The Beginning at Last (Wylde 1998)

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?’

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.

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.

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

Shark Fest II

Shark Fest was amazing! Today was such a cool, interesting and fun day. All the major shark research groups and charities of the UK turned out for a shark filled day. One thing that surprised me was there was something for everyone, regardless of academic background. This event worked great as a public engagement event to raise awareness of shark conservation, and getting younger generations exited about not just sharks but conserving the marine ecosystem as a whole. Furthermore, shark fest had plenty to offer for academics, it was a great opportunity for undergraduates, graduates and even post grad students to network and give advice on how to get into shark research. I met so many talented and interesting science students, studying at various universities around the UK. I was able to ask current PhD students about their personal progressions from undergraduate student to a PhD student studying sharks. The event also gave me the opportunity to speak to organisations and charities who conduct research. Hopefully I have managed to sell myself enough to them, as a few people did tell me to contact them about ideas they want trying out. One example being attempting to get any DNA samples out of fossilized teeth, which personally I think would be so cool to try, as I have successfully extracted both mtDNA and nuclear DNA from modern shark teeth. I collected many business cards and leaflets and spent far too much money on a variety of sharky things, but I think a personal highlight was speaking to the non academic shark fanatics. Just hearing the passion people had for sharks, people who have not studied them but just have a passionate interest and healthy respect for these animals is something that really makes me happy. Especially as most people have a fear or even dislike of most shark species, which is usually due to media and just a limited understanding of these wonderful animals. It’s always great to see families, with young children getting really excited when learning more about sharks. Organisations like The Shark Trust, Sharks 4 Kids, The Gills Club, Wise Ocean, Shark Guardian, Shark Stuff (+many more) and of Course the hosts Fin Fighters can not be praised highly enough, the work these companies are doing to raise awareness, fund research and protect sharks and the marine ecosystem is truly inspiring. I can not wait to go to the next Shark Fest, and one year I would love to be one of the people running a stand or even giving a talk and hopefully inspiring the next generation of shark researchers.

Introducing the Tasselled Wobbegong

This remarkable little shark is brilliant example of an ambush predator. The tasselled wobbegong (Eucrossorhinus dasypogon) is a highly unusual looking shark, its patterning and coral like tassels on its head makes it blend in with sea beds and coral reefs. The latin name for the tasselled wobbegong (Eucrossorhinus dasypogon) roughly translates to ‘well fringed nose with shaggy beard’. This refers to the distinctive mass of branching skin flaps that run continuously around the jaws. The ‘beard’ helps this wonderful shark  blend into its habitat. This facial adaptation, coupled with lightning speed makes a nightmare for many reef fish, as the tasselled wobbegong is adapted to be the prefect ambush predator.

Growing to a maximum length of 117 – 125 cm, the tasselled wobbegong is found on the coastal reefs of eastern Indian Ocean and the western-central Pacific Ocean, around Indonesia, Papua New Guinea and Australia (Northern Territory, Queensland, Western Australia). This nocturnal hunter has a highly varied diet. It sits in the mouth of a cave and waits for squid, reef fish, crustaceans and cuttlefish to drift within range, and then pounces with lightening speed.

The wobbegong family is believed to have a very short-range, usually having several hunting spots on a single reef system. The flattened body helps this wonderful shark sink into the sand and remain unseen. Additionally, tasselled wobbegongs have a deadly behavioural adaptation, where it uses its flat tail to lure prey in. When the shark is laying in wait, buried in the sand, its flattened tail is held above the sea bed and it moves in the current, resembling a small fish. This tail movement draw in the sharks’ prey items.

The Teeth!

Note how the teeth of the wobbegong have no pointy bits at the side (lateral cusplets)  these cusplets are clear to see on other species like the grey nurse shark teeth (Carcharias taurus). Additionally the wobbegongs’ teeth are unsarated like the teeth of great white sharks (Carcharodon carcharias). I will write a blog on specific tooth adaptations of sharks in the next few days which will shed more light on why these teeth are so different.

The tasselled wobbegong has two rows of razor-sharp, smooth, fang-like teeth on the palatoquadrate (upper jaw) and three rows located on the Meckel’s cartilage (lower jaw). The teeth are angled backwards like most sharks to help hold the prey. Like many other carpet sharks. The teeth of tasselled wobbegong have strong media cusps, and as mentioned the lateral cusplets are often absent or variable.(refer to image above)

There has been debate around the evolutionary relationship of the tasselled wobbegong, morphological studies has led to the current thought that the tasselled wobbegong is among the more derived wobbegong species. However, mitochondrial and nuclear DNA analysis contradicted these morphological findings, suggesting that this species was a closer relative to all the other wobbegongs, except for the northern wobbegongs (Orectolobus wardi).

Due to the limited distributional range of these animals, the tasselled wobbegong’s conservation status should be of concern. As this species lives primarily on coral reefs, the biggest threat this shark faces is habitat destruction from pollution and unsustainable, destructive fishing practices. It is currently listed as near threatened by IUCN (world conservation union). Fortunately for the tasselled wobbegong most of its habitat resides inside MPAs (marine protection areas) which are in place to preserve the great barrier reef. The IUCN, governmental and non-governmental organizations act in a partnership which assess the conservation status and manage the conservation of this species.

Ted Talks!

So I’m sat here in the LJMU offices working Clearing 2016, we are having quite a slow day so I have been watching ted talks most of the day and I thought I’d post this one just because I find it quite interesting and its been a few days since I mentioned sharks. Enjoy !

