The Path from the RNA World

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history. Received: 14 January 1997 / Accepted: 19 May 1997     

Expression of Barstar as a selectable marker in yeast mitochondria

We describe a new and potentially universal selection system for mitochondrial transformation based on bacterial genes, and demonstrate its feasibility in Saccharomyces cerevisiae. We first found that cytoplasmically synthesized Barnase, an RNase, interferes with mitochondrial gene expression when targeted to the organelle, without causing lethality when expressed at appropriate levels. Next, we synthesized a gene that uses the yeast mitochondrial genetic code to direct the synthesis of the specific Barnase inhibitor Barstar, and demonstrated that expression of this gene, BARSTM, integrated in mtDNA protects respiratory function from imported barnase. Finally, we showed that screening for resistance to mitochondrially targeted barnase can be used to identify rare mitochondrial transformants that had incorporated BARSTM in their mitochondrial DNA. The possibility of employing this strategy in other organisms is discussed.Communicated by R. G. Herrmann     

The poetics of babytalk

Caretaker-infant attachment is a complex but well-recognized adaptation in humans. An early instance of (or precursor to) attachment behavior is the dyadic interaction between adults and infants of 6 to 24 weeks, commonly called "babytalk." Detailed analysis of 1 minute of spontaneous babytalk with an 8-week infant shows that the poetic texture of the mother’s speech—specifically its use of metrics, phonetics, and foregrounding—helps to shape and direct the baby’s attention, as it also coordinates the partners’ emotional communication. We hypothesize that the ability to respond to poetic features of language is present as early as the first few weeks of life and that this ability attunes cognitive and affective capacities in ways that provide a foundation for the skills at work in later aesthetic production and response. By linking developmental social processes with formal cognitive aspects of art, we challenge predominant views in evolutionary psychology that literary art is a superfluous byproduct of adaptive evolutionary mechanisms or primarily an ornament created by sexual selection. David S. Miall is Professor of English at the University of Alberta in Canada. He is the author of essays on British Romantic writers, empirical studies of readers’ responses to literature, hypertext and literary computing. Ellen Dissanayake is Visiting Scholar at the Walter Chapin Simpson Center for the Humanities, University of Washington. Her most recent book is Art and Intimacy: How the Arts Began (2000).     

Mutation Exposed: A Neutral Explanation for Extreme Base Composition of an Endosymbiont Genome

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (ATGC vs. GCAT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 ATGC:GCAT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of ATGC and GCAT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N_e in the molecular evolution of bacterial endosymbionts.Reviewing Editor: Dr. J. William Ballard     

小泡巨鼠对森林种子选择和贮藏的观察

小泡巨鼠是四川省都江堰林区一种占优势的鼠种,取食多种林木种子和果实,可能影响这些树种的更新。于2001年秋季,调查了小泡巨鼠对栓皮栎、袍树、栲树、石栎、青冈和油茶等6种重要林木种子的选择和贮藏,并初步探讨了其对森林更新的影响。结果表明,小泡巨鼠对上述6种林木种子有很强的选择性,种子的营养价值和单宁含量是影响其选择和贮藏的主要因素。小泡巨鼠喜好取食和贮藏单宁含量较低的栲树、油茶和石栎种子,而不喜好取食和贮藏单宁含量较高的袍树、青冈和栓皮栎种子。小泡巨鼠在围栏内分散贮藏了部分种子(特别是石栎和油茶种子),且绝大部分贮藏点仅有1粒种子。小泡巨鼠对种子的选择和贮藏可能对有关林木的更新产生积极影响。     

A New Retroposed Gene in <Emphasis Type="Italic">Drosophila</Emphasis> Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization

A genomic pattern of new gene origination is often dependent on a genomic method that can efficiently identify a statistically adequate number of recently originated genes. The heterochromatic regions have often been viewed as genomic deserts with low coding potential and thus a low flux of new genes. However, increasing reports revealed unexpected roles of heterochromatic regions in the evolution of genes and genomes. We identified recently retroposed genes that originated in heterochromatic regions in Drosophila, by developing microarray-based comparative genomic hybridization (CGH) with multiple species. This new gene family, named Ifc-2h, originated in the common ancestor of the clade of D. simulans, D. mauritiana, and D. sechellia. The sequence features and phylogenetic distribution indicated that Ifc-2h resulted from the retroposition from its parental gene, Infertile crescent (Ifc), and integrated into heterochromatic region of common ancester of the three sibling species 2 million years ago. Expression analysis revealed that Ifc-2h had developed a new expression pattern by recruiting a putative regulatory element from its target sequence. The distribution of indel variation in Ifc-2h of D. simulans and D. mauritiana revealed a significant sequence constraint, suggesting that the Ifc-2h gene may be functional. These analyses cast fresh insight into the evolution of heterochromatin and the origin of its coding regions. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

Do artificial substrates favor nonindigenous fouling species over native species?

