and biogeography of a spectacular Old World radiation of butterflies: the subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrini) Ullasa Kodandaramaiah, David C Lees, Chris J Müller, Elizabeth Torres, K Praveen Karanth, and Niklas Wahlberg PMCID: PMC2898688 Cooperators Unite! Assortative linking promotes cooperation particularly for medium sized associations Ádám Kun, Gergely Boza, and István Scheuring PMCID: PMC2898689 Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae) Karl N Magnacca and Mark JF Brown PMCID: PMC2891727 Evidence for an early evolutionary emergence of γ-type carbonic anhydrases as components of mitochondrial respiratory complex I Ryan MR Gawryluk and Michael W Gray PMCID: PMC2900272 Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation? J Mark Hipfner, Kristen B Gorman, Rutger A Vos, and Jeffrey B Joy PMCID: PMC2896374 Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice Michael Reagon, Carrie S Thurber, Briana L Gross, Kenneth M Olsen, Yulin Jia, and Ana L Caicedo PMCID: PMC2898691 The origin and evolution of ARGFX homeobox loci in mammalian radiation Guang Li and Peter WH Holland PMCID: PMC2894831 A new Early Cretaceous relative of Gnetales: Siphonospermum simplex gen. et sp. nov. from the Yixian Formation of Northeast China Catarina Rydin and Else Marie Friis PMCID: PMC2900273 Mastacembelid eels support Lake Tanganyika as an evolutionary hotspot of diversification Katherine J Brown, Lukas Rüber, Roger Bills, and Julia J Day PMCID: PMC2903574 Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model Zu-Guo Yu, Ka Hou Chu, Chi Pang Li, Vo Anh, Li-Qian Zhou, and Roger Wei Wang PMCID: PMC2898692 Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development Robert B Page, Meredith A Boley, Jeramiah J Smith, Srikrishna Putta, and Stephen R Voss PMCID: PMC2900274 Software BLAST-EXPLORER helps you building datasets for phylogenetic analysis Alexis Dereeper, Stephane Audic, Jean-Michel Claverie, and Guillaume Blanc PMCID: PMC2821324 SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees Tobias Hill, Karl JV Nordström, Mikael Thollesson, Tommy M Säfström, Andreas KE Vernersson, Robert Fredriksson, and Helgi B Schiöth PMCID: PMC2829038 WAMI: a web server for the analysis of minisatellite maps Mohamed Abouelhoda, Mohamed El-Kalioby, and Robert Giegerich PMCID: PMC2897807 Research Articles Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae) A Lovisa S Gustafsson, Christiano F Verola, and Alexandre Antonelli PMCID: PMC2905424 Comparison of translation loads for standard and alternative genetic codes Stefanie Gabriele Sammet, Ugo Bastolla, and Markus Porto PMCID: PMC2909233 Evolution of the CD163 family and its relationship to the bovine gamma delta T cell co-receptor WC1 Carolyn TA Herzig, Ray W Waters, Cynthia L Baldwin, and Janice C Telfer PMCID: PMC2906472 Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries Marie Pagès, Yannick Chaval, Vincent Herbreteau, Surachit Waengsothorn, Jean-François Cosson, Jean-Pierre Hugot, Serge Morand, and Johan Michaux PMCID: PMC2906473 Geographic variation in the damselfish-red alga cultivation mutualism in the Indo-West Pacific Hiroki Hata, Katsutoshi Watanabe, and Makoto Kato PMCID: PMC2905425 Positive selection of HIV host factors and the evolution of lentivirus genes Katarzyna Bożek and Thomas Lengauer PMCID: PMC2906474 The evolution of transcription-associated biases of mutations across vertebrates Paz Polak, Robert Querfurth, and Peter F Arndt PMCID: PMC2927911 Chromosome phylogeny of the subfamily Pitheciinae (Platyrrhini, Primates) by classic cytogenetics and chromosome painting Liane FM Finotelo, Paulo JS Amaral, Julio C Pieczarka, Edivaldo HC de Oliveira, Alcides Pissinati, Michaela Neusser, Stephan Müller, and Cleusa Y Nagamachi PMCID: PMC2905426 Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants