New Project

It’s been a while since I posted on here, I was planning on deleting this page but I thought I may as well keep it to help me understand what it is I am doing, also it writing on here helps me focus on the task at hand. It helps keep me motivated and also lets me look back at work I have done and what I thought of it at the time.

However sometimes I just need to rant, or vent my frustrations at stupid things that shouldn’t annoy me, but alas they do… very much so. Scientific communication is so important to scientists, usually we want to engage a wide audience. There is little point in discovering something amazing, or getting really interesting and novel results if no one can understand what it is that you have found.. and most scientists try their hardest to break down there discoveries. However, a lot of the time it is apparent that it can be misconstrued or in many cases information can be cherry picked out of a paper to make a good headline. By doing this, a lot of media folk actually miss the point of the paper, or create the discovery they want, what ever suits them or makes a headline that will sell…

Either way just thought I’d leave a link to my new blog which is going to be a composite of my rants when I see these type of headlines.

https://sciencevsmediablog.wordpress.com/

 

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Nothing like a trip to the country to really fry your noodle (Reed 2017)

This week I took a trip up the Marine Institute (MI) in Newport, Mayo with my PhD supervisor for a day packed full of  meeting and discussions about the project and plans for the next few weeks, months and years. It was a great trip don’t get me wrong, but my mind is going a mile a minute and my ‘noodle is well and truly fried’ (Reed 2017) because of the meetings. However, I do now know which direction I should be pushing my work in, and I have even more to think about in regards to the whole anadromy vs residency question regarding the trout.

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The Marine Institute 

Right, so what did we actually talk about up in ‘sunny’ Mayo?

Well first,I met the members of the MI that I hadn’t met yet, like the research assistants who are vital to the salmonid projects, the lecturers, PhD students and researchers based up in Newport who are working on similar research involving trout or salmon. The first meeting was between my supervisors and the staff of the MI, the aim of this meeting was to try to sculpt and structure the PhD and assess its overall aims.

The first meeting lead into a second in which I was brought up to speed on the background of the area, the population statistic before and after the fish farm induced collapse in 1989.

Back in 1975 there was a sea-trout run in the Burshoole river system was around 3,400 fish. However from 1989 to around the 2000’s approximately 160 fish were counted with a low points of sea-trout run of <100 individuals during this time. Additionally a 50% sea mortality was documented, which has repetitively been attributed to salmon farms. As they increase parasite loads, particularly with sea lice, which increases morbidity within the population which, in turn results in increased mortality.  (see below for image of sea lice infection)

 

After I was brought up to speed, there was a third meeting, for which many more researchers, PhDs and staff members joined us. The main point was to discuss the logistics and timing of the common garden and reciprocal transplant experiments that I have mentioned in an earlier blog.

Just to recap, the plan is to conduct a reciprocal transplant experiment to gain greater insight and understanding of the roles that genes and environment play when shaping facultative anadromy in good old brown trout. Through this experiment we plan to assess whether phenotypic differences among trout populations with alternate life history traits reflect genetic divergence. The experiment will involve crossing two populations of brown trout, one which shows naturally high rates of anadromy (Erriff river population) and the other which shows naturally low rates(Rough river population). The offspring, of pure and hybrids will be categorized into 6 groups:

  • Erriff female x Erriff male (pure)
  • Erriff female x Rough Below Falls male (hybrid)
  • Erriff female x Rough Above Falls male (hybrid)
  • Rough Below Falls female x Erriff male (hybrid)
  • Rough Below Falls female x Rough Below Falls male (pure)
  • Rough Below Falls female x Rough Above Falls male (pure)
erriff-aasleagh-falls
Erriff river

The offspring will be reared under completely wild conditions in both ‘home’ and ‘away’ river environments, each equipped with downstream traps to catch migrants.

Okay, so what’s new? Whats changed?

