Molecular Evolution Forum
Time 2021-10-18 20:06:16Web Name: Molecular Evolution Forum
WebSite: http://molecularevolutionforum.blogspot.com
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keywords: description:Introduction of notable papers and books
The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.
Friday, March 14, 2014 Horizontal Gene Transfer Takes a Turn: Expansins from Plants to their Bacterial and Eukaryotic ParasitesLabels:Horizontal gene transferContributed by: Dimitra Chalkia
Genetic material is inherited from parentsto offspring and this process is known as vertical transmission. Howevergenetic material can be transferred form one organism to another in a non-genealogicalfashion. Such type of transmission is defined as horizontal transmission or genetransfer (HGT) (1). Although mechanisms for the transfer of genetic materialbetween organisms were known from the early years of molecular biology andgenetics research, and the theoretical potential of cross-species gene transferin evolution was proposed in the 1980s, the concept of HGT emerged in the 1990s(2). It was invoked as an alternative explanation for rarely observed incongruentphylogenetic relationships between species (2). However, the recentavailability of genome sequence information and the thorough study of multiple pro-and eukaryotic genomes has revealed that HGT is pervasive and powerful amongmicrobes (1,2,3). Additionally, more recent studies have shown that HGT is alsoevident between animals and bacteria, with the bacteria being the donor species(4,5). In plants, HGT has been relatively well documented, and in most casesinvolves the transfer of genetic material from a parasite to its host plant. Yet,HGTs with the plant species being the donor have rarely been documented.
Recently Nikolaidis et al (6) reported arare case of HGT from plants to multiple plant parasites or free living microorganisms.Specifically, they found that members of the plant expansin gene family, whichcode for plant cell-wall loosening proteins and are comprised of two distinctprotein domains D1 and D2, were transferred from plants to bacteria, fungi, andunicellular eukaryotes (amoebozoa).
Having previously established that thebacterial protein EXLX1 from Bacillus subtilisis structurally and functionally very similar to plant expansins (7,8,9),Nikolaidis et al investigated the evolution of the expansin family in-depth. Todo so they used the bacterial EXLX1 sequence as their primary-sequence databaseinterrogator. Like expansins, EXLX1protein contains two domains, D1 and D2, which are tightly packed structurallywith a conserved open surface spanning both of them (Figure 1a,b). To ensurethat the resulted raw sequence alignments of their exhaustive similaritysearches are not random hits, the authors employed a set of established strict searchcriteria. Remarkably, they identified numeroussequences from bacteria, fungi, and amoebozoa that align to both EXLX1 domainsand therefore may share ancestry with it. If so, the identified sequences are EXLX1homologs. By employing proven phylogenetic tools and methods, as well asprotein domain and fold recognition programs, the authors confirmed that allidentified proteins contain both expansin domains, and showed that thepredicted protein structures are very similar to both B. subtilis EXLX1 and plant expansins, further supporting the homologyinference (Figures 1 and 2).
Figure 1. The EXLX1 homologsare predicted to contain two domains, fold similarly to the Zea mays EXPB1 (a) and the B. subtilis EXLX1 (b), and contain aconserved long hydrophobic surface. (c, d) structural alignments of thethree-dimensional models of the EXLX1 homologs from Ralstonia and Erwiniawith the EXLX1structure. Surface (e) and ribbon (f) representations of theEXLX1 structure are colored according to conservation in 70 EXP domainsequences from bacteria and fungi (blue to red with increasingconservation). From Nikolaidis et al. (2014) (6).
