Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotro...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Nagy, L. G., Riley, R., Tritt, A., Adam, C., Daum, C., Floudas, D., Sun, H., Yadav, J. S., Pangilinan, J., Larsson, K.-H., Matsuura, K., Barry, K., Labutti, K., Kuo, R., Ohm, R. A., Bhattacharya, S. S., Shirouzu, T., Yoshinaga, Y., Martin, F. M., Grigorie Tags: Discoveries Source Type: research
Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia
Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite data set genotyped in 22 populations to estimate...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Alves, I., Arenas, M., Currat, M., Sramkova Hanulova, A., Sousa, V. C., Ray, N., Excoffier, L. Tags: Discoveries Source Type: research
The Time Scale of Recombination Rate Evolution in Great Apes
We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, fu...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Stevison, L. S., Woerner, A. E., Kidd, J. M., Kelley, J. L., Veeramah, K. R., McManus, K. F., Great Ape Genome Project, Bustamante, C. D., Hammer, M. F., Wall, J. D. Tags: Discoveries Source Type: research
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available T...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Yeoh, Y. K., Sekiguchi, Y., Parks, D. H., Hugenholtz, P. Tags: Discoveries Source Type: research
Emergence of Antimicrobial-Resistant Escherichia coli of Animal Origin Spreading in Humans
In the context of the great concern about the impact of human activities on the environment, we studied 403 commensal Escherichia coli/Escherichia clade strains isolated from several animal and human populations that have variable contacts to one another. Multilocus sequence typing (MLST) showed a decrease of diversity 1) in strains isolated from animals that had an increasing contact with humans and 2) in all strains that had increased antimicrobial resistance. A specific B1 phylogroup clonal complex (CC87, Institut Pasteur schema nomenclature) of animal origin was identified and characterized as being responsible for the...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Skurnik, D., Clermont, O., Guillard, T., Launay, A., Danilchanka, O., Pons, S., Diancourt, L., Lebreton, F., Kadlec, K., Roux, D., Jiang, D., Dion, S., Aschard, H., Denamur, M., Cywes-Bentley, C., Schwarz, S., Tenaillon, O., Andremont, A., Picard, B., Mek Tags: Discoveries Source Type: research