Well Originally the plan was to have ~20,000 eggs from the 6 groups (~3,300 per group) which would be split; 10,000 deposited into the Rough and 10,000 in the Glendavock tributary of the Erriff. But, as often is the case in academia, there were a few problems during stripping (process of obtaining eggs and sperm of fish) as many of the fish returning from sea were finnock and not fully mature sea-trout. This coupled with higher mortality than we anticipated after mixing of the eggs and sperm, substantially reduced the counts of our eggs. Current estimate stand between 15,000 and 12,000 eggs. I know this sounds like lots of eggs, but when you factor the 2 rivers which divides the figure by two and then the additional divide between the 6 groups per river. We start to see that these number are not huge, and this is before factoring in an estimated 1% survival rate. So after weeks of debate and back and forth between my supervisors and experts in the field, a new plan was developed, which allowed us to keep the reciprocal transplant, with a back up of a common garden experiment. Now the plan is to deposit 10,ooo-12,000 unfed fry into the Rough, and 2,000 into the Glendavock. However, there is still degrees of dissonance about the correct course of action that we should take, so again this is still subject to change and I will update the blogs as decisions are made.

As the third meeting progressed we started to focus on interesting points for potential chapters for my PhD and further discussed the phenotype candidates and physiological markers for migration/anadromy including:

  • Growth rate*
  • Standard metabolic rate*
  • Maximum metabolic rate*
  • Aerobic scopes
  • Adipose measures
  • Fatty acid status/compositions
  • Otholith growth and analysis
  • Size/mass
  • Isotope comp
  • Feeding behaviour
  • Glycolysis
  • Quantitative trait locus (QTLs)  i.e MEP-2

So this got me thinking about the genes that are involved in regulating these physiological markers, and whether there is clear differential expression of these genes between anadromous and resident trout.

Many studies have looked into the role of differential gene expression resulting in plasticity in phenotype and even evolution of alternate life history tactics within sympatric populations. So the next step, would be to look into the different gene expression levels between sea-trout (anadromous brown trout) and residents. However, all of this got us thinking, wouldn’t it be cool to try to see when these changes happen? When are these genes being up or down regulated? is this something that is predetermined when growing in the egg? is it something that is switched on when a certain threshold is met? is there possibly a non-genetic component due to differential methylation patterns passed on through epigenetic inheritance?  All these points came up and were discussed during the meeting which was brilliant, however, it still left me thinking what should I do next?

Prior to going up to Mayo, ‘team trout UCC’ had a day in the lab. We sacrificed 20 fish which have shared origin to the fish in my experiment. Certain organs were harvested and stored in RNAlater, with the aim of looking at the gene expression of Na-K ATPase in the gills and other organs. We did this in order check for signs of smoltification in the fish housed at UCC for another PhD project which aims to gain insight into the extent of phenotypic plasticity in ALH tactics with respect to food and temperature and to see if there is there an interactive effect of food and temperature on life histories. As these fish are early life stage, we could repeat this over time to try to get an idea of the changes that occur between the ALH tactics and also to see if the levels of gene expression is different between not only anadromous and resident fish in general but also between the anadromous and resident fish from different populations (Erriff and Rough).

First Undergrad Deminstration

The other day I did the first few hours of my required 50 hours of undergraduate demonstration. Which involves being present at, and assisting with undergraduate practices. Luckily enough for me it was an old favorite of mine, the good old fish dissection. The aim of the practical was for the undergrads to familiarise themselves with morphometrics, dissection and otolith extraction. The dissection species was the Atlantic mackerel (Scomber scombrus) which were freshly caught.  S.scombrus are a commercially important pelagic fish in Europe. The pelagic schooling species can be found on both sides of the North Atlantic ocean. S.scombrus is by far the most common of the 10 species of the family caught in British waters. S.scombus is extremely common in huge shoals migrating towards the coast to feed on small fish and prawns during the summer. mackerel-atlantic-1

So as the practical got underway, I was wondering around the class occasionally answering questions or just watching the dissections. While one undergrad was asking if they had cut the fish correctly, which they had, we noticed some movement in the fishes muscle. It was a nematode, about 3-4 centimeters long, and then there was another and before you knew it there where worms crawling out of pretty much every fish in the class. Now it’s not surprising to find parasites in freshly caught marine animals, but the size of these worms was new to me. I know I’ve mentioned I’ve worked with nematodes before with Dr. Rae at good old LJMU, but them worms, Phasmarhabditis hermaphrodita were small rarely reaching 1cm. So seeing a 4cm worm coming out of the cavities and muscles of these fish did surprise me, and I know animals can have much larger parasites and worms, but I guess I just got used to seeing smaller worms such as Phas. 

