Molecular Biology, Genetics & Phylogeny
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Rescooped by Cyril Guibert from Genomics and metagenomics of microbes
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A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction | Molecular Biology, Genetics & Phylogeny | Scoop.it

Abstract: Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting or horizontal gene transfer. In this manuscript we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and incomplete lineage sorting, therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations in order to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.


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Rescooped by Cyril Guibert from Popular Science
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Stunning Videos of Evolution in Action

Stunning Videos of Evolution in Action | Molecular Biology, Genetics & Phylogeny | Scoop.it
The MEGA-plate allows scientists to watch bacteria adapting to antibiotics before their eyes.

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CRISPR is coming to agriculture — with big implications for food, farmers, consumers and nature

CRISPR is coming to agriculture — with big implications for food, farmers, consumers and nature | Molecular Biology, Genetics & Phylogeny | Scoop.it
Gene editing offers dramatic advances in speed, scope and scale of genetic improvement. It also offers an opportunity for more nuanced GMO governance.
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Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degra... - PubMed - NCBI

FEMS Microbiol Ecol. 2015 Jun;91(6). pii: fiv049. doi: 10.1093/femsec/fiv049. Epub 2015 May 4. Research Support, Non-U.S. Gov't

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A molecular phylogeny of birds

A molecular phylogeny of birds | Molecular Biology, Genetics & Phylogeny | Scoop.it
While much progress has been made with respect to the paleontological studies on the origin of birds within Dinosauria, comparable progress was lacking with respect to understanding the relationshi...
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Humble plants that hide surprising secrets

Humble plants that hide surprising secrets | Molecular Biology, Genetics & Phylogeny | Scoop.it
In this intriguing talk, biologist Ameenah Gurib-Fakim introduces us to rare plant species from isolated islands and regions of Africa. Meet the shape-shifting benjoin; the baume de l'ile plate, which might offer a new treatment for asthma; and the iconic baobab tree, which could hold the key to the future of food. Plus: monkey apples.
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Rescooped by Cyril Guibert from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Algorithms for Molecular Biology | Full text | Alignment-free phylogeny of whole genomes using underlying subwords

With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment. There are cases where these techniques cannot be applied, for example if two genomes do not share the same set of genes, or if they are not alignable to each other due to low sequence similarity, rearrangements and inversions, or more specifically to their lengths when the organisms belong to different species. For these cases the comparison of complete genomes can be carried out only with ad hoc methods that are usually called alignment-free methods.

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Ben Hetman's curator insight, October 21, 2013 12:31 PM

This is a lot faster way of producing phylogenies than trying to align everything, and may be more accurate when trying to compare recombinogenic sequences. 

Rescooped by Cyril Guibert from Genomics and metagenomics of microbes
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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits | Molecular Biology, Genetics & Phylogeny | Scoop.it
Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments.

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Rescooped by Cyril Guibert from Genomics and metagenomics of microbes
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Assembly of complex plant–fungus networks : Nature Communications : Nature Publishing Group

Assembly of complex plant–fungus networks : Nature Communications : Nature Publishing Group | Molecular Biology, Genetics & Phylogeny | Scoop.it

Species in ecological communities build complex webs of interaction. Although revealing the architecture of these networks is fundamental to understanding ecological and evolutionary dynamics in nature, it has been difficult to characterize the structure of most species-rich ecological systems. By overcoming this limitation through next-generation sequencing technology, we herein uncover the network architecture of below-ground plant–fungus symbioses, which are ubiquitous to terrestrial ecosystems. The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. In contrast to results for other ecological networks and theoretical predictions for symbiotic networks, the plant–fungus network shows moderate or relatively low levels of interaction specialization and modularity and an unusual pattern of ‘nested’ network architecture. These results suggest that species-rich ecological networks are more architecturally diverse than previously recognized.


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The Hologenome: How Our Relationship With Microbes Drives Our Evolution

The Hologenome: How Our Relationship With Microbes Drives Our Evolution | Molecular Biology, Genetics & Phylogeny | Scoop.it
Is the secret to human intelligence lurking in our guts? Recent studies suggest that it might. Together, your genes and the genes of your microbes make up the “hologenome,” a single entity that is molded and shaped by our environment. Read on to learn how microbes impact our evolutionary fitness and how they may have made our species what it is today.
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Rescooped by Cyril Guibert from Popular Science
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If viruses transfer wasp genes into butterflies, are they GM? | New Scientist

If viruses transfer wasp genes into butterflies, are they GM? | New Scientist | Molecular Biology, Genetics & Phylogeny | Scoop.it

Some claim that North America's famed monarch butterfly is a natural genetically modified organism owing to the transfer of wasp genes by tamed viruses


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Neelima Sinha's curator insight, September 18, 2015 6:48 AM
Are monarch butterflies GMOs?
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Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”

Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus” | Molecular Biology, Genetics & Phylogeny | Scoop.it
RT @OfficialSMBE: MBE latest: Phylogeny of Zebrafish, a "Model Species," within Danio, a "Model Genus" http://t.co/WF3efqjMZc
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What the people of the Amazon know that you don’t

What the people of the Amazon know that you don’t | Molecular Biology, Genetics & Phylogeny | Scoop.it
"The greatest and most endangered species in the Amazon rainforest is not the jaguar or the harpy eagle," says Mark Plotkin, "It's the isolated and uncontacted tribes." In an energetic and sobering talk, the ethnobotanist brings us into the world of the forest's indigenous tribes and the incredible medicinal plants that their shamans use to heal. He outlines the challenges and perils that are endangering them — and their wisdom — and urges us to protect this irreplaceable repository of knowledge
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Rescooped by Cyril Guibert from Genomics and metagenomics of microbes
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A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction | Molecular Biology, Genetics & Phylogeny | Scoop.it

Abstract: Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting or horizontal gene transfer. In this manuscript we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and incomplete lineage sorting, therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations in order to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.


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The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions

The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions | Molecular Biology, Genetics & Phylogeny | Scoop.it

In the microhabitat that surrounds fungal hyphae in soil, coined the mycosphere, carbonaceous compounds that are released from the hyphae stimulate the growth of heterotrophic bacteria, and thus activate organism-to-organism contacts through genetic interactions. Therefore, the mycosphere is postulated to constitute a gene transfer arena, in which a plethora of genes, including locally adaptive ones, are swapped across the resident microbial communities. Such genetic transfers may have plasmids, in particular ones with broad host ranges, as the basis. Indeed, evidence is increasing for the contention that plasmids play crucial roles as accelerators of evolution in the mycosphere, serving as a horizontal gene pool and, therefore, providing competence factors to local bacteria as well as fungi. The evidence so far points at mycosphere roles for two major plasmid classes, the IncP-1 and PromA groups. Moreover, recent data indicate that bacterium-to-fungus gene transfers are detectable and have been evolutionarily important. The large gene pool present in the mycosphere, coupled with the chances for cell-to-cell contact between mycosphere dwellers allows enhanced recombination frequencies, and as such, organisms are selected locally for enhanced fitness.


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Molecular basis of angiosperm tree architecture - Hollender - 2014 - New Phytologist - Wiley Online Library

Molecular basis of angiosperm tree architecture - Hollender - 2014 - New Phytologist - Wiley Online Library | Molecular Biology, Genetics & Phylogeny | Scoop.it
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