Xinguo Li, Harry X Wu, and Simon G Southerton PMCID: PMC2907377 Filoviruses are ancient and integrated into mammalian genomes Derek J Taylor, Robert W Leach, and Jeremy Bruenn PMCID: PMC2906475 Contrasting patterns of phylogeographic relationships in sympatric sister species of ironclad beetles (Zopheridae: Phloeodes spp.) in California's Transverse Ranges Maxi Polihronakis and Michael S Caterino PMCID: PMC2904329 A phylogenetic survey of myotubularin genes of eukaryotes: distribution, protein structure, evolution, and gene expression David Kerk and Greg BG Moorhead PMCID: PMC2927912 Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus) Daniel WA Noble, Yin Qi, and Jinzhong Fu PMCID: PMC2904330 Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus) Jorge Vieira, Pedro G Ferreira, Bruno Aguiar, Nuno A Fonseca, and Cristina P Vieira PMCID: PMC2909234 Rampant historical mitochondrial genome introgression between two species of green pond frogs, Pelophylax nigromaculatus and P. plancyi Kui Liu, Fang Wang, Wei Chen, Lihong Tu, Mi-Sook Min, Ke Bi, and Jinzhong Fu PMCID: PMC2909235 Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species Delphine Audigeos, Anna Buonamici, Laurent Belkadi, Paul Rymer, David Boshier, Caroline Scotti-Saintagne, Giovanni G Vendramin, and Ivan Scotti PMCID: PMC2906476 Predictable patterns of trait mismatches between interacting plants and insects Bruce Anderson, John S Terblanche, and Allan G Ellis PMCID: PMC2927919 Population genetic diversity and fitness in multiple environments Jeffrey A Markert, Denise M Champlin, Ruth Gutjahr-Gobell, Jason S Grear, Anne Kuhn, Thomas J McGreevy, Jr, Annette Roth, Mark J Bagley, and Diane E Nacci PMCID: PMC2927917 Evolutionary analysis of the kinesin light chain genes in the yellow fever mosquito Aedes aegypti: gene duplication as a source for novel early zygotic genes James K Biedler and Zhijian Tu PMCID: PMC2927918 Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins Jun Okada, Tomohiro Okamoto, Atsushi Mukaiyama, Takashi Tadokoro, Dong-Ju You, Hyongi Chon, Yuichi Koga, Kazufumi Takano, and Shigenori Kanaya PMCID: PMC2927913 Comparative analyses of the Conserved Oligomeric Golgi (COG) complex in vertebrates Rita Quental, Luísa Azevedo, Rune Matthiesen, and António Amorim PMCID: PMC2927914 Molecular basis of a novel adaptation to hypoxic-hypercapnia in a strictly fossorial mole Kevin L Campbell, Jay F Storz, Anthony V Signore, Hideaki Moriyama, Kenneth C Catania, Alexander P Payson, Joseph Bonaventura, Jörg Stetefeld, and Roy E Weber PMCID: PMC2927915 Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes Linda Y Rutledge, Brent R Patterson, and Bradley N White PMCID: PMC2927920 Ontogenetic convergence and evolution of foot morphology in European cave salamanders (Family: Plethodontidae) Dean C Adams and Annamaria Nistri PMCID: PMC2927916 The evolution of antennal courtship in diplazontine parasitoid wasps (Hymenoptera, Ichneumonidae, Diplazontinae) Seraina Klopfstein, Donald LJ Quicke, and Christian Kropf PMCID: PMC2927921 Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana Sophie Plouviez, Dominique Le Guen, Odile Lecompte, François H Lallier, and Didier Jollivet PMCID: PMC2924869 Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra) Fernando Rodríguez, Trinidad Pérez, Sabine E Hammer, Jesús Albornoz, and Ana Domínguez PMCID: PMC2923631 Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani Joshua M Hull, David P Mindell, Sandra L Talbot, Emily H Kay, Hopi E Hoekstra, and Holly B Ernest PMCID: PMC2927923 Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus Erika S Tavares, Gerard HJ de Kroon, and Allan J Baker PMCID: PMC2927924 History of myxozoan character evolution on the basis of rDNA and EF-2 data Ivan Fiala and Pavla Bartošová PMCID: PMC2927925 Intragenomic conflict in populations infected by Parthenogenesis