I was interested a few weeks ago about parasites that I could encounter when doing fieldwork on Brown trout (Salmo trutta). As I know there is a degree of dissonance between research groups in regard to the effect of salmon farms and sea lice infections, and while I was looking up parasites, I thought I may as well look at nematodes that affect these fish, a few different species came up, Anisakis and Phocanema decipiens  seemed to be the most cited, therefore I assume the most common in anadromous and marine fish. So I looked up some facts on these nematodes, both are zoonotic, therefore can be transmitted to humans. However are usually asymptomatic in healthy individuals, although they can cause diarrhea, vomiting and stomach pain. I knew that the giants that came out of the mackerel were probably not Anisakis as the species in this genus usually grow to around 1.5 to 2cm, and our worms were double this. So that narrowed it down, I remembered that P.decipiens grew to that length, so I looked up other large parasites in S.scombrus and all the literature was suggesting that it was indeed P.decipiens. I just thought it was really cool to see these parasites, and eventually so did the undergrads. It was amusing to see a lot of them going from looking horrified at these worms to actually being quite keen on adding to the petri dish that i was collecting a few of the worms in just to show other undergrads and talk about zoonotic infections and parasitology.

I just thought I’d blog about this as it reminded me of the work I did back with Dr. Rae in lab 333 in LJMU. I was just amused as I found myself getting as excited about these fish parasites in the same way he got excited by finding Phas or other slug and snail parasitic nematodes.

DNA Alignment, A Jar of Teeth, a Model Great White and a Whole Bunch of Other Shark and Trout Stuff.

Now that I have my office space at UCC, I thought I’d decorate it, however when look20170124_151745ing around at the things the other PhD students have
around their desks, I must say I could do a lot better. Plus I need some trout things! At least I am up and running here as a PhD student, well maybe not running, its more of a leisurely strolling pace if I am honest. My colleagues are telling me to enjoy this quiet time while it lasts. I have been enjoying reading the papers I have been given, along with the ones I am finding.

Additionally I have been playing around with some software I used for my undergraduate dissertation while looking into genes and regions of DNA that thought to be of importance regarding anadromy in Salmonids.

browntrout_river

I found an interesting paper by McCormick et al. (2008) on mineralocoricoid receptors, the study looked at the effects of in vivo cortisol, 11-deoxycorticosterone (DOC) and aldosterone on salinity tolerance, gill Na(=),K(+)-ATPase(NKA) activity and mRNA levels of NKA in atlantic salmon (Salmo salar). This study was undertaken in response to other recent studies that have shown that fish express a gene with a high sequence similarity to the mammalian mineralcorticoid receptor (MR). Which suggests that there could be a possibility that other hormones, other than cortisol could carry out some mineralocorticoid functions in fish.  The McCormick et al.(2008) study found that after cortisol exposure, physiological levels of cortisol increased, there was increased gill NKA activity and improved salinity tolerance. Where as DOC and aldosterone had no effect on gill NKA or salinity tolerance. Levels of NKA mRNA increased in response to freshwater and saltwater acclimation, it was observed that these increases were up-regulated by cortisol. Overall the results support the notion that cortisol and not DOC and aldosterone, is involved in regulating the mineralocorticoid functions of ion uptake and salt secretion in teleost fish.

So why am I finding this interesting?

Well, I thought it’d be interesting to see the ‘highly similar sequencing’ for my self so I found the Genbank reference, and compared it to the mammalian model, a mouse. I used blast to align the sequences and then downloaded them in FASTA format to look at the sequence similarity in Clustal X, sure enough it was pretty similar. So that got me thinking, what if I blast the fish sequence and look for similarities of around 80-100% matches. Scrolling though the results I started to notice something cool,  a lot of fish that exhibit anadromy where in the 97-99% similarity range. Now this isn’t too surprising as many of these fish belong to the same family so you would expect to see a degree of similarity. So I went looking for some strictly marine species and strictly freshwater species from different families to see how there sequences would compare and after a bit of adjustment sure enough the sequences aligned. Again high similarity, however there was much more variance in the sequence when considering these marine and freshwater fish.

anadromy-sequence
Fig.1 Clustal X output of the MR sequence for only Andaromous fish species, stars indicate nucleotide matches across all species.
untitled
Fig.2 Clustal X output of the MR sequence for all fish species (anadromy,marine and freshwater), stars indicate nucleotide matches across all species.

