Pondering Undergrad Research

Sand-tiger-shark-swimming

So I’m sat here for my 11th day of clearing, waiting for the very few calls that remain. I’m becoming increasingly aware that my time at Liverpool John Moores University is over, and the days left on my ljmu computer account are numbered. So I am emailing myself all the work that I feel I did well on, to keep as a reminder of uni. Additionally, I put a lot of hours into some of this work and it would be a shame to just let it be wiped from the system.

As I was clicking through the files, scanning the documents for signs of intelligent life, I came across my final year research project entitled:

‘The haplotype diversity and origin of captive sand tiger sharks (Carcharias taurus) based on mitochondrial DNA analysis: implications for management of captive and wild populations, with a previously un-suggested phylogenetic relationship between shark orders’…

Bit of a long name I know but it was quite and enjoyable project to do.

So why am I harping on about this? Well I started reading the work and started thinking about similar research in the field, from the likes of Adam Stow, a Senior Lecturer in Biology at Macquarie University. His work mainly focuses on wild populations of C.taurus and how the population structure varies based on geographical location. which in turn has implications for conservation management. My work built on his existing work, with the aim of finding the origins of captive populations, and looking if individuals are being housed in global aquaria with other individuals which originate from different water bodies, if not different oceans. Turns out a lot of aquaria were indeed housing individuals from different oceans, in some cases without knowing it…

Additionally, as I wanted extend the project I also looked into the phylogenetic relationships between some of the shark orders. This second part of the project is the part that really has me thinking at the moment and I will show you why.

treeThe picture above shows 4 existing hypothesise of the phylogenetic relationship among extant shark orders by various authors. The first tree is based on morphological studies conducted by Compagno in 1973. The other 3 are based of sequencing parts of either the genome or the mitochondrial genome to see how these orders are related.

However my work looked at a 520bp section of the mitochondrial D-loop, looking at 21 different species across 4 orders; Orectolobiformes, Heterodontiformes, Carcharhiniformes and Lamniformes.

The shark species had the 520bp region of the mitochondrial genome compared. To get the sequence data I used a site called genbank (http://www.ncbi.nlm.nih.gov/genbank/). So I   would spend hours looking for a sequence which had my tiny 520bp sequence in it. I’d then align the sequence using BLAST. Maximum likelihood analysis test were run using a multitude of bioinformatics tools and this was the end result.

tree 2.png

( I do understand the limits of this study, there would need to be many other tests ran with larger data sets, more species included ect. )

So you (the 3 people who actually read this page) may think, ‘okay but what the point in this article?’ I’ll make that clear now just bear with me.

I find my self wishing I had more resources and an unlimited budget and a university or institute backing me or funding the research, as I think if a full genome or mt-genome study could shed some light on the phylogenetic relationships between shark orders. I do find it odd that in spite of conservation efforts, a long evolutionary history and ecological and commercial importance, the evolutionary relationship between shark orders remains so poorly understood. As shown before many different teams have their own hypothesise but depending what part of the genome is sequenced and what species are looked at it can all change. I am not saying any one is right or wrong, I’m not suggesting my findings are the way to look shark orders, with my sample size that would be absurd. There is unfortunately a lot of missing data in not just my study but many of the phylogenetic studies involving shark orders. This is because sharks are notoriously hard to study, due to many different aspects of their biology.

So this has been on my mind all day, who knows maybe a team will figure it out or come up with a new phylogenetic tree that will settle the debate, or more likely just cause even more confusion. I may even find a university or institute that would be interested in this type of work and may advertise it on a post grad site. Hopefully Id stand a chance if it is advertised.

 

 

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