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Charles Darwin on December of 1833 during the Beagle voyage surveying along the Patagonia coastline navigated up a river where he set up camp nearby Darwin’s mirrors (photo) in Puerto Deseado (Santa Cruz, Argentina), where he described the topography, geo

Why then, and this is not only my particular case, does this barren land possess my mind? I find it hard to explain but it might partly be because it enhances the horizons of imagination. - Charles Darwin

Charles Darwin on December of 1833 during the Beagle voyage surveying along the Patagonia coastline navigated up a river where he set up camp nearby Darwin’s mirrors (photo) in Puerto Deseado (Santa Cruz, Argentina), where he described the topography, geology, fauna, flora and collected fossils.
The reasons for their existence of operons have remained controversial. Operon conservation is inversely correlated to the abundance of transcription factors in the genome suggesting a negative association between the complexity of genetic networks and operon conservation. Results in Nuñez et al. showed that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization suggesting that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.

A fluorescent image of three consecutive stages of oogenesis in <i>Drosophila melanogaster</i>.

A fluorescent image of three consecutive stages of oogenesis in Drosophila melanogaster. Cells were stained to reveal reactive oxygen species in green and DNA in blue. Polyploid nurse cells and the single oocyte have quiescent mitochondria, and nuclear DNA gives them their blue color. In contrast, mitochondria of the surrounding diploid follicle cells, active in respiration, produce reactive oxygen species, and so green predominates. John F. Allen and colleagues, in Female and Male Gamete Mitochondria Are Distinct and Complementary in Transcription, Structure, and Genome Function, demonstrate that female germline mitochondria in fruit flies and zebrafish suppress transcription and oxidative phosphorylation. This adaptation may protect the mitochondrial genetic template from free radical-mediated mutation. Allen’s fascinating question is whether the separation of the mitochondrial properties of male and female gametes, serving motility and hereditary functions, respectively, could explain the origin of sexual dimorphism in multicellular animals.

The growth of Mount Etna, Sicily (depicted top) may have led to the rapid divergence of <i>Senecio chrysanthemifolius</i> (depicted lower left) and <i>S. aethnensis</i> (depicted lower right) which are now found on the volcano at low and high altitudes re

The growth of Mount Etna, Sicily (depicted top) may have led to the rapid divergence of Senecio chrysanthemifolius (depicted lower left) and S. aethnensis (depicted lower right) which are now found on the volcano at low and high altitudes respectively, as discussed in Owen G. Osborne,Thomas E. Batstone, Simon J. Hiscock, and Dmitry A. Filatov: Rapid Speciation with Gene Flow Following the Formation of Mt. Etna. Image of Mt. Etna by BenAveling (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons.

Emergence of phenotypic innovations following a regulatory-based parallel mechanism. Dots represent human orthologs, colored according to their origin, which integrate genetic modules thanks to regulatory interactions (lines).

Emergence of phenotypic innovations following a regulatory-based parallel mechanism. Dots represent human orthologs, colored according to their origin, which integrate genetic modules thanks to regulatory interactions (lines). Phenotypic innovations driven by such genetic modules can be latent (no background), labile (purple background) or stable (grey background). See details in the paper by Wenger and Galliot: Punctuated Emergences of Genetic and Phenotypic Innovations in Eumetazoan, Bilaterian, Euteleost and Hominidae ancestors. Genome Biology and Evolution (2013).

An adult Chamaeleo chamaeleon (common chameleon) from Israel.

An adult Chamaeleo chamaeleon (common chameleon) from Israel. C. chamaeleon is an arboreal lizard, adapted for hunting insects. Some of the chameleon’s unique characters include a long, retractable tongue to capture prey, independently rotating eyes, allowing 360˚vision, juxtaposed digits for gripping branches, prehensile tail and its color change, according to physiological condition, social communication and camouflage requirements. The first chameleon transcriptome is presented in Bar-Yaacov et al. This transcriptome sequence is the first genomic-scale resource for C. chamaeleon. Along with transcriptome sequences from 34 vertebrates, this resource allowed comparative genomic analysis of the entire oxidative phosphorylation system. From The First Chameleon Transcriptome: Comparative Genomic Analysis of the OXPHOS System Reveals Loss of COX8 in Iguanian Lizards by Dan Bar-Yaacov, Amos Bouskila, and Dan Mishmar.

Complex Patterns of Local Adaptation in Teosinte

Complex Patterns of Local Adaptation in Teosinte. Image by Dan Graur, based on the research article Complex Patterns of Local Adaptation in Teosinte by Tanja Pyhäjärvi, Sofiane Mezmouk, Matthew Hufford, and Jeffrey Ross-Ibarra.

Dr. Masatoshi Nei, co-founder of SMBE, awarded the 2013 Kyoto Prize in Basic Sciences.

Dr. Masatoshi Nei, co-founder of the journal Molecular Biology and Evolution and co-founder of the Society for Molecular Biology and Evolution, was awarded the 2013 Kyoto Prize in Basic Sciences. This cover design is based on Dr. Nei’s pioneering book, Molecular Population Genetics and Evolution (1975) and the logos of the Kyoto Prize and the Inamori Foundation. Cover Design by Dan Graur, Ph.D. student of Dr. Nei (1980-1985).

Conservation of gene spacing is highly predictive of gene function in fungi.

Conservation of gene spacing is highly predictive of gene function in fungi. The genomic context of one gene, Aspergillus nidulans stuA, is depicted as a simplified alignment, highlighting an exceptionally large upstream intergenic region that has been maintained within the Ascomycota for approximately 600 Myr. From Fungal Genes in Context: Genome Architecture Reflects Regulatory Complexity and Function by Luke M. Noble and Alex Andrianopoulos.

Female of the hybrid butterfly species <i>Papilio appalachiensis</i>

Female of the hybrid butterfly species Papilio appalachiensis, photographed in Spruce Knob, West Virginia. Photo by Krushnamegh Kunte. Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies, by Zhang et al.

The Annual Conference of the Society for Molecular Biology and Evolution, Chicago, Illinois, July 7-11, 2013.

The Annual Conference of the Society for Molecular Biology and Evolution, Chicago, Illinois, July 7-11, 2013. Cover design by Dan Graur.

A <i>Drosophila suzukii</i> female perched on a raspberry during her search for an oviposition site.

A Drosophila suzukii female perched on a raspberry during her search for an oviposition site. Unlike most other Drosophila, D. suzukii lays eggs and feeds on undamaged, ripening fruits, posing a serious threat to fruit cultivation. The draft genome sequence and transcriptome of this species is described in Ometto et al., along with thorough analyses of patterns of molecular evolution and field observations that reveal the evolutionary history of its behavioral innovation.Photo by Umberto Salvagnin, Fondazione Edmund Mach.

Sequence similarity network of the 1,455 CRP/FNR-type transcription regulators in prokaryote.

Sequence similarity network of the 1,455 CRP/FNR-type transcription regulators in prokaryote. Circles represent each transcription regulator and the colors indicate regulators from the same group. Stepwise evolution of the sequence similarity networks of the groups is also shown as a dendrogram in the background. See details in the paper Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks by Matsui et al. Genome Biology and Evolution 5(2):267-282 (2013). Artwork by Motomu Matsui (Keio University, Japan).

Among the dominant members of the oceanic picoplankton, rhodopsin-containing marine microbes such as flavobacteria play a pivotal role in the biogeochemical cycle of the euphotic zone.

Among the dominant members of the oceanic picoplankton, rhodopsin-containing marine microbes such as flavobacteria play a pivotal role in the biogeochemical cycle of the euphotic zone. The genome sequence of the marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis), isolated from the surface seawater collected between the two main islands of Dokdo in the East Sea of Korea, was determined to unveil a phylogenetically distinct class of rhodopsin, with a characteristic NQ motif, that apparently functions in sodium-adapted lifestyle. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a cytophaga, a deinococcus, and even a eukaryote diatom, suggesting the horizontal gene transfer within and between domains of life. The full story is described in Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins by Kwon et al., 2013. Design of the illustration by Soon-Kyeong Kwon, Jihyun F. Kim, and Eun Joo Kim; SEM image of N. dokdonensis from Jung-Hoon Yoon.

