Abstract  The rapidly evolving mitochondrial control region remains an important source of information on phylogeography and demographic history for cetaceans and other vertebrates, despite great uncertainty in the rate of nucleotide substitution across both nucleotide positions and lineages. Patterns of variation in linked markers with slower rates of evolution can potentially be used to calibrate the rate of nucleotide substitution in the control region and to better understand the interplay of evolutionary and demographic forces across the mitochondrial genome above and below the species level. We have examined patterns of diversity within and between three baleen whale species (gray, humpback, and Antarctic minke whales) in order to determine how patterns of molecular evolution differ between cytochrome b and the control region. Our results show that cytochrome b is less variable than expected given the diversity in the control region for gray and humpback whales, even after functional differences are taken into account, but more variable than expected for minke whales. Differences in the frequency distributions of polymorphic sites and in best-fit models of nucleotide substitution indicate that these patterns may be the result of hypervariability in the control region in gray and humpback whales but, in minke whales, may result from a large, stable or expanding population size coupled with saturation at the control region. Using paired cytochrome b and control region data across individuals, we show that the average rate of nucleotide substitution in the control region may be on average 2.6 times higher than phylogenetically derived estimates in cetaceans. These results highlight the complexity of making inferences from control region data alone and suggest that applying simple rules of DNA sequence analyses across species may be difficult.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9193-2
• Authors
  • S. Elizabeth Alter, Stanford University Department of Biological Sciences, Hopkins Marine Station 120 Oceanview Boulevard Pacific Grove CA 93950 USA
  • Stephen R. Palumbi, Stanford University Department of Biological Sciences, Hopkins Marine Station 120 Oceanview Boulevard Pacific Grove CA 93950 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Chimeric RNAs have been reported in varieties of organisms and are conventionally thought to be produced by trans-splicing of two or more distinct transcripts. Here, we conducted a large-scale search for chimeric RNAs in the budding yeast, fruit fly, mouse, and human. Thousands of chimeric transcripts were identified in these organisms except in yeast, in which five chimeric RNAs were observed. RT-PCR experiments for a sample of yeast and fly chimeric transcripts using specific primers show that about one-third of these chimeric RNAs can be reproduced. The results suggest that at least a considerable amount of chimeric RNAs is unlikely from aberrant transcription or splicing, and thus formation of chimeric RNAs is probably a widespread process and can greatly contribute to the complexity of the transcriptome and proteome of organisms. However, only a small fraction (<20%) of these chimeric RNAs has GU-AG at the junction sequences which fits the classical trans-splicing model. In contrast, we observed that about half of the chimeric RNAs have short homologous sequences (SHSs) at the junction sites of the source sequences. Our sequence mutation experiments in yeast showed that disruption of SHSs resulted in the disappearance of the corresponding chimeric RNAs, suggesting that SHSs are essential for generating this kind of chimeric RNA. In addition to the classical trans-splicing model, we propose a new model, the transcriptional slippage model, to explain the generation of those chimeric RNAs synthesized from templates with SHSs.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9187-0
• Authors
  • Xin Li, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS) CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution Kunming 650223 China
  • Li Zhao, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS) CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution Kunming 650223 China
  • Huifeng Jiang, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS) CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution Kunming 650223 China
  • Wen Wang, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS) CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution Kunming 650223 China

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Genetic miscoding lesions can cause inaccuracies during the interpretation of ancient DNA sequence data. In this study, genetic miscoding lesions were identified and assessed by cloning and direct sequencing of degraded, amplified mitochondrial DNA (mtDNA) extracted from human remains. Forty-two individuals, comprising nine collections from five geographic locations, were analyzed for the presence of DNA damage that can affect the generation of a correct mtDNA profile. In agreement with previous studies, high levels (56.5% of all damage sites) of proposed hydrolytic damage products were observed. Among these, type 2 transitions (cytosine → thymine or guanine → adenine), which are highly indicative of hydrolytic deamination, were observed in 50% of all misincorporations that occurred. In addition to hydrolytic damage products, oxidative damage products were also observed in this study and were responsible for approximately 43.5% of all misincorporations. This level of misincorporation is in contrast to previous studies characterizing miscoding lesions from the analysis of bone and teeth, where few to no oxidative damage products were observed. Of all the oxidative damage products found in this study, type 2 transversions (cytosine → adenine/guanine → thymine or cytosine → guanine/guanine → cytosine), which are commonly formed through the generation of 8-hydroxyguanine, accounted for 30.3% of all genetic miscoding lesions observed. This study identifies the previously unreported presence of oxidative DNA damage and proposes that damage to degraded DNA templates is highly specific in type, correlating with the geographic location and the taphonomic conditions of the depositional environment from which the remains are recovered.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9184-3
• Authors
  • Ryan Lamers, Lakehead University Department of Biology Thunder Bay ON Canada
  • Shana Hayter, Lakehead University Department of Biology Thunder Bay ON Canada
  • Carney D. Matheson, Lakehead University Department of Biology Thunder Bay ON Canada