Inducing Wolbachia ends with irreversible loss of sexual reproduction Richard Stouthamer, James E Russell, Fabrice Vavre, and Leonard Nunney PMCID: PMC2927591 Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus Muktak Aklujkar and Derek R Lovley PMCID: PMC2923632 Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins Angela Lek, Monkol Lek, Kathryn N North, and Sandra T Cooper PMCID: PMC2923515 Strong reproductive barriers in a narrow hybrid zone of West-Mediterranean green toads (Bufo viridis subgroup) with Plio-Pleistocene divergence Caroline Colliard, Alessandra Sicilia, Giuseppe Fabrizio Turrisi, Marco Arculeo, Nicolas Perrin, and Matthias Stöck PMCID: PMC2923517 Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma Audrius Menkis, Carrie A Whittle, and Hanna Johannesson PMCID: PMC2923516 Introducing the refined gravity hypothesis of extreme sexual size dimorphism Guadalupe Corcobado, Miguel A Rodríguez-Gironés, Eva De Mas, and Jordi Moya-Laraño PMCID: PMC2924870 Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms Raquel Tavares, Mathilde Cagnon, Ioan Negrutiu, and Dominque Mouchiroud PMCID: PMC2924871 Expression breadth and expression abundance behave differently in correlations with evolutionary rates Seung Gu Park and Sun Shim Choi PMCID: PMC2924872 Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets Arong Luo, Huijie Qiao, Yanzhou Zhang, Weifeng Shi, Simon YW Ho, Weijun Xu, Aibing Zhang, and Chaodong Zhu PMCID: PMC2925852 Untangling spider silk evolution with spidroin terminal domains Jessica E Garb, Nadia A Ayoub, and Cheryl Y Hayashi PMCID: PMC2928236 Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences Guy Baele, Yves Van de Peer, and Stijn Vansteelandt PMCID: PMC2928787 Mating system drives negative associations between morphological features in Schistosomatidae Sophie Beltran, Yves Desdevises, Julien Portela, and Jérôme Boissier PMCID: PMC2928788 Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes Sylvia Schäffer, Stephan Koblmüller, Tobias Pfingstl, Christian Sturmbauer, and Günther Krisper PMCID: PMC2930640 An evolutionary analysis of cAMP-specific Phosphodiesterase 4 alternative splicing Keven R Johnson, Jessie Nicodemus-Johnson, and Robert S Danziger PMCID: PMC2929239 Identification, classification and evolution of Owl Monkeys (Aotus, Illiger 1811) Albert N Menezes, Cibele R Bonvicino, and Hector N Seuánez PMCID: PMC2931504 Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods Jon Bohlin, Lars Snipen, Axel Cloeckaert, Karin Lagesen, David Ussery, Anja B Kristoffersen, and Jacques Godfroid PMCID: PMC2928237 Phenotypic plasticity in the range-margin population of the lycaenid butterfly Zizeeria maha Joji M Otaki, Atsuki Hiyama, Masaki Iwata, and Tadashi Kudo PMCID: PMC2931505 Methodology Articles Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes Chenhong Li, Jean-Jack M Riethoven, and Lingbo Ma PMCID: PMC2853542 Bootstrap-based Support of HGT Inferred by Maximum Parsimony Hyun Jung Park, Guohua Jin, and Luay Nakhleh PMCID: PMC2874802 Algorithmic approaches to aid species' delimitation in multidimensional morphospace Thomas HG Ezard, Paul N Pearson, and Andy Purvis PMCID: PMC2898690 Corrections Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae Daniel B Sloan, Bengt Oxelman, Anja Rautenberg, and Douglas R Taylor PMCID: PMC2820449 Corrects: Daniel B Sloan, et al. Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae. BMC Evol Biol. 2009; 9: 260. Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii) Bailey D McKay, Herman L Mays, Jr, Yi-Wen Peng, Kenneth H Kozak, Cheng-Te Yao, Hsiao-Wei Yuan, Pei-Fen Lee, and Fu-Hsiung Hsu PMCID: PMC2880302 Corrects: Bailey D McKay, et al. Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii) BMC Evol Biol. 2010; 10: 71. Other Issues: Journal List
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