Figure 2. TheBacillus subtilis EXLX1protein has manyhomologs in bacteria, fungi, and amoebozoa. (a) Phylogeneticrelationships of representativeB. subtilisEXLX1 homologs. Twodifferent phylogenetic methods (NJ and ML) were used with gamma-distributeddistances from the WAG substitution model withα= 1.72.Alignment gaps were excluded and the total number of sites used to constructthe trees was 176. The numbers at the nodes are bootstrap values (NJ/ML). Thebiology of each species is shown with different symbols next to the speciesname. Species names abbreviations are given insupplementary table S1, SupplementaryMaterialonline. Only sequences producing BLAST hits with E-values lowerthan 104and query coverage higher than 80% were used for theconstruction of these trees (b). Many EXLX1homologs contain additionaldomains. The domain organization of the EXLX1 homologs was identified using theConserved Domains Database (CDD) database from NCBI coupled to fold recognitionanalysis. We define as expansin the domain that contains both D1 and D2 domainsaccording to the EXLX1structure (Kerff et al. 2008;Georgelis et al. 2013).From Nikolaidis et al. (2014) (6).
However, sequence similarity is not sufficient forshowing the genetic-material-transmission typevertical or horizontal. Five significantobservations led the authors to support the HGT type: a) the sporadicdistribution of organisms harboring expansin homologs, b) the biologicalfeatures of these organisms plant pathogens, soil inhabitants, or celluloseproducers, c) the incongruence between the phylogenetic tree derived from EXLX1and its homologs and the established bacterial or fungal species tree, d) thefusion of additional and shared protein domains (cellulase GH5 orcarbohydrate-binding modules) in several EXLX1 homologs, and e) the functionalsimilarities between microbial and plant expansins, especially the lack ofcatalytic activity. The latter observation argues against convergence (independentfusion of D1 and D2 domains) because such a scenario would require the biochemicallyand evolutionarily improbable independent loss and gain of the same amino acidresidues in multiple distant phyla.
Relaxing the criteria of their sequence similaritysearches, the authors also examined whether sequences similar to each one ofthe two expansin domains exist. Their results were positive for both domains. Applyingtheir phylogenetic/protein fold recognition methodology to the sequencessimilar only to the second expansin domain (D2), the authors showed that thefungal swollenin protein family is homologous to expansins. Swollenin proteinsare composed of two domains, too. Interestingly, although their N-terminal D1domain contains many conserved insertions and therefore bears very low similaritywith the expansin D1 domain, the folding patterns are very similar.
Regarding the timing of the expansin HGT, the lack ofany differences in parametric measures such as GC-content, amino acid ornucleotide usage, etc., in the EXLX1 homologs allowed the authors to concludeit was not recent. Two additional observations augmented this conclusion.First, the phylogenetic patterns revealed that the HGT of expansins wasfollowed by vertical transfers during certain fungal or amoebozoan speciesevolution. Second, several bacterial and fungal distant species containexpansin genes fused with cellulose GH5 and carbohydrate-binding domains,respectively. According to the authors phylogenetic analysis these extradomains were most likely acquired independently by convergence. Therefore theHGT of expansins from plants to other organisms preceded the long-lasting andslow events of convergence and speciation. Hence it must be ancient.
Regarding the origin of the expansin gene family, theauthors, following a reductio ad absurdumargumentation, favor the scenario of a single origin in the common ancestor ofplants and subsequent horizontal transmission to non-plant species. The patchy distributionof EXLX1 homologs in a small percentage of the tested bacterial (128/4,281 or3%) and fungal (28 /543 or 5.2%) genomes argues against a single origin inbacteria and subsequent vertical transmission, since such a scenario demandsthe absurd assumption of multiple independent gene losses. Additionally, the authors previouslyreported functional similarities between plant and microbial expansins (8,9) arguesagainst convergence, and therefore augments the single origin scenario.
Nikolaidis et al., offer a long list of logical andtightly woven arguments for the HGT scenario of non-plant expansins. However they do admitthe difficulty of proving it beyondreasonable doubt. Another taskyet harder in the case of expansinsis to determineprecisely the donor and recipient species, as well as its mechanism and timing.As more genomes are being sequenced we will probably be able to define at leasta plant lineage that contributed its expansins to its intimately associated parasites.If so, then investigation for the potential mechanisms of HGT will be somehoweased. A current plausible suchmechanism includes a plasmid-mediated transfer (10).