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  The enzymes catalyzing the first two reactions in the sulfate activation pathway, ATP-sulfurylase (S) and APS-kinase (K), are fused as ‘KS’ in animals but are fused as ‘SK’ in select bacteria and fungi. We have discovered a novel triple fusion protein of K, S, and pyrophosphatase (P) in several protozoan genomes within the Stramenopile lineage. These triple domain fusion proteins led us to hypothesize that pyrophosphatase enzymes and sulfate activation enzymes physically interact to impact the thermodynamics of the sulfate activation pathway. In support of this hypothesis, we demonstrate through biochemical assays that separately encoded KS and P proteins physically interact and that KS/P complexes activate more sulfate than KS alone. We also conclude on the basis of phylogenetic analyses that all known KS fusions originate from a single fusion event early in the eukaryotic lineage. Strikingly, our analyses support the same conclusion for all known SK fusions. These observations indicate that the patchwork of fused and nonfused S and K genes observed in modern-day eukaryotes and prokaryotes are the result of the two ancestral fusion genes evolving by an assortment of gene fissions, duplications, deletions, and horizontal transfers in different lineages. Our integrative use of genomics, phylogenetics, and biochemistry to characterize pyrophosphatase as a new member of the sulfate activation pathway should be effective at identifying new protein members and connections in other molecular pathways.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9181-6
• Authors
  • Michael E. Bradley, University of Chicago Department of Pediatrics 5841 South Maryland Avenue, WCH C519A Chicago IL 60637 USA
  • Joshua S. Rest, University of Chicago Department of Human Genetics Chicago IL 60637 USA
  • Wen-Hsiung Li, University of Chicago Department of Ecology and Evolution Chicago IL 60637 USA
  • Nancy B. Schwartz, University of Chicago Department of Pediatrics 5841 South Maryland Avenue, WCH C519A Chicago IL 60637 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Evolutionary rates of sites can be independent of one another or correlated in some fashion. Significant spatial autocorrelation was observed for site amino acid replacement rates in vasopressin receptor family proteins (VPRs). Spatial autocorrelation of rates is the propensity of residues to lie near other residues of similar rate in the folded protein structure. Optimal correlation occurred at a distance suggesting that residues in contact had correlated rates. As another way to study the same phenomenon, VPR was partitioned into >40 × 10 Å3 contiguous spatial clusters for amino acid replacement rate estimation. Partitioning was done without preconception of functional regions of the protein and with a random partition control. Cluster rates exhibited an overdispersed distribution suggesting that rates were not randomly distributed in the spatial partitions. In tests, cluster partitioning improved maximum likelihood and Bayesian likelihood models for VPR evolution. Spatial clusters with outlier rates, or lineage-specific clusters differing in rate, proved to contain VPR features likely to be under selection. Thus the spatial autocorrelation observed is probably not just a statistical finding, but likely has an evolutionary basis in protein function.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9183-4
• Authors
  • Lorraine Marsh, Long Island University Department of Biology Brooklyn NY 11201 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Although thousands of in vitro selection and evolution experiments have been performed to seek different types of targets, most of them have only inspected the terminal evolutionary pool for patterns. In addition, to rapidly obtain the most favorable target, many experiments have been carried out under increasing selection pressure. However, increasing selection pressure seldom occurs in natural evolution. We studied the dynamic features of DNA in vitro evolution in the presence of the Mnt repressor under sequential constant selection pressure. When evolving under a constant pressure from an initial random pool of DNA, our system showed a clear, sharp, and reproducible crossover from a random population to an advantageous population (higher binding affinities of DNA sequences to the Mnt repressor). This crossover occurs after a long latent period during which there are no obvious changes in the population phenotype. We demonstrated that the existence of the crossover is caused by a significant sequence-nonspecific binding in the repressor–DNA system. After the crossover, the population settled in a stationary distribution of genotypes, which responded immediately to a subsequent sudden increase in selection pressure. We also experimentally tested the linear correlation between the evolution speed and sequence diversity (Fisher’s theorem) in our system.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9182-5
• Authors
  • Xiaojing Yang, Peking University Center for Theoretical Biology Beijing 100871 China
  • Xili Liu, Peking University Center for Theoretical Biology Beijing 100871 China
  • Chunbo Lou, Peking University Center for Theoretical Biology Beijing 100871 China
  • Jianguo Chen, Peking University Center for Theoretical Biology Beijing 100871 China
  • Qi Ouyang, Peking University Center for Theoretical Biology Beijing 100871 China