As can be seen from Figures 1 and 2 above this region of the gene is similar across all the species, however similarity rates are greater in Fig.1 than in Fig.2 (even when excluding the gap caused by the 5th species down in Fig.2). The increased number of stars in Fig.1 has got me interested. As this is just the result of me playing around with genbank and these alignment software I have no idea what it could mean, if it means anything at all.

So it inspired me to look a little further into genes and regions of the genome associated with anadromy, and I didn’t have to look to far as in the same paper I noted the sodium/potassium ATPase mRNA alpha sub unit 1 isoform a1a, or NKAa1a for short, was linked with changing gill morphology which increases salt tolerance in fish. Which is very important if you’re a fish practicing anadromy.

So back to Genbank I go! I found a sequence for good old brown trout (Salmo trutta) and put the FASTA sequence into blast and got a lot of matches and 99% similarity results. So I downloaded them and found the same thing, Salmo salar,  Oncorhynchus masou, Oncorhynchus mykiss, Oncorhynchus nerka and a bunch more salmonids. These results are not surprising as all of these fish are closely related, however it is interesting that these genes are very highly conserved across the anadromous species and less so when looking at marine and strictly freshwater species.

nak-anadromy
Fig.3 Clustal X output of the NKAa1a sequence for only anadromous fish species, stars indicate nucleotide matches across all species.
nak-all
Fig.4 Clustal X output of the NKAa1a sequence for all fish species (anadromous, fresh water and marine), stars indicate nucleotide matches across all species.

Fig.3 shows a much higher match rate than Fig.4, this may be a result of all the anadromous fish being salmonids. However, this data does represent species from different genera: OncorhynchusSalmo and Salvelinus. Additionally, it is believed that the split between Oncorhynchus and Salmo occurred well before the Pliocene some even suggest it may have gone back as far as the early Miocene about 20 mya.

Again I must that I am just playing with data and the software therefore these results don’t particularly show anything at this current time. I do plan to look at a few other regions that I have on my list and to scan though the current literature and scan for other regions to add to that list. Eventually I would like to run some stats to see if there is any significance between the differences in the number of single nucleotide polymorphisms (SNPS), represented by the absence of stars in Fig.1,2,3 and 4, in anadromous species and marine and freshwater species.

The Beginning at Last (Wylde 1998)

bees_logo_screen_colour_high

Now that I’m over here in Cork, I can finally start working on this PhD. This is both very exciting and also if I am honest, a little bit daunting. Just because I know that this is going to be a new challenge for me and I assume that I will be working at a much faster pace from now on. So lately I have been looking over all the papers, reviews and podcasts that my new supervisor has recommended along with a few papers I have found, that either help explain unfamiliar topics or, that are just generally interesting.

My PhD is a part of a much bigger project that is running over a 60 months period at University College Cork (UCC). The overall aims of this project are to gain a deeper understanding of how genetic, environmental and physiological factors interactively shape alternate life histories and how this in turn affects a populations demographic. (told you there would be science on here at some point.)

Right so what does this mean? and what does this have to do with facultative anadromy in brown trout? To answer the former of the questions I should probably talk a little about the basics of evolution.  Life history theory in ecology and evolution refers to the timing of key events in an organism’s lifetime, as shaped by natural and/or sexual selection. As we know natural selection is a driving force of evolution. Traits of an organisms are selected for or against, thus affecting the Darwinian fitness of said organism. The organism with traits that are selected for pass their genes on, thus the genetic lineage and the trait survives. However, ecosystems are not a static concept, an organisms’ environment is constantly changing. This can give rise to environmentally triggered alternative phenotypes. Most phenotypic traits that have influence on the adaptive fit between an organism and its environment are influenced by a multitude of interacting genes which are expressed dependent on the developmental stage and extrinsic factors. This further complicates the phenotype to genotype map as different genes, or gene combinations may produce the same particular trait (phenotype) in different environments, this is known as counter-gradient variation. Although the same genotype can produce very different phenotypes in response to environmental factors or cues.