Exotic species are prominent constituents of fouling communities. If exotic fouling organisms colonize or compete better on a wider range of substrate types than native species, this may partially account for their high abundance in estuaries and bays. We used four artificial and four naturally occurring substrate types to compare initial settlement and percent cover of native and exotic fouling species through six months of community development. Both the identity of common taxa and the total number of species colonizing artificial versus natural substrate types were similar. Despite the similarities in species richness, relative abundance patterns between natural and artificial substrate types varied, particularly as the communities developed. Native species were initially in equal abundance on natural and artificial substrate types. Initially, the two most common exotic species, the colonial tunicates, Botrylloides violaceus Ritter and Forsyth and Botryllus schlosseri (Pallas), were also in similar, but low, abundance on artificial and natural substrates. As the communities developed, there was little change in abundance of exotic or native species on natural substrates. However, on artificial substrates the exotic tunicates increased dramatically and native species declined in abundance. Artificial surfaces may provide a novel context for competitive interactions giving exotic species a more “level playing field” in an environment for which they otherwise might not be as well adapted compared to long-resident native species. Additions of artificial substrates to nearshore environments may disproportionately favor exotic species by increasing local sources of exotic propagules to colonize all types of substrates.     

Optimizing selection for function-valued traits

We consider a function-valued trait z(t) whose pre-selection distribution is Gaussian, and a fitness function W that models optimizing selection, subject to certain natural assumptions. We show that the post-selection distribution of z(t) is also Gaussian, compute the selection differential, and derive an equation that expresses the selection gradient in terms of the parameters of W and of the pre-selection distribution. We make no assumptions on the nature of the “time” parameter t.      

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

Genome-wide methods offer a powerful approach to detect signatures of drug selection. However, limited availability of suitable reference genomes and the difficulty of obtaining field populations with well-defined, distinct drug treatment histories mean there is little information on the signatures of selection in parasitic nematodes and on how best to detect them. This study addresses these knowledge gaps by using field populations of Haemonchus contortus with well-defined benzimidazole treatment histories, leveraging a recently completed chromosomal-scale reference genome assembly. We generated a panel of 49,393 genomic markers to genotype 20 individual adult worms from each of four H. contortus populations: two from closed sheep flocks with an approximate 20 year history of frequent benzimidazole treatment, and two populations with a history of little or no treatment. Sampling occurred in the same geographical region to limit genetic differentiation and maximise the detection sensitivity. A clear signature of selection was detected on chromosome I, centred on the isotype-1 β-tubulin gene. Two additional, but weaker, signatures of selection were detected; one near the middle of chromosome I spanning 3.75 Mbp and 259 annotated genes, and one on chromosome II spanning a region of 3.3 Mbp and 206 annotated genes, including the isotype-2 β-tubulin locus. We also assessed how sensitivity was impacted by sequencing depth, worm number, and pooled versus individual worm sequence data. This study provides the first known direct genome-wide evidence for any parasitic nematode, that the isotype-1 β-tubulin gene is quantitatively the single most important benzimidazole resistance locus. It also identified two additional genomic regions that likely contain benzimidazole resistance loci of secondary importance. This study provides an experimental framework to maximise the power of genome-wide approaches to detect signatures of selection driven by anthelmintic drug treatments in field populations of parasitic nematodes.     

Mean time to resolution of gene duplication

The mean time to resolution of gene duplication (T_r) is studied in this paper under the double null recessive (DNR) and haplo-insufficient (HI) models within the same analytical and simulation framework. We show that when population size is not too small (more precisely Nμ > 0.1), T_r for unlinked duplication is usually larger than that for linked and T_r for unlinked duplication under the HI model might be greatly prolonged, which were consistent with previous observations. Furthermore, by analytical approach we here indicate the primary underlying mechanism is that the frequency of the original (or wild-type) chromosomal haplotype of the linked duplication decreases nearly exponential to zero with time while that of the unlinked decreases quickly to an quasi-equilibrium; and this phenomenon is particularly profound under the HI model, because the quasi-equilibrium frequency of the original chromosomal haplotype (x₀) under the HI model is higher than that under the DNR model. These results suggest that recombination and HI model might jointly contribute to the marked prolongation of T_r even in a modest population. The prolonged T_r and higher quasi-equilibrium frequency of the original allele at both duplicated loci might have offered more opportunities for the emergence of novel genes.