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2 February 2018

Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data [PLOS One]

Subject Areas : phylogeography, speciation, species delimitation, phylogenetics; paleogenetics, frogs, population genetics, taxonomy

Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon’s range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot.(...)

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1 February 2018

Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces [Scientific Reports]

Keywords : genomics, population genetics

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate host DNA from majority-bacterial samples.(...)

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1 February 2018

Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates [New Phytologist]

Keywords : decomposition, functional diversity, fungal niche, secondary metabolism, symbiosis

The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability.(...)

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31 January 2018

A genome for gnetophytes and early evolution of seed plants [Nature Plants]

Keywords : plant evolution, plant genetics

Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes.(...)

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31 January 2018

Building adaptive capacity to climate change in tropical coastal communities [Nature Climate Change]

Keywords : developing world, interdisciplinary studies, social sciences

To minimize the impacts of climate change on human wellbeing, governments, development agencies, and civil society organizations have made substantial investments in improving people’s capacity to adapt to change. Yet to date, these investments have tended to focus on a very narrow understanding of adaptive capacity. Here, we propose an approach to build adaptive capacity across five domains: the assets that people can draw upon in times of need; the flexibility to change strategies; the ability to organize and act collectively; learning to recognize and respond to change; and the agency to determine whether to change or not.

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