How to: Create rdf input files for Network (www.fluxus-engineering.com)

This is a faster and easier way to produce directly the .rdf input file for Network (v4.6.1.3).
 
1. Open your alignment in DnaSP (I use version 5.10.01).
 
2. From the file menu, click on the “Options for Saving (Nexus Format) and select the default settings.

3. From the file menu, save/export data as Roehl file format and select from the “Generate” menu: Roehl data file (Network software).
 

Save and your .rdf file is ready for use J

(Step by step process here)
 

 

Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

This is a very interesting paper! Here we add to the global availability of barcoded, culturable marine-derived fungi useful for biodiscovery and detailed future genomic and physiological studies. Most importantly, we expose an immense micro-word of marine fungi characterized by virtually unlimited levels of diversity (and I can explain why).

 

From a technical perspective though, this paper  demonstrates the amount of bias and confusion an ordinary biodiversity survey can carry forward and introduce into public databases simply because of improper use of sequence alignment algorithms and genetic distance corrections. We have tested the performance of the automatic barcode gap finder (ABGD) method and its accuracy and comparability of estimating Operational Taxonomic Units (OTUs) against combinations of commonly used alignment algorithms (such as CLUSTAL, KALIGN, MUSCLE and MUFFT) and commonly used genetic distance measures (such as p-distance, K2P correction and the General Time reversible model). Well, in algorithmic OTU delineation, there are big differences in the number of OTUs delivered by each of the combinations between an alignment algorithm and a genetic distance calculation. IN biodiversity surveys the choice of the algorithm really matters.

 

• Andreakis N, Høj L, Kearns P, Hall MR, Ericson G, Cobb RE, et al. (2015) Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters. PLoS ONE 10(8): e0136130. doi:10.1371/journal.pone.0136130

Morphological description of Asparagopsis and Falkenbergia (the marine asparagus and its fluffy pom-pom)

Species and cryptic lineages of the red seaweed Asparagopsis are well-known for their use in biodiscovery, in aquaculture as biological filters but also as notorious invaders and pests causing decline in biodiversity worldwide. The species in this genus, A. armata and the cryptic species complex A. taxiformis, which embraces at least four genetic lineages, share nearly identical tetrasporophytes (i.e., the Falkenbergia stage). One of the A. taxiformis cryptic lineages, the so-called invasive lineage 2, is equipped with unique ecophysiological features. When conditions are met, in short amounts of time, lineage 2 takes over on other, less aggressive, non-native or even local endemics and leaves behind either “dense purple gametophyte forests” or “dense purple tetrasporophyte mats”.

 

 

However, not all of the A. taxiformis cryptic lineages are invasive. Very often, not all of the Asparagopsis gametophytes or tetrasporophytes from within the “purple forest” or the “purple mat” belong to the same lineage. Obviously the prompt identification of a pest is crucial in support of its sustainable management especially when the pest is hidden within morphologically identical conspecifics. In the case of Asparagopsis, only DNA sequencing could tell gametophytes and tetrasporophytes of the cryptic lineages apart. But not anymore! Marianela Zanolla (UMA) in her recently published paper was able to identify morphologically tetrasporophytes and gametophytes of Asparagopsis species and cryptic lineages collected from the Mediterranean Sea and the Hawaiian Islands. Basically these are the places where multiple Asparagopsis lineages are found within few hundred yards. But please pay attention! If you are a marine aquaria lover, you still need to purchase a microscope or a PCR for some DNA analyses. Read more here…