Besides the mechanism and timing of expansins HGT,their adaptive significance for the recipient species is of essence. Experimentalstudies on the physiological role of non-plant expansins have started to shedlight on this topic. The authors report several such studies and propose that theHGT of expansin proteins in plant-interacting microbes contributed new oralternative tools for colonization or infection. The latter hypothesis impliesan adaptive advantage for the plant-infecting organisms and together with theresults of other reports on the role of HGT to the emergence of new diseasessuggests that the observed rarity of HGT is not indicative of its importance inorganismal evolution.
Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbialplant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.
References1.Goldenfeld N, Woese C (2007) Biologys next revolution. Nature 445, 3692.Boto L (2010) Horizontal gene transfer in evolution: facts and challenges. Proc R Soc B 277, 8198273.Syvanen M (2012) Evolutionary Implications of Horizontal Gene Transfer. Annu Rev Genet 46, 3413584.Dunning Hotopp JC (2011) Horizontal gene transfer between bacteria and animals.Trends Genet 27, 157163 5.Boto L (2014) Horizontal gene transfer in the acquisition of novel traits by metazoans. Proc R Soc B 281: 20132450http://dx.doi.org/10.1098/rspb.2013.24506.Nikolaidis N, Doran N, DJ Cosgrove (2014) Plant Expansins in Bacteria and Fungi: Evolution by Horizontal Gene Transfer and Independent Domain Fusion. Mol Biol Evol 31(2), 3763867.Kerff F, Amoroso A, Herman R, et al. (2008) Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization. Proc Natl Acad Sci U S A 105:16876168818.Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. 2011. Structure-function analysis of the bacterial expansin EXLX1. JBiol Chem 286: 16814168239.Georgelis N, Yennawar NH, Cosgrove DJ. 2012. Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin. Proc Natl Acad Sci US A 109:148301483510.Laine MJ, Haapalainen M, Wahlroos T, Kankare K, Nissinen R, et al. 2000. Thecellulase encoded by the native plasmid of Clavibacter michiganensis ssp. sepedonicus plays a role in virulence and contains an expansin-like domain. Physiol Mol PlantPathol 57, 221233
0comments Friday, February 21, 2014 Evolution of a Behavioral Character in a Sparrow SpeciesLabels:Behavioral evolution Althoughthe mutational study of behavioral characters was initiated by Seymour Benzerin the 1960s, his study was concerned primarily with laboratory mutations of fruitfliesand did not give much insight into the evolutionary mechanisms of behavioralcharacters in the wild. For this reason, many authors are now investigatingthis problem at the molecular level. Horton et al. (2014) recently published aninteresting result with respect to the social behavior in the white-throatedsparrow Zonotrichia albicollis.
In thewhite-throated sparrow there are two polymorphic phenotypes with respect to thecolor pattern of the head crown: (1) tan-striped (TS) and (2) white-striped (WS)(Fig. 1). The male WS phenotype isknown to be more aggressive than the male TSwith respect to territoriality and mate-finding. In song-birds, these behaviorsare typically dependent on sex steroid during the breeding season. WS birds have higher plasma testosteronethan the same sex TS birds. However, morphdifferences in behavior cannot be entirely explained by these hormones, becausethe differences persist even when plasma levels are experimentally equalized. Therefore,individual variation in steroid-dependent behavior may be better explained byneural sensitivity to the hormones, for example by variation in thedistribution and abundance of steroid receptors (Horton et al., 2014). From Horton et al. (2014).
By the way, the WS and TS are associated with two inversion haplotypes of chromosome 2(Thomas et al. 2008). That is, the genes controlling WS and TS are apparently locatedin the inverted segment of haplotypes ZAL2mand ZAL2. However, because WS is dominant over TS and the frequency of ZAL2mis relatively low, individuals can roughly be divided into two groups, WS (ZAL2m/ZAL2,) and TS (ZAL2/ZAL2), genotype ZAL2m/ZAL2m,being practically absent. It has also been inferred that ZAL2m was derived from ZAL2 about 2 million years ago by chromosomal inversion and thereforethe polymorphism has existed for a long time. Note also that there is practicallyno recombination between two inverted chromosomes. Horton et al.(2014) looked for steroid receptor genes in the inverted segment and found thatthe gene (ESR1) encoding estrogenreceptor α (ERα) is located in theinverted segment and that the two proteins encoded by the ESR1 genes from the WSand TS phenotypes showed one aminoacid difference but this difference did not affect the gene expression pattern appreciably.They then hypothesized that the phenotypic difference between WS and TS is caused by the difference in the gene regulatory region of thegene. In fact, when the binding sites of transcription factors in the cis-regulatory region upstream of the ESR1 gene were examined by a computerprogram, there was considerable difference between the WS and TS haplotypes(Fig. 2A).
