Week 7: Mimics and maniacs!

I want to start off by saying that everyone should now be able to make a comment with or without an account. I have also put a survey on the website and some ratings on each post, please feel free to comment with questions and rate so that I can improve my posts, I wont bite!  

Really, I wont bite!

Linux penguin, Tux

This week started off with some great new that I had officially been accepted onto the PhD program. Now I bet a lot of you are asking, having you already been working for around 2 months and you were not officially accepted? Nope, not until this Monday where I found out that the project plan that I told you all about last week had been accepted. So now not only am I an employee for Nord university I am also a student (yes I know that sounds strange)!

During this week of work my energy was very low, this is because I am temporarily a single parent for the next few weeks, however I have been getting work done as best as I can. Most of the week consisted of reading and I have nearly covered most of the literature on my specific topic. I was also preparing my computer for the course I will be going on in two weeks time near Gothenburg. I had to install several bioinformatic programs along with installing a virtual computer so that I could run Linux on my Windows PC.

larval fish(mimics) mimicking jellyfish/gelatinous larvae
 (models) (Greer et al. 2016) .

This week was also time for another journal club, with this week’s presentation being done by Amalia Mailli on the paper “Larval fishes utilize Batesian mimicry as a survival strategy in the plankton” (Greer et al. 2016).  Batesian mimicry is a form of mimicry where a harmless species has evolved to imitate the warning signs of a harmful species for protection from predation. In this paper, they looked at larval fish(mimics) mimicking jellyfish/gelatinous larvae (models) for protection (See image). The jellyfish larvae are poisonous to predator fish and will be avoided, so the mimics are protected from predation. There are many crazy different examples and is almost as interesting as hybridization. There is so much more I could talk about on this topic but due to my low energy levels I believe it is best to keep it short, instead I will link some interesting sites at the bottom of this post.

One of the many  interesting examples of  Batesian mimicry,
one which I have always thought about as a child, the hover fly
and the wasps! 1- German Wasp, 2 - Hoverfly, 3 - Hoverfly,
4 - Wasp Beetle, 5 - Sawfly, 6 - Hoverfly.
http://alexhyde.photoshelter.com/image/I0000fkOVUVljQXg

Finally, in my free time I have been working to improve my scientific writing and my portfolio. It is a piece of side work that I am hoping to submit for an Evolutionary Digest and once my work has been submitted I will go into more details. Once again, thank you so much for everyone who is reading my posts, please comment and leave feedback, I would very much like to hear what you think, but until next week, I hope you all have a great one!    

Journal: https://www.researchgate.net/publication/301826265_Larval_fishes_utilize_Batesian_mimicry_as_a_survival_strategy_in_the_plankton

Interesting sites:

 https://en.wikipedia.org/wiki/Batesian_mimicry

http://www.nature.com/subjects/batesian-mimicry

http://blennywatcher.com/2013/08/05/mimicry-the-filefish-and-the-puffer/

Week 6: My project and why it is interesting!

The 5 PhD students that started along side me. From top left,
Arseny Dubin, Kyle Rogers, Maeve Mcgovern, Peter Schulze,
Solveig Sorensen and me!.  

Greetings once again from my PhD journey, this week was not very exciting and consisted of a lot of reading and learning how to use the command-line on my computer. So in this week’s blog post will be dedicated to letting you all know what exactly the idea is behind my PhD. I will also decorate the post with pictures from my week and I will try to keep it clear and understandable for everyone. So please sit back, relax and enjoy the presentation!

We have always wanted to know the mechanisms behind speciation (the formation of species), but there are so many different factors that leads one species to become two species. It is also becoming more complex and the reason for this is that we have started look at speciation as a continuum (something that goes through a gradual change). One thing that we do know for sure and that is the process of local adaptations where populations evolve to better fit local conditions. When a species evolves there are changes in its DNA, but they usually accumulate in specific parts of the DNA sequence.

The northern lights dancing around the moon this week.

In my research, I will be looking at reproductive barriers, reproductive barriers stop species reproducing and when this happens is key to establishing when a species becomes a species. Reproductive barriers can be a result of many different factors and can be either before an embryo is form or after.  One other key aspect of my research is hybrid zones and the formation of hybrids thought he process of hybridization. When reproductive barriers form between hybridizing species it is very interesting and complex due to the nature of hybridization. Hybridization allows genetic information to be move and shared between the two species, known as “intergression”. Due to intergression, this makes hybrid zones the perfect natural experiment to study the forces that select specific genes which lead to reproductive isolation and ultimately speciation.

Autumn is here and someone is happy about it!

The species I will study, if you had not guessed it already, is the macroalgal (sea weed) Fucus, in particular, Fucus serratus and Fucus distichus. These species provide me the ideal system in which to study the mechanisms of speciation. It has been shown that these two species can produce hybrids in the wild, the sperm from F. serratus can fertilise the eggs of F. disichus. The next important factor about these species is that there are a few hybrid zones, some that have existed for 100 years and one that has existed for around 10,000 years. The reason that this is important is because the older hybrid zone does not produce hybrids whereas the younger hybrid zones do. The reason for this is that hybrids have been shown to be less efficient than either parental species and so natural selection has over time selected individuals that do not produce hybrids or produces less and this process is known as reinforcement. The genes behind this effect are unknown and this is where my research comes in.

My first fish here in Norway!

The central aim of my project is to understand how reproductive isolation mechanisms evolve in the Fucus speciation continuum, from a local adaptation to complete reproductive isolation. And that ladies and gentlemen is the idea behind my PhD.  I hope that you all were able to follow the post to this point and if you had any questions please feel free to ask, I would be very happy to answer them.  But until next time, have a great week everyone!

Week 5

After my first month as a PhD was so exciting and jam packed with things to do, I hoped this week would slow down, so that I had the time to sort out all those little things that get pushed aside when you have big projects to work on. Some of the topics in this week’s post may get a little scientific, so I will make the words or phrase in bold and leave some links at the bottom of the post for any of you that are interested in reading more.

Spangled Darter (Etheostoma obama) named after Barack Obama.
A common tread of the Darter fish, is they are named after a
USA presidents. 

The week started with the usual meetings with the unit and lab team, I found out that I was accepted onto the genomics workshop in Český Krumlov, Czech Republic and was followed by my very first session of Journal club. Journal club is a very interesting concept, were people present interesting journals that could be very different from their own topic, but still relevant to our departments field. It is something I will definitely take part in when I find a paper I enjoy enough to take the time to present. This week Alexander Jüterbock gave a very good presentation on an extremely interesting, but a not so statistically significant paper. The paper was called “Epigenetic divergence as a potential first step in darter speciation” (Also linked at the bottom of this post).

Epigenetics, for those of you that don’t know it is the study of genetic effects that are not caused by DNA itself and may be a result of environmental factors, that switch genes on and off and change how a cell works. If it is still a little confusing let me give you a quick example, every cell in your body has all the DNA within them that makes you, you. Your skin cell is a skin cell and not a white blood cell for example, because only certain genes are being expressed. In this paper it focused on a particular type of epigenetics known as “DNA methylation”, which is when methyl groups (a chemical compound) are added to DNA, which in turn modifies how it functions. The papers results, simply put, tried to show that epigenetic changes such as DNA methylation, could influence or be the first step in speciation (evolution).

The excited little scientist! 

As I mentioned previously the paper was extremely interesting, but the paper seemed to be lacking in significant statistical evidence. I could write an entire paper on how modern science has become too focused on significant statistics that we are blind to papers like this, but I won’t go into that here! However, one very interesting thing this paper did for me, was that I started thinking about how it could affect my own project and if I could look at this DNA methylation in my own subject genus Fucus. After speaking to my supervisor, it turns out that we don’t even know if Fucus use DNA methylation, something we plan to find out about in the near future. This could open up a lot more questions, which I would be very excited to answer!

Finally, at the end of the work week I worked on fixing a computer with Linux, I finally got around to apply to Research Gate, ARCTOS and applying to be a SSB student representative, but I was mainly working on my CV. This was something I didn’t think I would need to do since I was offered the PhD, but I could not have been more wrong and have already submitted it 4 times since I started in September!

Although this week was not as exciting as my last, I hope you still enjoyed my post! Please feel free to leave me feedback and comment and have a great week and I will see you all in my next post!

Pictures from the grand finale of the Researchers Battle
in Stormen last week. From top lefts, Me, Peter Schulze,
Asan Mohideen and Helene Rønquist Knutsen.    

Article

https://www.researchgate.net/publication/292949637_Epigenetic_divergence_as_a_potential_first_step_in_darter_speciation

Societies

ARCTOS - https://arctos.uit.no/home

SSB - http://www.systbio.org/

Interesting links

Český Krumlov - https://en.wikipedia.org/wiki/%C4%8Cesk%C3%BD_Krumlov

Epigenetics - https://en.wikipedia.org/wiki/Epigenetics

DNA methylation - https://en.wikipedia.org/wiki/DNA_methylation

Fucus -  https://en.wikipedia.org/wiki/Fucus

Research Gate - https://www.researchgate.net/

       

Welcome to the blog and my first month as a PhD student!

Hello and welcome to my PhD blog! 