Often is the case that two or more discrete phenotypes occur within an interbreeding population (sympatry). These phenotypes can be defined by morphology, distinct life history, or physiology. Here is where the brown trout come in. Brown trout (Salmo trutta) populations can show facultative anadromy. Anadromy is defined as the migration of fish, from salt water to fresh water, as adults. However in brown trout individuals migrating to sea to mature (sea-trout) while others remain in the river (river-residents). Now this is why I waffled on about all that phenotype jargon… Within the same river system these two environmentally triggered alternative phenotypes may co-exist within one population. To further complicate things there is no clear indication of what influences the ‘decision’ to go to sea. Why is it that within one population some trout go to sea and some stay? and although there is a tendency to track parental life history, why can environmental ques change the ‘decision’ to track the ‘choice’ of its parents? What happens when you crossbreed the phenotypes? or change the environment? limit the resources? decrease competition? introduce a predator? All these questions have been buzzing around in my head over the last few months, hopefully over the next few years there will be answers (but inevitably there will be many more complicated and puzzling questions…).

So what am I going to be doing? Well many of my family have been trying to explain that to there colleagues and friends by saying either:

‘It is something to do with fish in Ireland’  or my personal favorite.. ‘Err…Trout?’

rs-leaping_sea_trout-c-rupert-fleetingly

But seriously what will I be doing?

Well my main experiment will  involve a reciprocal transplant of trout between the two river systems, the Erriff and the Burrishoole system. These systems are ideal for this study as one (Burrishoole) has typically <10% anadromy in recent years and the other (Erriff) has typically over 90%. Additionally both systems have streams with downstream traps which monitor migration. Reciprocal transplant experiments are useful as they can gain deeper insight into whether phenotypic differences among populations have a genetic basis. Considering genetic and environmental influences, Burrishoole trout should show lower incidence of anadromy when reared in the Burrishoole system. However, they should show higher rates of anadromy when reared in the Erriff system. Meanwhile we should see the same pattern in the Erriff trout, that being, Erriff trout, reared in the Erriff system should have a higher rate of anadromy, and when they are reared in Burrishoole we should see a lower rate. The experimentally created hybrid families are expected to exhibit intermediate patterns compared to the pure families in each environment. The aforementioned traps will catch any migrating individuals, the fish will be examined for morphological indicators of smoltification and a sample will be taken for genetic and genomic analysis. Additionally, there will be extensive, strategic sampling of the non-migrating population.

When aiming to understand alternate life histories are shaped, genetic and genomic techniques are often employed. In spite of the recent advancements and increased understand of evolutionary ecology of migration, relatively little is known about the genetic architecture of migration related traits. When looking into the genetic basis of alternate life history tactics in brown trout, we will use two complimentary genomic approaches: genome wide association study (GWAS) and microarray technology will be used. GWAS will allow for loci associated with the propensity for anadromy to be identified, whereas the microarray will help us gain greater understanding of what genes are being expressed. I must add here that I am still currently reading the ins and outs of how this will be done and plan to write a detailed blog about it in a few months after a few chats with my supervisor and the genomics team, hopefully I’ll be up to speed about the genomic and quantitative genetic components by then.

All in all, I am looking forward to getting suck in and although I still have a few worries and nerves about the academic pacing of the project, I am happy to finally reach the beginning at last.

From Liverpool to Cork

From LJMU to UCC

Okay, I have been really quiet over the last few months, a lot has changed…

First, I must say, I no longer live in the United Kingdom, I’m now over the water and down a bit from my former stomping grounds. I have relocated to Cork in Ireland, and I must say it’s a lovely city. I moved down here as the lovely people at the University Collage Cork offered me a fully funded PhD. I will get on to what the PhD focuses on a little later, I promise there will be some science posts on here eventually, I don’t plan to ramble too much today. I have moved into a lovely house on a hill and am living with 3 Geology PhD students who are all very kind.

I have fallen in love with Ireland, it is such a friendly and unique place, additionally, I am pleasantly surprised on how close to home it is, not just geographically. Cork shares many characteristics with Liverpool, its a friendly and funny city full of great food, interesting people and places. The flights to and fro are not only short, around 35-60 minutes, but also very cheap. Which means I wont have to be away from my friends and family back in Liverpool for too long. My family and girlfriend have been a great help over the last few weeks and I can not praise them enough for all the help, love and support they have given to make the move a smooth and comfortable transition.

 

 

Wellies, Mud, Algae, Crabs and A Seal Named Rodrigo!