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker’s snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9179-0
• Authors
  • R. David Russell, Simon Fraser University Department of Molecular Biology and Biochemistry 8888 University Drive Burnaby BC Canada V5A 1S6
  • Andrew T. Beckenbach, Simon Fraser University Department of Biological Sciences 8888 University Drive Burnaby BC Canada V5A 1S6

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9149-6
• Authors
  • Manuela Marz, University of Leipzig Bioinformatics Group, Department of Computer Science Härtelstrasse 16-18 04107 Leipzig Germany
  • Toralf Kirsten, Interdisziplinäres Zentrum für Bioinformatik, University of Leipzig Härtelstrasse 16-18 04107 Leipzig Germany
  • Peter F. Stadler, University of Leipzig Bioinformatics Group, Department of Computer Science Härtelstrasse 16-18 04107 Leipzig Germany

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  The eukaryotic Mutator family of transposable elements is widespread in plants. Active or potentially active copies are also found in fungi and protozoans, and sequences related to this family have been detected in metazoans as well. Members of this family are called Mutator-like elements (MULE s). They encode transposases, which contain a region conserved with transposases of the IS256 prokaryotic family, known to harbor a DDE catalytic domain. Different DDE or D34E motifs have been proposed in some groups of eukaryotic MULEs based on primary sequence conservation. On a large number of protein sequences related to, and representative of, all MULE families, we analyzed global conservation, the close environment of different acidic residues and the secondary structure. This allowed us to identify a potential DDE motif that is likely to be homologous to the one in IS256-like transposases. The characteristics of this motif are depicted in each known family of MULEs. Different hypotheses about the evolution of this triad are discussed.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9178-1
• Authors
  • Aurélie Hua-Van, Centre National de la Recherche Scientifique Laboratoire Evolution, Génomes et Spéciation UPR9034 91198 Gif-sur-Yvette France
  • Pierre Capy, Centre National de la Recherche Scientifique Laboratoire Evolution, Génomes et Spéciation UPR9034 91198 Gif-sur-Yvette France

