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Welcome to The Pipeline

...a blog for members of AustralianBioinformatics.net to share ideas, insights, questions...

Thursday
Jan152015

Potential Publications in Fish Phylogeography Project

Are you

  •       Interested in evolution?
  •       Experienced in bioinformatics, computational biology or statistics?
  •       Free to focus on the phylogeographic analysis of sequence data for 3-4 weeks?
  •       Keen to get a high-impact publication?

…then read on

We are looking for a collaborator to work with on our interesting, novel, well-funded evolutionary biology project with high publication expectations (at Monash University). Specifically we are seeking someone to assist us with the analysis of genetic sequencing data. This is an excellent opportunity for a recent PhD graduate, or an early career researcher with experience in bioinformatics, computational biology or statistics. 

The crater lakes in Nicaragua’s Pacific Basin region are proving to be one of the most fertile areas in the world for novel biological research. In addition to the rugged beauty of the surrounding terrain and the lush tropical forest, underneath the lake’s surfaces evolutionary processes are occurring that many once considered incredibly implausible and that still remain highly controversial today. Specifically, several species of closely related cichlid fish (Amphilophus sp.) are co-existing in sympatry, with speciation events having occurred despite a lack of geographical barriers to prevent gene flow. Despite more than 150 years passing since the publication of The Origin of Species, the relative importance of the mechanisms generating and shaping organismal diversity still continue to be debated vigorously. Understanding these mechanisms that maintain and promote variation in traits under natural selection is therefore a major challenge for evolutionary theory.

Cichlid fishes are a diverse group that are well known for their ability to rapidly evolve and diversify. Closely related species often only vary conspicuously in regard to body colour and trophic characteristics, with differences also occurring within species. We travelled to Nicaragua earlier last year to sample Amphilophus cichlids from Nicaragua’s two great lakes, Lake Nicaragua and Managua. We specifically targeted two species, Amphilophus labiatus and Amphilophus citrinellus. These two species are closely related, however they differ in their diet and key aspects of their trophic morphology. In particular A. labiatus has large fleshy lips, a trait that pops up in several cichlid species across their range (mainly Africa and South/Central America).

Amphilophus labiatus has a patchy distribution, with populations often isolated by tens of kilometres. Elsewhere in Nicaragua, phenotypically similar forms of thick-lipped Amphilophus cichlid (found in different small crater lakes) appear to have occurred due to independent parallel adaptation, within a remarkable short time period. Which leads to the question did the thick-lipped phenotype arise once in the Nicaraguan great lakes or multiple times (in parallel) across the lakes in response to local environmental conditions? Amphilophus citrinellus lives in sympatry with A. labiatus, however it does not possess thick lips, it also has a significantly different diet and a much wider distribution. Importantly, A. citrinellus has two distinct forms that coexist together across much of the lakes. These forms differ in their general body colour, diet and also in the shape and size of the lower pharyngeal jaw, which is thought to be a fundamental cause of phenotypic differentiation and ecological speciation in cichlids via divergent evolution.

We (PhD Candidate Will Sowersby and Assoc. Prof. Bob Wong) have collected samples across the lakes for diet, morphometric and genetic analysis. This work is begin conducted as part of an international collaboration with Dr. Marta Barluenga (Museo Nacional de Ciencias Naturales, Spain), Prof. Walter Salzburger (University of Basel, Switzerland) and Dr. Topi Lehtonen (University of Turku, Finland), who all have multiple publications on Amphilophus cichlids in high impact factor journals. The genetic samples have been prepared for RAD tag sequencing analysis in Europe and the data will be available for analysis shortly.

Specifically we are looking for someone to generate the phylogeography of the two species from multiple locations in both lakes and at the level of gene flow between and within locations.

All samples have been collected and are currently being analysed, we estimate that this will be a short-term commitment. We are looking for a collaborator to work with us for a matter of weeks, starting in March, however we are somewhat flexible with dates at this stage.  You should have a PhD in a relevant subject area (e.g. computational biology, bioinformatics, statistics and genomics).

If you are interested please contact Will Sowersby for any further information: william.sowersby@monash.edu

Monday
Dec152014

Are you working with non-model organisms?

  • Tired of fellow bioinformaticians cheerfully aligning their reads to the umpteenth draft of a reference genome before lunchtime?
  • Faced by masses of diverse data with hardly any structure to prop it up?
  • Sick of reminding folks that the genome you are studying is an autodecaploid, two orders of magnitude larger than Homo sapiens motley assortment of DNA?

Well, help is at hand!

Actually, no.

But at least the folks at TGAC and Bioplatforms want to find out more about the ordeal confronting you.

Click here to answer a short (10 minute) survey...

Friday
Nov142014

You too can post to AustralianBioinformatics.net!

We're fairly sure Lord Kitchener would want you to post to AustralianBioinformatics.net tooAs part of the evolution of the Australian Bioinformatics Network, I am encouraging others to do what Tony Papenfuss, Liam Elbourne and one or two others have done: ...post!

Yes! Any registered member of AustralianBioinformatics.net can post jobs, events, articles, what have you.

And the more who do, the more benefit we can deliver via this online platform.

We've already provided some instructions on how to do this.

For those of you who prefer a walk-though, here's how...

 

 

 

 

Tuesday
Nov112014

This is what 110 people said about ABiC

Bring on the pie charts!!! Arrrgh!Many thanks to those who shared thoughts and ideas about ABiC 2014 and beyond.

Results are in and you can read them in summary by clicking here, or why not analyse them yourself with this raw data?

Congratulations to Nathan Watson-Haigh, Nicholas Blackburn and Monther Alhamdoosh winners of the survey's amazing prizes (ABN T-shirts... yeah, stay calm folks).

Onwards to 2015!

Monday
Nov102014

The Australian Bioinformatics Network evolves...

Another great moment in evolutionOne of the hallmarks of robust biological networks is their ability to absorb and adapt to change, ideally becoming even more successful in the process.

Discussions are underway to do just that with The Australian Bioinformatics Network as its Director, Dr David Lovell steps down to accept a new role as Professor and Head of the School of Electrical Engineering and Computer Science at Queensland University of Technology.

This coincides with the establishment of the Australian Bioinformatics And Computational Biology Society (ABACBS), so the discussions are now underway between the ABN’s funding partners (CSIRO, EMBL Australia and Bioplatforms Australia) and ABACBS about building on the ABN’s achievements and infrastructure under the stewardship of the Society.

Over the past two-and-a-half years, The Australian Bioinformatics Network has grown steadily, with over 700 members registered at AustralianBioinformatics.net, the “information hub” established to support Australian bioinformatics communities.

The ABN has supported and encouraged leaders and members of Australian bioinformatics communities through funding and communication for events including the Sydney Bioinformatics Research Symposia, Bob Kuhn’s UCSC Browser Roadshows, and the recent (and well received) Australian Bioinformatics Conference.

The ABN has been instrumental in the establishment of ABACBS and for the Network now to become part of this professional Society is a very natural and desirable evolution indeed.

David looks forward to participating in and contributing to the Australian Bioinformatics Community in his new role.