Today, (well sorta yesterday now) me and my girlfriend decided to take a day out as she had a day off from doing uni work. So we went to Hilbre Islands in West Kirby, which is a lovely scenic area of the Wirral, just over the water from Liverpool.

Hilbre islands are an archipelago consisting of three small islands at the mouth of the of the River Dee. It is an area of natural beauty and interest, the islands play an important role in the ecosystem as there is quite an extreme tidal system (as can be seen below).

(Left: High tide, Right: Low tide)

As the rocks and sea bed is exposed for half of the time, both the flora and fauna have had to adapt to avoid desiccation (fancy science word for dehydration). I could go off on one here rambling about many different species and how they are all uniquely adapted in their own way and so on… People have literally written books on these species and how they are adapted. So I will not list all the plants and animals, but I will talk briefly about some algae I find interesting.

I know this is primarily a zoology blog, but I can’t help but mention Fucus algae when talking about desiccation preventative adaptations, when it comes to staying alive at low tide these guys really are the kings. I know there are plenty of species I could waffle on about but I will just chose my favourite species (how cool… I have a favourite species of algae…) Fucus vesiculosus, commonly known as Bladderwrack. Fucus vesiculosus has multitude of morphological adaptations that are extremely beneficial. The organism, like many algal species,  has evolved what is called a holdfast. This works as a root-like structure which connects the entire organism to the substrate or ground.

Bladderwrack has also evolved extremely flat blades that allow it to soak up as much sunlight as possible without having to sacrifice many nutrients.  making it somewhat of a specialist in surface area to volume ratio. This adaptation also aids the osmotic processes that the alga relies on for its survival as it hasn’t evolved vascular tissue like plants have.

F. vesiculosus is known for the air bladders found in pairs on its blades. My girlfriend enjoyed using the dead detached blades as an organic bubble wrap, getting endless joy from popping the air bladders. Besides keeping Hol entertained  these bladders provide buoyancy for the brown algae, keeping it afloat when the tide comes in so photosynthesis can continue at a more productive rate. The bladders are filled an oxygen rich mucus and mostly O2.

Okay now that I’m done waffling about algae, back to zoology!

I had actually planned to go during the summer break however, I just never got around to it. The reason I’ve wanted to back to Hilbre, is to see the wild life and also its really quite a nice place to be (weather permitting). I went during my second year of uni for an optional enrichment field trip for a marine biology course. Although it was great going with uni and I did learn a lot I remember thinking it would be really cool to spend the whole day here and really have a good look at the wild life in the inter-tidal zones. To look at the life in the rock pools and see how it changed, the closer we got to the water. The change was subtle at first; the crustaceans got progressively larger, the presence of larger groups of bigger sand gobies, Pomatoschistus minitus and common gobies Pomatoschistus microps was more frequent. Additionally, the scattered remains of the bivalves that the gulls had devoured became more sparse as we approached the algae covered rocks. Sparse patches of black and brown slowly replaced the sand, and above the dull blacks and browns, specs of green appeared, as you walk closer to the water these specs become fields until its lost to the waves.

Being the big kids that we are, we went rock pooling. Trudging through the mud in our newly bought wellies, gently turning over rocks and smiling like fools when we saw a bunch of crabs scurry for cover. Making sure to put the rocks back as we found them, so not to upset the rock pools inhibitors any more than we needed to. Disappointingly, I wasn’t able to find a large velvet swimmer crab, Necora puber, (see below) although I was able to find a young one which very impressive colouration. I don’t know why but I do have a liking for these evil eyed, bad-tempered little guys. I think it may be the effort that these guys put in to really try to get you if you manage to annoy one.

Velvet-swimming-crab-in-defensive-position.jpg

Another reason me and Hol wanted to go was to see the main attractions, the seals. Hilbre Islands are a great place to see gray seals Halichoerus grypus and harbour or common seals Phoca vitulina. It was quite exciting to watch their little heads pop up out of the water, then disappear moments later, only to reappear after a minute or so either 6 foot closer to you or a good way away if it had drifted into a slip stream. We sat on a cliff face and ate some lunch watching and naming the seals.  All in all it was a great day, was good to get back into a nature/ecology setting, even if it was just a silly day out of rock pooling and looking at seals called Rodrigo.

Left: Gray seal. Right: Harbour seal