From Horton et al. (2014).
However, to provethat this difference is indeed responsible for the behavioral difference, itwas necessary to show that the expression level of the ESR1 gene is higher in haplotype ZAL2m than in ZAL2.For this purpose, Horton et al. used several molecular techniques such as theluciferase reporter method with HeLa cells and radioimmunoassay. Their results showedthat the expression level of the ESR1gene is about 1.5 times higher in haplotype ZAL2mthan in ZAL2 (Fig. 2B,C).This findingindicates that the difference in expression level of a single major genegenerates a clear phenotypic difference, which in turn affects an importantbehavioral character. At the present time, this type of data is rare, but it ispossible that many behavioral characters are controlled by similar molecularmechanisms, and it is desirable that more studies will be conducted in thefuture. In practice, behavioral characters are generally controlled by manygenes, and eventually we may be able to understand the molecular basis of the characters.Yet, the basic principle of gene expression could be simpler than our intuitionsuggests as in the case of the above example. In their significancestatement, Horton et al. write:
In this series ofstudies, we provide a rare illustration of how a chromosomal polymorphism hasaffected overt social behavior in a vertebrate. White-throated sparrows occurin two alternative phenotypes, or morphs, distinguished by a chromosomalrearrangement. That the morphs differ in territorial and parental behavior hasbeen known for decades, but how the rearrangement affects behavior is not understood.Here we show that genetic differentiation between the morphs affects thetranscription of a gene well known to be involved in social behavior. We thenshow that in a free-living population, the neural expression of this genepredicts both territorial and parental behavior. We hypothesize that thismechanism has played a causal role in the evolution of alternative life-historystrategies.
References
0comments Wednesday, February 5, 2014 Symbiosis and Genome Degeneration: Micro-niche EvolutionLabels:Genomic evolution Symbioticassociation of bacteria with animals and plants are ubiquitous, and about 15%of insect species have been estimated to harbor bacterial species as symbionts(Oakeson et al. 2014). These bacterial symbionts generally have reduced genomesize compared with ancestral free-living bacteria (McCutcheon and Moran 2011). However,these symbionts produce nutrients that are essential for survival of the host,and therefore a mutualistic symbiosis is generated. In many of these bacteria,the initiation of symbiosis occurred a long time ago, so that it is difficultto know how the genome size reduction occurred. In these bacteria, the rate ofamino acid substitution is generally higher than that of ancestral free-livingbacteria (Moran 1996; Lynch 1996), and this high rate has been attributed toadvantageous mutation (Fares et al. 2002) or to Mullers ratchet effect (Lynch1996). However, Itoh et al. (2002) and Dale et al. (2003) suggested that theloss of DNA repair enzymes in these bacteria is responsible for the high rateof amino acid substitution. To resolve this controversy, however, it is importantto know how gene loss occurs in the early stage of evolution of endosymbiosis.
Table 1. General features of thestrain HS, SOPE, andS. glossinidiusgenome sequences
Claytonet al. (2012) and Oakeson et al. (2014) sequenced the genomes of HS and SOPE and compared the genomic sequences with the sequence of S. glossinidius, which was availablefrom the literature. The results indicated that the number of pseudogenes hasincreased substantially in the symbiont bacteria whereas the number of intactgenes (supposedly functional genes) has been reduced (see Table 1 and Fig. 1).Furthermore, a large number of mobile insertion sequences (IS) and a substantialnumber of duplicate genes have accumulated in the symbiotic bacteria.
