Is Speciation Accompanied by Rapid Evolution? Insights from Comparing Reproductive and Nonreproductive Transcriptomes in Drosophila

The tempo and mode of evolutionary change during speciation have remained contentious until recently. While much of the evidence claiming speciation is an abrupt and rapid process comes from fossil data, recent molecular phylogenetics show that the background of gradual evolution is often broken by accelerated rates of molecular evolution during speciation. However, what kinds of genes affect or are affected by speciation remains unexplored. Our analysis of 4843 protein-coding genes in five species of the Drosophila melanogaster subgroup shows that while ~70% of genes follow clock-like evolution, between 17–19.67% of loci show signatures of accelerated rates of evolution in recently formed species. These genes show 2-3-fold higher rates of substitution in recently diverged species compared to older species. This fraction of loci affects a diverse range of functions. Only a small proportion of reproductive genes experience speciation-related accelerated changes but many sex-and -reproduction related genes show an interesting pattern of persistent rapid evolution suggesting that sex-and-reproduction related genes are under constant selective pressures. The identification of loci associated with accelerated evolution allows us to address the mechanisms of rapid evolution and speciation, which in our study appears to be a combination of both selection and rapid demographical changes

Increased Substitution Rates Surrounding Low-Complexity Regions within Primate Proteins

Previous studies have found that DNA-flanking low-complexity regions (LCRs) have an increased substitution rate. Here, the substitution rate was confirmed to increase in the vicinity of LCRs in several primate species, including humans. This effect was also found among human sequences from the 1000 Genomes Project. A strong correlation was found between average substitution rate per site and distance from the LCR, as well as the proportion of genes with gaps in the alignment at each site and distance from the LCR. Along with substitution rates, dN/dS ratios were also determined for each site, and the proportion of sites undergoing negative selection was found to have a negative relationship with distance from the LCR

Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila

<p>Abstract</p> <p>Background</p> <p>Karl Ernst Von Baer noted that species tend to show greater morphological divergence in later stages of development when compared to earlier stages. Darwin originally interpreted these observations via a selectionist framework, suggesting that divergence should be greatest during ontogenic stages in which organisms experienced varying 'conditions of existence' and opportunity for differential selection. Modern hypotheses have focused on the notion that genes and structures involved in early development will be under stronger purifying selection due to the deleterious pleiotropic effects of mutations propagating over the course of ontogeny, also known as the developmental constraint hypothesis.</p> <p>Results</p> <p>Using developmental stage-specific expressed sequence tag (EST) libraries, we tested the 2 hypotheses by comparing the rates of evolution of 7,180 genes obtained from 6 species of the <it>Drosophila melanogaster </it>group with respect to ontogeny, and sex and reproduction-related functions in gonadal tissues. Supporting morphological observations, we found evidence of a pattern of increasing mean evolutionary rate in genes that are expressed in subsequent stages of development. Furthermore, supporting expectations that early expressed genes are constrained in divergence, we found that embryo stage genes are involved in a higher mean number of interactions as compared to later stages. We noted that the accelerated divergence of genes in the adult stage is explained by those expressed specifically in the male gonads, whose divergence is driven by positive selection. In addition, accelerated gonadal gene divergence occurs only in the adult stage, suggesting that the effects of selection are observed primarily at the stages during which they are expected occur. Finally, we also found a significant correlation between temporal specificity of gene expression and evolutionary rate, supporting expectations that genes with ubiquitous expression are under stronger constraint.</p> <p>Conclusion</p> <p>Taken together, these results support both the developmental constraint hypothesis limiting the divergence of early expressed developmentally important genes, leading to a gradient of divergence rates over ontogeny (embryonic < larval/pupal < adult), as well as Darwin's 'selection opportunity' hypothesis leading to increased divergence in adults, particularly in the case of reproductive tissues. We suggest that a constraint early/opportunity late model best explains divergence over ontogeny.</p

Genome-Wide Analysis of Human Long Noncoding RNAs:A Provocative Review

Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

<p>Abstract</p> <p>Background</p> <p>Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode <it>Caenorhabditis elegans </it>is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three <it>Caenorhabditid </it>nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human) we sought to identify orthologous TFs and characterized their patterns of evolution.</p> <p>Results</p> <p>We identified 988 TF genes in <it>C. elegans</it>, and inferred corresponding sets in <it>C. briggsae </it>and <it>C. remanei</it>, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set), approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types) and HOX family members. Examination of the TF genes in <it>C. elegans </it>and <it>C. briggsae </it>identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in <it>Drosophila melanogaster</it>, <it>Mus musculus </it>and <it>Homo sapiens </it>revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species.</p> <p>Conclusion</p> <p>Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription factors even across distant evolutionary lineages and form the basis for future experiments to examine TF gene function in nematodes and other divergent phyla.</p

MicroRNA Profiling in the Weddell Seal Suggests Novel Regulatory Mechanisms Contributing to Diving Adaptation

Background:The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving... (See full abstract in article)

Reproductive interference and Satyrisation: Mechanisms, outcomes and potential use for insect control

Reproductive Interference occurs when interactions between individuals from different species disrupt reproductive processes, resulting in a fitness cost to one or both parties involved. It is typically observed between individuals of closely related species, often upon secondary contact. In both vertebrates and invertebrates, Reproductive Interference is frequently referred to as ‘Satyrisation’. It can manifest in various ways, ranging from blocking or reducing the efficacy of mating signals, through to negative effects of heterospecific copulations and the production of sterile or infertile hybrid offspring. The negative fitness effects of Satyrisation in reciprocal matings between species are often asymmetric and it is this aspect, which is most relevant to, and can offer utility in, pest management. In this review, we focus on Satyrisation and outline the mechanisms through which it can operate. We illustrate this by using test cases, and we consider the underlying reasons why the reproductive interactions that comprise Satyrisation occur. We synthesise the key factors affecting the expression of Satyrisation and explore how they have potential utility in developing new routes for the management and control of harmful insects. We consider how Satyrisation might interact with other control mechanisms, and conclude by outlining a framework for its use in control, highlighting some of the important next steps

Roadblock: Improved annotations do not necessarily translate into new functional insights

The advent of cost-effective high-throughput nucleotide sequencing means that information about the transcriptome is accruing at an exponential rate, rapidly refining our understanding of the diversity of gene products. It is important that these findings are readily accessible to the wider scientific community to maximise their impact. However, there are multiple barriers to their efficient dissemination and their translation into functional insights. Here, we outline how the status quo can result in information becoming siloed and/or ambiguous, using the CACNA1C gene, which encodes a voltage-gated calcium channel, as an example. We highlight three areas that pose potential barriers to effective information transfer and offer suggestions as to how these may be addressed: firstly, a lack of clarity about the strength of the evidence for individual transcripts in current annotations; secondly, limitations to the transfer of information between nucleotide and protein databases; thirdly, challenges relating to the nomenclature used for transcriptional events and RNA modifications, both for genomic researchers and the wider scientific community

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene’s expression, parameterize the distribution of each gene’s optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease

Evolution of miRNA-binding sites and regulatory networks in cichlids

The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA-binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analyzing the selective constraints driving evolution of miRNA and transcription factor (TF)-binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA- and TF-binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared with subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA- and TF-binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired, for example, clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions, and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits