Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo
Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing prese...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Brucato, N., Kusuma, P., Cox, M. P., Pierron, D., Purnomo, G. A., Adelaar, A., Kivisild, T., Letellier, T., Sudoyo, H., Ricaut, F.-X. Tags: Discoveries Source Type: research
Annual Killifish Transcriptomics and Candidate Genes for Metazoan Diapause
We report the diapause transcriptome of the annual killifish Nematolebias whitei, and compare gene expression between diapause embryos and free-living larvae to identify a candidate set of 945 differentially expressed "diapause" genes for this species. Similarity of transcriptional patterns among N. whitei and other diapausing animals is striking for a small set of genes associated with stress resistance, circadian rhythm, and metabolism, while other genes show discordant patterns. Although convergent evolution of diapause may require shared molecular mechanisms for fundamental processes, similar physiological phenotypes a...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Thompson, A. W., Orti, G. Tags: Discoveries Source Type: research
Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont
While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytoso...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Hehenberger, E., Burki, F., Kolisko, M., Keeling, P. J. Tags: Discoveries Source Type: research
Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance
Ohnologs –paralogous gene pairs generated by whole genome duplication– are enriched for dosage sensitive genes, that is, genes that have a phenotype due to copy number changes. Dosage sensitive genes frequently occur in the same metabolic pathway and in physically interacting proteins. Accumulating evidence reveals that functionally related genes tend to co-localize in the three-dimensional (3D) arrangement of chromosomes. We query whether the spatial distribution of ohnologs has implications for their dosage balance. We analyzed the colocalization frequency of ohnologs based on chromatin interaction datasets o...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Xie, T., Yang, Q.-Y., Wang, X.-T., McLysaght, A., Zhang, H.-Y. Tags: Discoveries Source Type: research
Coevolution between Stop Codon Usage and Release Factors in Bacterial Species
Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abu...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Wei, Y., Wang, J., Xia, X. Tags: Discoveries Source Type: research
The Defensins Consist of Two Independent, Convergent Protein Superfamilies
The defensin and defensin-like proteins are an extensive group of small, cationic, disulfide-rich proteins found in animals, plants, and fungi and mostly perform roles in host defense. The term defensin was originally used for small mammalian proteins found in neutrophils and was subsequently applied to insect proteins and plant -thionins based on their perceived sequence and structural similarity. Defensins are often described as ancient innate immunity molecules and classified as a single superfamily and both sequence alignments and phylogenies have been constructed. Here, we present evidence that the defensins have not ...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Shafee, T. M. A., Lay, F. T., Hulett, M. D., Anderson, M. A. Tags: Discoveries Source Type: research
Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus)
The sea lamprey (Petromyzon marinus) is a basal vertebrate that undergoes developmentally programmed genome rearrangements (PGRs) during early development. These events facilitate the elimination of ~20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. Thus far only a handful of germline-specific genes have been definitively identified within the estimated 500 Mb of DNA that is deleted during PGR, although a few thousand germline-specific genes are thought to exist. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predict...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Bryant, S. A., Herdy, J. R., Amemiya, C. T., Smith, J. J. Tags: Discoveries Source Type: research
Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata
We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a var...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Leger, M. M., Eme, L., Hug, L. A., Roger, A. J. Tags: Discoveries Source Type: research
The Role of Deleterious Substitutions in Crop Genomes
In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also repo...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Kono, T. J. Y., Fu, F., Mohammadi, M., Hoffman, P. J., Liu, C., Stupar, R. M., Smith, K. P., Tiffin, P., Fay, J. C., Morrell, P. L. Tags: Discoveries Source Type: research
Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Warnefors, M., Hartmann, B., Thomsen, S., Alonso, C. R. Tags: Discoveries Source Type: research
Evolutionary Consequences of DNA Methylation in a Basal Metazoan
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower s...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Dixon, G. B., Bay, L. K., Matz, M. V. Tags: Discoveries Source Type: research
Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation
At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communities maintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Cox, M. P., Hudjashov, G., Sim, A., Savina, O., Karafet, T. M., Sudoyo, H., Lansing, J. S. Tags: Discoveries Source Type: research
Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages
Understanding how new species form requires investigation of evolutionary forces that cause phenotypic and genotypic changes among populations. However, the mechanisms underlying speciation vary and little is known about whether genomes diversify in the same ways in parallel at the incipient scale. We address this using the nematode, Pristionchus pacificus, which resides at an interesting point on the speciation continuum (distinct evolutionary lineages without reproductive isolation), and inhabits heterogeneous environments subject to divergent environmental pressures. Using whole genome re-sequencing of 264 strains, we e...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: McGaughran, A., Rödelsperger, C., Grimm, D. G., Meyer, J. M., Moreno, E., Morgan, K., Leaver, M., Serobyan, V., Rakitsch, B., Borgwardt, K. M., Sommer, R. J. Tags: Discoveries Source Type: research
The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution
Protein evolution often occurs at unequal rates in different sites along an amino acid chain. Site-specific evolutionary rates have been linked to several structural and functional properties of proteins. Previous analyses of this phenomenon have involved relatively small datasets and, in some cases, the interaction among multiple structural factors is not evaluated. Here, we present the results of a large-scale phylogenetic and statistical analysis, testing the effects and interactions of three structural properties on amino acid replacement rates. We used sequence-based computational methods to predict (i) intrinsic diso...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Ahrens, J., Dos Santos, H. G., Siltberg-Liberles, J. Tags: Discoveries Source Type: research
microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes
We presented evidence that abundance of miRNAs in the same clusters were highly correlated and those miRNAs exerted cooperative repressive effects on target genes in human tissues. By transfecting miRNAs into human and fly cells and extensively profiling the transcriptome alteration with deep-sequencing, we further demonstrated the functional co-adaptation between new and old miRNAs in the miR-17–92 cluster. Our population genomic analysis suggest that positive Darwinian selection might be the driving force underlying the formation and evolution of miRNA clustering. Our model provided novel insights into mechanisms a...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Wang, Y., Luo, J., Zhang, H., Lu, J. Tags: Discoveries Source Type: research