Figure 1. Alignments ofthree regions of theS. glossinidius, strain HS, and SOPEchromosomes. Alignments of threeregions of theS. glossinidius, strain HS, and SOPE chromosomes,corresponding to SG0948SG0977 (A), ps_SGL0466SG0918 (B) andps_SGL0318ps_SGL0330 (C) in the most recentS. glossinidiusannotation[25]. Putative ORFs and intergenic regions are drawn according to scale,oriented according to their inferred direction of transcription and color-codedaccording to COG functional categories. While all of the depicted strain HS genes have intact reading frames, thestatus of their orthologs inS. glossinidiusand SOPE are shown in the outer bars (green= intact, purple = inactivated). Nonsense mutations (premature stop codons) aredepicted by purple diamonds, and frameshifting indels are depicted by purpletriangles. Light grey connecting bars are syntenic nucleotide alignments, whilebrown bars illustrate IS-element acquisitions that occur more frequently in SOPE.
Theseresults suggest that when free-living bacteria entered into a host insect manygenes of the free-living bacteria was nonfunctionalized because they were notnecessary in the insect host. At the same time normally harmful IS elementshave accumulated because the destruction of many functional genes by IS elementsappear to be harmless under the condition of symbiosis. It is interesting tonote that these evolutionary changes have occurred very rapidly because in theinitial stage of symbiosis many useless genes can be pseudogenized but thepseudogenes may be retained in the genome for some time. (In the present casesymbiosis was estimated to have occurred only about 28,000 years ago, thoughthis estimate seems to be too low; Concord et al. 2008.) This rapid regressiveevolution occurred apparently because a small number of free-living bacteriacolonized in the bacteriocytes of the host and the number of verticallyinherited bacteria has remained to be small. I would like to call this type ofevolution small-niche or micro-niche evolution. In micro-niche evolution, thebacterial population was effectively homozygous, and many mutational changesare expected to be fixed at the rate of mutation unless they are deleterious underthe symbiotic condition.
References
13.Jeffery WR. 2009. Regressive evolution in Astyanax cavefish. Annu Rev Genet 43:25-47.
14.Yoshizawa, M., Yamamoto, Y., OQuin, K. E., Jeffery, W. R. (2012).Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish. BMC Biology10:108.15.Nei, M. (2013). Mutation-driven evolution. Oxford University Press, Oxford.0comments Friday, December 20, 2013 Selective Advantage of New Mutations May Depend on Mutations in Other SitesLabels:Adaptation
Contributed by: Zhenguo Zhang
Advantageous mutations may facilitate the adaptation of organisms to new environments. However, a single mutation which is advantageous in a given genetic background may be deleterious in another genetic background. This occurs when gene interaction or epistasis exists (1). An interesting case of epistatic interaction was recently observed in the hemoglobin of the deer mouse, Peromyscus maniculatus (2).