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  The plastid genome of Trifolium subterraneum is 144,763 bp, about 20 kb longer than those of closely related legumes, which also lost one copy of the large inverted repeat (IR). The genome has undergone extensive genomic reconfiguration, including the loss of six genes (accD, infA, rpl22, rps16, rps18, and ycf1) and two introns (clpP and rps12) and numerous gene order changes, attributable to 14–18 inversions. All endpoints of rearranged gene clusters are flanked by repeated sequences, tRNAs, or pseudogenes. One unusual feature of the Trifolium subterraneum genome is the large number of dispersed repeats, which comprise 19.5% (ca. 28 kb) of the genome (versus about 4% for other angiosperms) and account for part of the increase in genome size. Nine genes (psbT, rbcL, clpP, rps3, rpl23, atpB, psbN, trnI-cau, and ycf3) have also been duplicated either partially or completely. rpl23 is the most highly duplicated gene, with portions of this gene duplicated six times. Comparisons of the Trifolium plastid genome with the Plant Repeat Database and searches for flanking inverted repeats suggest that the high incidence of dispersed repeats and rearrangements is not likely the result of transposition. Trifolium has 19.5 kb of unique DNA distributed among 160 fragments ranging in size from 30 to 494 bp, greatly surpassing the other five sequenced legume plastid genomes in novel DNA content. At least some of this unique DNA may represent horizontal transfer from bacterial genomes. These unusual features provide direction for the development of more complex models of plastid genome evolution.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9180-7
• Authors
  • Zhengqiu Cai, The University of Texas at Austin Austin TX 78712 USA
  • Mary Guisinger, The University of Texas at Austin Austin TX 78712 USA
  • Hyi-Gyung Kim, The University of Texas at Austin Austin TX 78712 USA
  • Elizabeth Ruck, The University of Texas at Austin Austin TX 78712 USA
  • John C. Blazier, The University of Texas at Austin Austin TX 78712 USA
  • Vanity McMurtry, The University of Texas M. D. Anderson Cancer Center Houston TX 77030 USA
  • Jennifer V. Kuehl, DOE Joint Genome Institute Walnut Creek CA 94598 USA
  • Jeffrey Boore, DOE Joint Genome Institute Walnut Creek CA 94598 USA
  • Robert K. Jansen, The University of Texas at Austin Austin TX 78712 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9158-5
• Authors
  • Valeria Itskovich, Laboratory of Analytical Bio-Organic Chemistry, Limnological Institute of the Siberian Branch of the Russian Academy of Sciences Ulan-Batorskaya 3 664 033 Irkutsk Russia
  • Andrey Gontcharov, Institute of Biology and Soil Science of the Far Eastern Branch of the Russian Academy of Sciences pr. 100-leti Vladivostoka 159 690022 Vladivostok Russia
  • Yoshiki Masuda, Kawasaki Medical School Department of Biology Kurashiki 701-0192 Japan
  • Tsutomu Nohno, Kawasaki Medical School Department of Biology Kurashiki 701-0192 Japan
  • Sergey Belikov, Laboratory of Analytical Bio-Organic Chemistry, Limnological Institute of the Siberian Branch of the Russian Academy of Sciences Ulan-Batorskaya 3 664 033 Irkutsk Russia
  • Sofia Efremova, St. Petersburg State University Laboratory of Ontogenesis, Biological Research Institute Oranienbaumskoe sch. 2, Stary Peterhoff 198 904 St. Petersburg Russia
  • Martin Meixner, SMB R.- Breitscheidstr. 70 15562 Ruёdersdorf Germany
  • Dorte Janussen, Forschungsinstitut und Naturmuseum Senckenberg Frankfurt am Main Germany

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  In the yeast or nematode, the proportion of essential genes in duplicates is lower than in singletons (single-copy genes), due to the functional redundancy. One may expect that it should be the same in the mouse genome. However, based on the publicly available mouse knockout data, it was observed that the proportion of essential genes in duplicates is similar to that in singletons. The most straightforward interpretation, as claimed in a recent study, is that duplicate genes may have a negligible role in the mouse genetic robustness. Here we show that in the current mouse knockout dataset, recently duplicated genes have been highly underrepresented, leading to an overestimation of the proportion of essential genes in duplicates. After estimating the duplication time of mouse duplication events, we have developed a simple bias-correcting procedure and shown that the bias-corrected proportion of essential genes in mouse duplicates is significantly lower than that in singletons.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9170-9
• Authors
  • Zhixi Su, Fudan University Institutes of Biomedical Sciences Shanghai 200032 China
  • Xun Gu, Fudan University Institutes of Biomedical Sciences Shanghai 200032 China

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  We have performed a genome-wide analysis of the mimp family of miniature inverted-repeat transposable elements, taking advantage of the recent release of the F. oxysporum genome sequence. Using different approaches, we detected 103 mimp elements, corresponding to 75 nonredundant copies, half of which are located on a single small chromosome. Phylogenetic analysis identified at least six subfamilies, all remarkably homogeneous in size and sequence. Based on high sequence identity in the terminal inverted repeats (TIRs), mimp elements were connected to different impala members. To gain insights into the mechanisms at the origin and amplification of mimps, we studied the potential of impala to cross-mobilize different mimps, native but also created de novo by inserting a short DNA segment between two TIRs. Our results show that TIR sequences are the main requirement for mobilization but that additional parameters in the internal region are likely to influence transposition efficiency. Finally, we show that integration site preference of native versus newly transposed mimps greatly varies in the host genomes used in this study.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9164-7
• Authors
  • Mara Bergemann, Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621 91405 Orsay France
  • Olivier Lespinet, Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621 91405 Orsay France
  • Sarrah Ben M’Barek, Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621 91405 Orsay France
  • Marie-Josée Daboussi, Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621 91405 Orsay France
  • Marie Dufresne, Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621 91405 Orsay France

