New Study Reveals Adaptations for Snub-Nosed Monkeys
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
The Great Evolutionary Smoke out: An Advantage for Modern Humans?
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Every Grain of Rice: Ancient Rice DNA Data Provides New View of Domestication History
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Snake Eyes: New Insights into Visual Adaptations
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Lives in the Balance: Why Do We Hold onto Potentially Harmful, Disease-Causing Mutations?
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One reason is that TE abundance needs to be studied at the population level, but sequencing individuals on a population scale is still too expensive to characterize TE abundance in multiple populations. Although sequencing pools of individuals dramatically reduces sequencing costs, a comparison of TE abundance between pooled samples has been difficult, if not impossible, due to various biases. Here, we introduce a novel bioinformatic tool, PoPoolationTE2, which is specifically tailored for the comparison of TE abundance among pooled popul...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Kofler, R., Gomez-Sanchez, D., Schlötterer, C. Tags: Resources Source Type: research
Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats
Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA–DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated t...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Fungtammasan, A., Tomaszkiewicz, M., Campos-Sanchez, R., Eckert, K. A., DeGiorgio, M., Makova, K. D. Tags: Methods Source Type: research
Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure.
Key words: phylogenetics, evolution, tree metrics, genetics, sequencing. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Kendall, M., Colijn, C. Tags: Methods Source Type: research
Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees
The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Kalaghatgi, P., Pfeifer, N., Lengauer, T. Tags: Methods Source Type: research
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Pinosio, S., Giacomello, S., Faivre-Rampant, P., Taylor, G., Jorge, V., Le Paslier, M. C., Zaina, G., Bastien, C., Cattonaro, F., Marroni, F., Morgante, M. Tags: Discoveries Source Type: research
The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them
High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. T...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Zhang, Y., Xia, R., Kuang, H., Meyers, B. C. Tags: Discoveries Source Type: research
Intron Length Coevolution across Mammalian Genomes
Although they do not contribute directly to the proteome, introns frequently contain regulatory elements and can extend the protein coding potential of the genome through alternative splicing. For some genes, the contribution of introns to the time required for transcription can also be functionally significant. We have previously shown that intron length in genes associated with developmental patterning is often highly conserved. In general, sets of genes that require precise coordination in the timing of their expression may be sensitive to changes in transcript length. A prediction of this hypothesis is that evolutionar...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Keane, P. A., Seoighe, C. Tags: Discoveries Source Type: research
Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys
Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats ...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Zhou, X., Meng, X., Liu, Z., Chang, J., Wang, B., Li, M., Wengel, P. O.-t., Tian, S., Wen, C., Wang, Z., Garber, P. A., Pan, H., Ye, X., Xiang, Z., Bruford, M. W., Edwards, S. V., Cao, Y., Yu, S., Gao, L., Cao, Z., Liu, G., Ren, B., Shi, F., Peterfi, Z., Tags: Discoveries Source Type: research
Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome
In this study, we analyzed ELVgv integrations at several genomic locations in four distinct colugo specimens covering all the extant dermopteran species. We confirmed ELVgv integrations in all the specimens examined, which implies that the virus originated before the dermopteran diversification. Using a locus-specific dermopteran substitution rate, we estimated that the proviral integrations occurred 21–40 Ma. Using phylogenetic analysis, we estimated that ELVgv invaded an ancestor of today’s Dermoptera in an even more distant past. We also provide evidence of selective pressure on the TRIM5 antiviral restricti...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Hron, T., Farkasova, H., Padhi, A., Paces, J., Elleder, D. Tags: Discoveries Source Type: research
Divergent Ah Receptor Ligand Selectivity during Hominin Evolution
We have identified a fixed nonsynonymous sequence difference between humans (Val381; derived variant) and Neandertals (Ala381; ancestral variant) in the ligand-binding domain of the aryl hydrocarbon receptor (AHR) gene. In an exome sequence analysis of four Neandertal and Denisovan individuals compared with nine modern humans, there are only 90 total nucleotide sites genome-wide for which archaic hominins are fixed for the ancestral nonsynonymous variant and the modern humans are fixed for the derived variant. Of those sites, only 27, including Val381 in the AHR, also have no reported variability in the human dbSNP databas...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Hubbard, T. D., Murray, I. A., Bisson, W. H., Sullivan, A. P., Sebastian, A., Perry, G. H., Jablonski, N. G., Perdew, G. H. Tags: Discoveries Source Type: research