Figure 1. The 3-D structure (PDB ID: 1GZX) ofhuman Hemoglobin. The -chainsand -chains are in purple and cyan,respectively. The heme groups are in green and the bound oxygen moleculars arein red.Hemoglobin is the oxygen transporter in red blood cells of all vertebrates. It can load oxygen from the respiratory organs (such as lungs and gills) and release it in other tissues (such as muscles), where oxygen is utilized for generating energy. Hemoglobin is a tetramer consisting of two -chains and two -chains, encoded by - and -globin genes, respectively (Fig. 1). It has been known that the hemoglobin of high-altitude deer mouse populations has a high hemoglobin-oxygen affinity, which enhances the physiological performance under hypoxia. However, the molecular mechanism of this high oxygen affinity was unknown. Natarajan et al. compared the hemoglobins of deer mice living in highland (Rocky Mountains) and lowland (Great Plains) populations and identified 12 key amino acid mutations, among which 8 mutations occurred in the -globin and 4 in the -globin (Fig. 2). These 12 mutations were separated into three regions of the genes based on the linkage disequilibrium information: 5 mutations in -globin exon 2, 3 mutations in -globin exon 3, and 4 mutations in -globin (Fig. 2). The allelic group for each region was denoted by the letter H or L, depending on whether it came from the highland (H) or lowland (L) population. The notation HH-H thus represents a combination of the highland allelic groups in the three regions (-globin exon 2, -globin exon 3, and -globin). To test the epistasis among the mutations at these regions, Natarajan et al. constructed eight recombinant hemoglobins by permuting all (23 = 8) combinations of allelic group variants (Fig. 2), and tested the oxygen affinity of the recombinant proteins in vitro with or without allosteric effectors (Cl- and DPG).Figure 2. The 8 genotypes of the recombinantdeer mouse hemoglobin. (From Natarajan etal., Science, 2013). Each line denotes the amino acids of one recombinanthemoglobin at the polymorphic sites with the amino acids from the highlandpopulation in blue and those from the lowland population in red. The results of this experiment clearly showed that epistasis occurred among the allelic groups of the three regions (Table 1). For example, under the condition with the Cl- anion (the +KCl line in Table 1), changing from the L to H allelic group in any region in the LL-L background decreased oxygen affinity (corresponding to a higher P50 value), but the simultaneous changes in all three regions to the H allelic group (i.e., HH-H) increased oxygen affinity, contrary to the expectation from the additive effect model. As shown in the lower half of Table 1, the sensitivity of recombinant hemoglobins to the allosteric effectors (denoted by ΔlogP50) is also modulated by epistatic interactions of these three regions. 3-D structural analysis of different hemoglobin variants indicated no direct interactions among these mutational sites, but different sets of hydrogen bonds formed in each recombinant hemoglobin (2). This implies that the epistatic interactions of these mutations may be mediated by coordinated changes of protein topology.
Table 1(From Natarajan et al., Science, 2013. P50 represents the oxygen pressurewhen 50% of the hemes of hemoglobins are saturated with oxygen. The genotype ofeach recombinant hemoglobin is denoted by three letters, for example, LH-Lrepresenting the L allele for -globin exon 2, H allele for -globin exon 3, and L allele for -globin. H and Ldenote the alleles present in the highland and lowland populations,respectively)This study (2) demonstrates that the effect of a mutation on the oxygen affinity depends on the genetic background. Since epistasis is prevalent in the genome (3), it is important to take into account the genetic background when one wants to know the evolution of a complex character with epistatic effect. In this case there are several possible ways of evolution from low-altitude hemoglobins to high-altitude hemoglobins or vice versa, as in the case of other proteins (4, 5). Genetic drift and environmental changes also may have played important roles.
Abstract of the original paperEpistaticinteractions between mutant sites in the same protein can exert a stronginfluence on pathways of molecular evolution. We performed protein engineeringexperiments that revealed pervasive epistasis among segregating amino acid variantsthat contribute to adaptive functional variation in deer mouse hemoglobin (Hb).Amino acid mutations increased or decreased Hb-O2 affinity dependingon the allelic state of other sites. Structural analysis revealed thatepistasis for Hb-O2 affinity and allosteric regulatory control isattributable to indirect interactions between structurally remote sites. Theprevalence of sign epistasis for fitness-related biochemical phenotypes hasimportant implications for the evolutionary dynamics of protein polymorphism innatural populations.
References1. LehnerB: Molecular mechanisms of epistasis within and between genes. TrendsGenet 2011, 27(8):323-331.2. NatarajanC, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF: Epistasis among adaptive mutations in deer mouse hemoglobin. Science 2013, 340(6138):1324-1327.3. Nei M, Ebooks Corporation: Mutation-driven evolution. In., 1st edn. Oxford: Oxford UniversityPress; 2013: 1 online resource.4. Salverda ML, Dellus E, Gorter FA,Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JA: Initial mutations direct alternative pathways of protein evolution. PLoSGenet 2011, 7(3):e1001321.5. Lozovsky ER, Chookajorn T, Brown KM,Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL: Stepwise acquisition of pyrimethamine resistance in the malaria parasite. ProcNatl Acad Sci U S A 2009, 106(29):12025-12030.
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