MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega. The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command l...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Kumar, S., Stecher, G., Tamura, K. Tags: Resources Source Type: research
A Simple, General Result for the Variance of Substitution Number in Molecular Evolution
The number of substitutions (of nucleotides, amino acids, etc.) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of substitutions during molecular evolution of a sequence can be estimated for a given substitution model, no simple solution exists for the variance of this random variable. We show in this article that the computation of the variance is as simple as that of the mean number of substitutions for both short and long times. Apart from its fundamental importance, this result can be used to investigate ...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Houchmandzadeh, B., Vallade, M. Tags: Methods Source Type: research
Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss
We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v. We consider the limiting case known as the infinitely ...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Zamani-Dahaj, S. A., Okasha, M., Kosakowski, J., Higgs, P. G. Tags: Methods Source Type: research
Are There Rab GTPases in Archaea?
A complex endomembrane system is one of the hallmarks of Eukaryotes. Vesicle trafficking between compartments is controlled by a diverse protein repertoire, including Rab GTPases. These small GTP-binding proteins contribute identity and specificity to the system, and by working as molecular switches, trigger multiple events in vesicle budding, transport, and fusion. A diverse collection of Rab GTPases already existed in the ancestral Eukaryote, yet, it is unclear how such elaborate repertoire emerged. A novel archaeal phylum, the Lokiarchaeota, revealed that several eukaryotic-like protein systems, including small GTPases,...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Surkont, J., Pereira-Leal, J. B. Tags: Discoveries Source Type: research
Evolution of the APETALA2 Gene Lineage in Seed Plants
Gene duplication is a fundamental source of functional evolutionary change and has been associated with organismal diversification and the acquisition of novel features. The APETALA2/ETHYLENE RESPONSIVE ELEMENT-BINDING FACTOR (AP2/ERF) genes are exclusive to vascular plants and have been classified into the AP2-like and ERF-like clades. The AP2-like clade includes the AINTEGUMENTA (ANT) and the euAPETALA2 (euAP2) genes, both regulated by miR172. Arabidopsis has two paralogs in the euAP2 clade, namely APETALA2 (AP2) and TARGET OF EAT3 (TOE3) that control flowering time, meristem determinacy, sepal and petal identity and fru...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Zumajo-Cardona, C., Pabon-Mora, N. Tags: Discoveries Source Type: research
Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics
Experimental studies have found the involvement of certain conserved noncoding sequences (CNSs) in the regulation of the proximal protein-coding genes in mammals. However, reported cases of long range enhancer activities and inter-chromosomal regulation suggest that proximity of CNSs to protein-coding genes might not be important for regulation. To test the importance of the CNS genomic location, we extracted the CNSs conserved between chicken and four mammalian species (human, mouse, dog, and cattle). These CNSs were confirmed to be under purifying selection. The intergenic CNSs are often found in clusters in gene deserts...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Babarinde, I. A., Saitou, N. Tags: Discoveries Source Type: research
Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species
C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Emms, D. M., Covshoff, S., Hibberd, J. M., Kelly, S. Tags: Discoveries Source Type: research
The Complex Admixture History and Recent Southern Origins of Siberian Populations
Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether it remained habitable during the extreme cold of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, because commonly used methods assume a tree-like population history and at most single admixture events. Here we analyze geogenetic maps and use other approaches to distinguish the effects of shared ancestry ...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Pugach, I., Matveev, R., Spitsyn, V., Makarov, S., Novgorodov, I., Osakovsky, V., Stoneking, M., Pakendorf, B. Tags: Discoveries Source Type: research
Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory
The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscapes. Conformational dynamics, which is essential for protein function, has received little attention in the context of evolutionary analyses. Here we employ NMR spectroscopy, the chief experimental tool to describe protein dynamics at atomic level in solution at room temperature, to study the intrinsic dynamic features of a metallo-β-lactamase enzyme and three variants...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Gonzalez, M. M., Abriata, L. A., Tomatis, P. E., Vila, A. J. Tags: Discoveries Source Type: research
Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens
Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ~2.2–3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population e...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Wang, J., Street, N. R., Scofield, D. G., Ingvarsson, P. K. Tags: Discoveries Source Type: research
Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels
We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits (e.g., metabolites and transcripts). Following the approach, we show that a reduction in unsaturated fatty acids was associated with selection during domestication of emmer (primary domestication). We also show that changes in the amino acid content due to selection mark the domestication of durum wheat (secondary domestication). These effects were found to be partially independent of the associations that unsaturated fatty acids and amino acids have with other domestication-related kernel traits. Changes in contents...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Beleggia, R., Rau, D., Laido, G., Platani, C., Nigro, F., Fragasso, M., De Vita, P., Scossa, F., Fernie, A. R., Nikoloski, Z., Papa, R. Tags: Discoveries Source Type: research
Positive Selection on a Regulatory Insertion-Deletion Polymorphism in FADS2 Influences Apparent Endogenous Synthesis of Arachidonic Acid
This study is consistent with previous in vitro data suggesting that the insertion allele enhances n-6 LCPUFA synthesis and may confer an adaptive advantage in South Asians because of the traditional plant-based diet practice. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Kothapalli, K. S. D., Ye, , K., Gadgil, M. S., Carlson, S. E., OBrien, K. O., Zhang, J. Y., Park, H. G., Ojukwu, K., Zou, J., Hyon, S. S., Joshi, K. S., Gu, Z., Keinan, A., Brenna, J. T. Tags: Discoveries Source Type: research
The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography
This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Lapierre, M., Blin, C., Lambert, A., Achaz, G., Rocha, E. P. C. Tags: Discoveries Source Type: research
Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships
Identification of relationships among protein families or superfamilies is a challenge. However, functionally essential protein regions typically retain structural integrity, even when the corresponding protein sequences evolve. Consequently, comparison of protein structures enables deeper phylogenetic analyses than achievable through the use of sequence information only. Here, we focus on a group of distantly related viral and cellular enzymes involved in nucleic acid or nucleotide processing and synthesis. All these enzymes share an apparently similar protein fold at their active site, which resembles the palm subdomain ...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Mönttinen, H. A. M., Ravantti, J. J., Poranen, M. M. Tags: Discoveries Source Type: research
Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering
The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces "sensu stricto" species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Naseeb, S., Carter, Z., Minnis, D., Donaldson, I., Zeef, L., Delneri, D. Tags: Discoveries Source Type: research