You might be wondering why I am starting a PhD blog, and why now? The reason I am wanted to start a PhD blog is because during the three years of my PhD, many things are going to happen and this way I can note them down so that I don’t forget (you never know it could be useful one day!). Also I get to talk about what I have learnt and allow my friends, family and anyone else who is interested, know about my progress during my PhD and anyone interested in Fucus research. So you might be wondering why start now, you are already a month into your PhD? Well I had thought with the idea of writing a PhD blog, but the move to Norway and adjusting to my life here got in the way. Now that things have settled down I feel I have some time to sit down and type away. I would also like to point out that this blog will be for fun, so I will not go back and check with a microscope for spelling or grammatical mistakes, I am dyslexic, there are going to be some. 

Although it has just been my first month there has been a lot that has happened and to post everything in to this blog post might be long. I will be making a post dedicated to what I plan to do during my PhD at a later date as the project plan is still a work in progress.

Just before I started my PhD, one of my colleges needed help to collect samples early in the morning. I used this opportunity to get to know one of the loveliest people I have met so far here in Bodø (Chloé Maréchal), snap a few photos and collect a few samples. 

My samples!

Cyanea lamarckii

Chloé Maréchal sampling.

My first week was a mix of getting settled in both the administration side of my PhD and the project side. On the administration side you need to get used to the university, how it works and getting your office and computer up and running. On the project side I was getting to know my research team and reading papers, so that I can get my roots in the topic I will be working on for the next three years. At the end of the first week we had a gathering for all the PhD students as there was around 6/7 new PhDs all starting at the same time. I cannot tell you how lucky I am to be working around such a lovely group of people. They are all intelligent, kind, and likeminded people whose topics range far and wide.    

At the start of my second week I had my first meeting with my supervisor and co-supervisor to discuss the direction of the project. It is a strange thing starting a PhD, especially if it’s in a new field of study. The first port of call is to write a project plan, which requires you to know everything and plan the entire 3 years of you PhD, which includes the timing of all experiments, data analysis, writing, courses and so on. The rest of my week was mainly filled with searching for the courses that I will need to take during my degree. At this point in time, I have applied for a one-week course in Gothenburg, Sweden on “An introduction to bioinformatic tools for metagenetic and population genomic data analysis” and a two, two-week workshop in Cesky Krumlov, Czech Republic on “genomics” and “phylogenomics”. I am very excited and hopeful, as both will be a great kick start to my PhD and will give me the skills I need to do great work. Also during the week, we had a meeting about an upcoming event, in which I put forward a few ideas to make it more exciting for young children. At the end of my second week I went to a local event to support my research team present their work to the local community of Valnesfjord and even ended up in the local newspaper!   

Some of the helpful people at Valnesfjord. 

My son enjoying the marine creatures.

My week three was a little bit of everything, I started with a couple of meetings and followed by some applications to be a member of some scientific communities (ForBio, ARCTOS and Evolution digests). I also found out that I had been accepted onto the Swedish course and so had to organise my trip to Gothenburg. As this was my first time during my PhD I had to learn all the do’s and don’ts when traveling for work. Near the end of the work week I was working on my presentation about hybridisation for the “Research Battle” qualifying round on Monday next week. Finally, at the end of the week I took my family to the university's research stations "open day" and it was great. My son was able to take a look and get his hands on some marine creatures, such as starfish and jellyfish which he enjoyed. In the meeting last week, I suggested hiding some finding nemo/dory toys inside the tanks/mesocosms to encourage the young children to look into them to win a prize and it seemed to go down very well.

The final presentation.

Last week, week 4, was a crazy week! It started on Monday with the qualifying rounds of the “Research Battle”. I presented my PhD topic "Hybridization" to the public at the local student bar for science week. I have never presented to such a large crowed and have never had to make my complicated topic understandable to the public. Only the top 7 presentations got through to the next round, but me and a few of my friends (Helene Knutsen, Asan Sahib and Peter Schulze) managed to get through to the final! On the Wednesday we had a course on how to improve your presentation skill, so that we could put on a good show for Fridays final of the "research battle". We started by jumping around, making weird noises and then some improvisation and although very similar to fatherhood, it was a very different work day than I was used to. The course improved all of the finalist’s presentations exponentially and so it was going to be a tight competition for Fridays final. The finals for the “research battle” were held in the cities library Stormen and the attitude was a lot more serious than the qualifying rounds on Monday. My presentation went very well and I had improved a lot since Monday and managed to get 4^th place, with my amazing friend Helene Knutsen stealing the show and coming in 1st place.

Now that you are all caught up on what has happened so far in my PhD I am sure the future posts will be far smaller and on a weekly basis (I hope). I hope you enjoyed the read and I hope you will join me on this amazing ride that will be my PhD.