Exploring the origins of Australian marine endemic diversity

This is an evolutionary understanding of Australia’s marine fauna that can explain the modern bio-geographic patterns and assist vulnerability-risk assessments of fish families to present and future environmental changes. It is interesting that the Australian continent emerges as a reservoir of biodiversity for the indo-Pacific Ocean in geological periods and as a Noah’s Ark’ for biodiversity in modern days. Read the full NERP report here. In the photo a fossil of an extinct ray. The maskrays originated after the collision of the Australian and Eurasian plates and their speciation may have been accelerated by falls in sea level millions of years ago (Image by John Adamek). 

 

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