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  All striated muscles respond to stretch by a delayed increase in tension. This physiological response, known as stretch activation, is, however, predominantly found in vertebrate cardiac muscle and insect asynchronous flight muscles. Stretch activation relies on an elastic third filament system composed of giant proteins known as titin in vertebrates or kettin and projectin in insects. The projectin insect protein functions jointly as a “scaffold and ruler” system during myofibril assembly and as an elastic protein during stretch activation. An evolutionary analysis of the projectin molecule could potentially provide insight into how distinct protein regions may have evolved in response to different evolutionary constraints. We mined candidate genes in representative insect species from Hemiptera to Diptera, from published and novel genome sequence data, and carried out a detailed molecular and phylogenetic analysis. The general domain organization of projectin is highly conserved, as are the protein sequences of its two repeated regions—the immunoglobulin type C and fibronectin type III domains. The conservation in structure and sequence is consistent with the proposed function of projectin as a scaffold and ruler. In contrast, the amino acid sequences of the elastic PEVK domains are noticeably divergent, although their length and overall unusual amino acid makeup are conserved. These patterns suggest that the PEVK region working as an unstructured domain can still maintain its dynamic, and even its three-dimensional, properties, without the need for strict amino acid conservation. Phylogenetic analysis of the projectin proteins also supports a reclassification of the Hymenoptera in relation to Diptera and Coleoptera.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9177-2
• Authors
  • Agnes J. Ayme-Southgate, College of Charleston Department of Biology 66 George Street Charleston SC 29401 USA
  • Richard J. Southgate, College of Charleston Department of Biology 66 George Street Charleston SC 29401 USA
  • Richard A. Philipp, College of Charleston Department of Biology 66 George Street Charleston SC 29401 USA
  • Erik E. Sotka, College of Charleston Department of Biology 66 George Street Charleston SC 29401 USA
  • Catherine Kramp, College of Charleston Department of Biology 66 George Street Charleston SC 29401 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Ants live in crowded nests with interacting individuals, which makes them particularly prone to infectious diseases. The question is, How do ants cope with the increased risk of pathogen transmission due to sociality? We have studied the molecular evolution of defensin, a gene encoding an antimicrobial protein, in ants. Defensin sequences from several ant species were analyzed with maximum likelihood models of codon substitution to infer selection. Positive selection was detected in the mature region of defensin, whereas the signal and pro regions seem to be evolving neutrally. We also found a significantly higher rate of nonsynonymous substitutions in some phylogenetic lineages, as well as d N /d S  > 1, suggesting varying selection pressures in different lineages. Earlier studies on the molecular evolution of insect antimicrobial peptide genes have focused on termites and dipteran species, and detected positive selection only in duplicated termicin genes in termites. These findings, together with our present results, provide an indication that the immune systems of social insects (ants and termites) and dipteran insects may have responded differently to the selection pressure caused by microbial pathogens.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9173-6
• Authors
  • Lumi Viljakainen, University of Oulu Department of Biology and Biocenter Oulu P.O. Box 3000 Oulu 90014 Finland
  • Pekka Pamilo, University of Oulu Department of Biology and Biocenter Oulu P.O. Box 3000 Oulu 90014 Finland