Genome-wide co-occurrence of short repeats, indels, and point mutations in whole chloroplast genomes of family Araceae.

Genome-wide co-occurrence of short repeats, indels, and point mutations in whole chloroplast genomes of family Araceae. From Mutational Dynamics of Aroid Chloroplast Genomes by Ahmed et al.

An adult drosophilid fly <i>Scaptomyza flava</i> on a leaf of its host plant, <i>Arabidopsis thaliana</i> Col-0.

An adult drosophilid fly Scaptomyza flava on a leaf of its host plant, Arabidopsis thaliana Col-0, as discussed in the paper Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly by Whiteman N, et al.

Cover design by Dan Graur, based on Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes by F. Murat, Y. Van de Peer, and J. Salse.

Cover design by Dan Graur, based on Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes by F. Murat, Y. Van de Peer, and J. Salse.

Celebrating the 2012 SMBE conference in Dublin, Ireland, June 23-26

The arms of Dublin feature a Viking raven (Corvus corax), a hurdle (Baile Átha Claith), and a pyre epitomizing the city’s motto “Beart do réir ár mbríathar (Action to match the words). Two Celtic shields signify the endosymbiotic events at the origin of eukaryotes and plants. Three Oghan characters, for yew (Taxus baccata), blackthorn (Prunus spinosa), and ash (Fraxinus excelsior), are shown as terminal branches within Plantae. The symbol for apple (Malus domestica) is shown as a terminal branch within Dinophyceae, indicating that uncertainties in multiple sequence alignments may cause phylogenetic misplacement. The large Celtic knot denotes the limits of the phylogenetic-tree metaphor. At the end of the rainbow, two prokaryotic genomes stand for the leprechaun’s pot o’ gold. A snake is seen leaving the tableau after being banished by St. Patrick at the end of a 40-day fast. Because of St. Patrick, order Squamata is represented in Ireland by only two species, the viviparous lizard (Zootoca vivipara) and the newly introduced slow worm (Anguis fragilis). Green, orange, and white constitute the tricolor of the Republic of Ireland. Green symbolizes the Gaelic community, orange represents the Orange community, and white represents peace between them. For technical reasons related to the limitation of glossy paper, large swathes of white could not be accommodated in the design. (Dan Graur)

An adult female aye-aye at Nosy Mangabe, Madagascar

An adult female aye-aye at Nosy Mangabe, Madagascar (photograph: Edward Louis, Omaha's Henry Doorly Zoo). The aye-aye, a nocturnal lemur with continuously-growing incisors used to gnaw through tree bark to extract grubs with a very thin, flexible, middle finger, is considered one of the most unusual primates. A draft sequence and analysis of the aye-aye genome is presented in Perry et al., A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Advance Access published December 7, 2011 doi:10.1093/gbe/evr132.

Przewalski's horse

Przewalski's horse, the only surviving wild horse. Sequencing and analysis of its complete mitochondrial and partial nuclear genomes are reported in Goto et al. Genome Biol Evol (2011) 3:1096-1106. doi: 10.1093/gbe/evr067
Credit: Zoological Society of San Diego.

Pufferfish chromosomes

Pufferfish chromosomes with telomeres and centromeres labelled by flourescence in situ hybridization.
Image kindly provided by: Dr. Kiyoshi Kikuchi, Fisheries Laboratory, University of Tokyo

Cover_Competition_winner

Cover illustration by Dan Graur as a gesture of thanks to the organizers of the SMBE Annual Meeting 2011 in Kyoto. The symbols allude to Kyoto, Mishima, Sakura, and genome evolution.

Image taken by Denis Kunkel Microscopy, Inc., cells provided by Sarah and Seth Bordenstein, and false-colouring drawn by Rob Brucker.

Image taken by Denis Kunkel Microscopy, Inc., cells provided by Sarah and Seth Bordenstein, and false-colouring drawn by Rob Brucker.

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Cells inside cells at infinitum by Odra Noel, Scientific Artist (www.odranoel.eu).

Cover design and graphics kindly supplied by Ford Doolittle

Cover design and graphics kindly supplied by Ford Doolittle.