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of amino acid substitutions in the plant gene eIF4E to evaluate the performance of these methods in detecting site-specific positive selection. We documented for the first time a molecular signature of positive selection within a recessive resistance gene in plants. We then used two statistical platforms, Phylogenetic Analysis Using Maximum Likelihood and Hypothesis Testing Using Phylogenies (HyPhy), to look for site-specific positive selection. Their relative power and accuracy are assessed by comparing the sites they identify as being positively selected with those of resistance-determining amino acids. Our results indicate that although both methods are surprisingly accurate in their identification of resistance sites, HyPhy appears to more accurately identify biologically significant amino acids using our data set.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9172-7
• Authors
  • J. R. Cavatorta, Cornell University Department of Plant Breeding and Genetics Ithaca NY USA
  • A. E. Savage, Cornell University Department of Ecology and Evolutionary Biology Ithaca NY USA
  • I. Yeam, Cornell University Department of Plant Breeding and Genetics Ithaca NY USA
  • S. M. Gray, Cornell University United States Department of Agriculture-Agricultural Research Station (USDA-ARS), Department of Plant Pathology Ithaca NY USA
  • M. M. Jahn, Cornell University Department of Plant Breeding and Genetics Ithaca NY USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  The divergent domain D8 of the large ribosomal RNA is very variable and extended in vertebrates compared to other eukaryotes. We provide data from 31 species of echinoderms and present the first comparative analysis of the D8 in nonvertebrate deuterostomes. In addition, we obtained 16S mitochondrial DNA sequences for the sea urchin taxa and analyzed single-strand conformation polymorphism (SSCP) of D8 in several populations within the species complex Echinocardium cordatum. A common secondary structure supported by compensatory substitutions and indels is inferred for echinoderms. Variation mostly arises at the tip of the longest stem (D8a), and the most variable taxa also display the longest and most stable D8. The most stable variants are the only ones displaying bulges in the terminal part of the stem, suggesting that selection, rather than maximizing stability of the D8 secondary structure, maintains it in a given range. Striking variation in D8 evolutionary rates was evidenced among sea urchins, by comparison with both 16S mitochondrial DNA and paleontological data. In Echinocardium cordatum and Strongylocentrotus pallidus and S. droebachiensis, belonging to very distant genera, the increase in D8 evolutionary rate is extreme. Their highly stable D8 secondary structures rule out the possibility of pseudogenes. These taxa are the only ones in which interspecific hybridization was reported. We discuss how evolutionary rates may be affected in nuclear relative to mitochondrial genes after hybridization, by selective or mutational processes such as gene silencing and concerted evolution.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9171-8
• Authors
  • Anne Chenuil, Université Aix-Marseille II, Université de la Méditerranée, Centre d’Océanologie de Marseille, Station marine d’Endoume Laboratoire DIMAR, diversité, évolution, écologie fonctionnelle marine, CNRS UMR6540 rue de la batterie des Lions 13007 Marseille France
  • Emilie Egea, Université Aix-Marseille II, Université de la Méditerranée, Centre d’Océanologie de Marseille, Station marine d’Endoume Laboratoire DIMAR, diversité, évolution, écologie fonctionnelle marine, CNRS UMR6540 rue de la batterie des Lions 13007 Marseille France
  • Caroline Rocher, Université Aix-Marseille II, Université de la Méditerranée, Centre d’Océanologie de Marseille, Station marine d’Endoume Laboratoire DIMAR, diversité, évolution, écologie fonctionnelle marine, CNRS UMR6540 rue de la batterie des Lions 13007 Marseille France
  • Hélène Touzet, LIFL, CNRS UMR 8022, Université Lille 1 Villeneuve d’Ascq France
  • Jean-Pierre Féral, Université Aix-Marseille II, Université de la Méditerranée, Centre d’Océanologie de Marseille, Station marine d’Endoume Laboratoire DIMAR, diversité, évolution, écologie fonctionnelle marine, CNRS UMR6540 rue de la batterie des Lions 13007 Marseille France

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  The naked carp (Gymnocypris przewalskii) is a native teleost of Lake Qinghai (altitude, 3.2 km) on the Qinghai-Tibet Plateau in China. Hypoxia-inducible factor (HIF)-1α of Gymnocypris przewalskii was cloned and a phylogenetic tree for vertebrate HIF-1α was constructed. By analysis of maximum likelihood models of codon substitutions for HIF-1α, three positive sites in the branch lineages of crucian carp, eelpout, and flounder, and a higher proportion of neutral sites in naked carp, antarctic eelpout, rainbow trout, and grayling, were detected among all teleosts. It seems that low habitat temperatures relax the purifying selection of HIF-1α in these stenothermal coldwater fish, and both cold and hypoxic lake water contributed to the evolution of the HIF-1α gene in the naked carp. Furthermore, Glut 1 mRNA, a gene downstream from HIF-1α, has a time-course- and tissue-specific dependent response to hypoxic challenge.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9175-4
• Authors
  • Yi-Bin Cao, Zhejiang University Division of Neurobiology and Physiology, College of Life Sciences Hangzhou 310058 China
  • Xue-Qun Chen, Zhejiang University Division of Neurobiology and Physiology, School of Medicine Hangzhou 310058 China
  • Shen Wang, Zhejiang University Division of Neurobiology and Physiology, College of Life Sciences Hangzhou 310058 China
  • Yu-Xiang Wang, Queen’s University Department of Biology Kingston ON Canada K7L 3N6
  • Ji-Zeng Du, Zhejiang University Division of Neurobiology and Physiology, College of Life Sciences Hangzhou 310058 China

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Genetic robustness, insensitivity of the phenotype facing genetic mutations, is a fundamental and ubiquitously observed property of biological systems. In this study, we investigate the genetic robustness of the structural elements within native miRNA genes on a genome-wide scale. MicroRNAs (miRNAs) are a large family of endogenous noncoding RNAs that regulate gene expression at the posttranscriptional level. We examine the neutrality of the structural element in 1082 native pre-miRNAs from six species and demonstrate that the structural elements in native pre-miRNAs exhibit a significantly higher level of genetic robustness in comparison with structural elements within random pseudo pre-miRNAs. Hence, this excess robustness of structural elements in pre-miRNAs goes beyond the intrinsic robustness of the stem-loop structure. Furthermore, we show that it is not a by-product of a base composition bias. Interestingly, our data also demonstrate a difference in increased levels of average neutrality between structural elements. Remarkably, differential genetic robustness between structural elements is observed in both native and pseudo pre-miRNAs. Our results are much in agreement with previous experimental observations, and suggest that the genetic robustness of secondary structural elements in native pre-miRNAs, under different evolutionary selection pressures, may evolve due to its own selective advantage.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9174-5
• Authors
  • Wenjie Shu, Beijing Institute of Radiation Medicine Beijing 100850 China
  • Ming Ni, Beijing Institute of Radiation Medicine Beijing 100850 China
  • Xiaochen Bo, Beijing Institute of Radiation Medicine Beijing 100850 China
  • Zhiqiang Zheng, National University of Defense Technology College of Electro-Mechanic and Automation Changsha Hunan 410073 China
  • Shengqi Wang, Beijing Institute of Radiation Medicine Beijing 100850 China

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844

Abstract  Prokaryotic organisms preferentially utilize less energetically costly amino acids in highly expressed genes. Studies have shown that the proteome of Saccharomyces cerevisiae also exhibits this behavior, but only in broad terms. This study examines the question of metabolic efficiency as a proteome-shaping force at a finer scale, examining whether trends consistent with cost minimization as an evolutionary force are present independent of protein function and amino acid physicochemical property, and consistently with respect to amino acid biosynthetic costs. Inverse correlations between the average amino acid biosynthetic cost of the protein product and the levels of gene expression in S. cerevisiae are consistent with natural selection to minimize costs. There are, however, patterns of amino acid usage that raise questions about the strength (and possibly the universality) of this selective force in shaping S. cerevisiae’s proteome.

• Content Type Journal Article
• DOI 10.1007/s00239-008-9162-9
• Authors
  • Douglas W. Raiford, Southern Methodist University Department of Computer Science and Engineering P.O. Box 750122 Dallas TX 75275 USA
  • Esley M. Heizer, Wright State University Department of Biological Sciences 3640 Colonel Glenn, Highway Dayton OH 45435 USA
  • Robert V. Miller, Oklahoma State University Department of Microbiology and Molecular Genetics Stillwater OK 74078 USA
  • Hiroshi Akashi, Pennsylvania State University Department of Biology University Park PA 16802 USA
  • Michael L. Raymer, Wright State University Department of Computer Science and Engineering Dayton OH 45435 USA
  • Dan E. Krane, Wright State University Department of Biological Sciences 3640 Colonel Glenn, Highway Dayton OH 45435 USA

• Journal Journal of Molecular Evolution
• Online ISSN 1432-1432
• Print ISSN 0022-2844