 

 

Haldane, Biogeography and the ‘Incomplete’ Fossil Record

J.B.S Haldane once said that he would give up his belief in evolution if someone found fossil rabbits in the Precambrian. Although this witty comment will bring a smirk to the face of many biologists. Through my time working with many high schools, colleges and sixth forms, and even to an extent at university, I felt that the significance of this bold statement is seemingly undervalued by many pupils and even undergraduates.

 

 

The statement actually underlines and highlights the constraining predictions of the evolutionary view. There are requirements which make the theory of evolution so elegant and so un-falsafiable. One of which is the general emergence of organic complexity from simpler systems in a relatively predictable way.

For example the progression of evolution (in a very simplistic watered down way) is generally understood to be as follows:

Single celled organisms > multicellular organisms (cell differentiation)>(insert ~1.5 billion years here)> Aquatic invertebrates (no rabbits!!)> Aquatic vertebrates> lungfish like creatures(still no rabbits)> Primitive quadrupedal, semi-terrestrial vertebrates which over the next few hundreds of millions of years diversified into amphibians, reptiles and eventually mammals. (and some way down the line we finally we get rabbits). *

(*I know it’s a little more complex than how I have briefly put it but I’m just putting forward a watered down model to paint a simplified picture)

Haldane made the rabbit statement as he knew, as many of us know, that the layering of the fossils we find is non random, it’s no coincidence that we find specific fossils where we would expect to find them. There is a chronological order of fossils, implied by stratigraphic layering which is reconfirmed by radiometric carbon dating. The results of the carbon dating precisely matches the chronological order of the fossils.

The evolutionary process requires a continuous genetic flow throughout the ages. There can be no inexplicable disjunction. Additionally evolution requires the same continuous gene flow through space. It sound simple when you think about it. Gene flow must be continuous, the organism must pass on its DNA to continue its lineage. To do this reproduction must take place, which generally implies, with few exceptions, that two individuals must be within a relative proximity to each other at the same time.

Therefore we could say, in a similar way to Haldane, that we could abandon the idea of evolution if we found animals in a place were we wouldn’t naturally expect to find them. For example if we were to find elephant fossils in the canary islands, or koalas in France, Tasmanian tigers in Scotland… you get the point. Each of these occurrences would represent an unacceptable and explained spatial disjunction. A reality in which these occurrences are true would be just as problematic for evolution as the temporal disjunction presented by Haldane’s Precambrian rabbit.

The chronological order of fossils has logical constraints which allow us to make accurate predictions, as mentioned earlier. Furthermore, the continuous gene flow which validates the evolutionary theory constrains the possible location of plants and animals.

Show Me The Missing Link

People who deny the facts and therefore deny evolution like to smugly point out gaps in the fossil record. Insisting that there must be observable intermediates for the theory to be true. Proudly claiming that ‘there is no evidence for evolution without observable macro evolution’ or as its more commonly put ‘I’ve never seen a chimp give birth to a human’…

There are obviously so many problems to this argument, too many to cover today, maybe one day I shall blog about more of the problems with denying evolution in the future, but today I will attempt to keep focus.

One main issue that the evolution deniers have with the theory of evolution is, as stated the fossil record has ‘gaps’. However, I can see a flaw in this request to plug the gaps, every time an ‘intermediate’ is found it will of course require two more ‘intermediates’ for example:

Denier: The fossil record has too many gaps, too many missing links, find a fossil, until you do there is no proof…

Species A—*(‘Missing link’)*—Species B

We found a fossil!! we found your ‘proof’

Species A—*(Species I)* —Species B

Denier: Hey! where is the missing link for species A and I and the link between I and B. This proves nothing!

*repeat over and over until you headbutt the wall…*

What many of the evolution deniers fail to see or understand is fossil records are not a great example of evidence for evolution. That’s not to say we can not support evolution from this evidence from the fossil record as discussed before, Haldane, biogeography etc.

But seeing as many of these people are obsessed with seeing intermediates, many examples do spring to mind, the one I have chosen is the one of the most cited and possibly the best example of a ring species that has been documented.

 Ensatina eschscholtzii the living intermediates!

On the Western coast of America, the rich coastal forests of California to the Western reaches of Nevada there is a rich habitat for amphibian life. It is here that we find one of the most compelling evidence of evolution happening before our eyes in the ensatina salamander (Ensatina eschscholtzii ).We can see observable aesthetic change as we progress from north to south.

To put it simply, as the population of salamander moved south, it was met by a geographical barrier which divided to populations. These two populations were split and are referred to being in reproductive isolation. Two populations of the same organism divided by the central valley. Both groups were exposed to different selection pressures created from the slightly differed environments. As the populations travelled further south, over time these different selection pressures have altered the phenotypes of these animals (How they look). Although these changes do alter how these animals look, the genome is not altered beyond the point where postzygotic barriers arise. Each population can breed freely with the neighbouring populations producing hybrids, this is true except for one pair. These pairs inhabit the region located south of the geographic barrier. The yellow blotted ensatina salamander and the Monterey salamander are sub species of Ensatina eschscholtzii. Therefore the reproductive isolation of the eastern valley salamanders has resulted in the diversification of one species, into two subspecies through a process called allopatric speciation.  

I guess in summary the point I am trying to make is evolution is a wonderful, beautifully constructed and most importantly true idea. It’s thought-provoking and inspiring, one of natures great puzzles. Although we know natural selection is true, there is still a lot to learn. Progress is being made, universities and research institutes continue to make new discoveries and more religious groups are excepting the theory of evolution as fact. The phrase ‘well its only a theory!’ is becoming more of a rarity in today’s society. Science is making more of a strive, new generations of intrigued pupils enter the educational system every year. There are more younger people getting involved in science, getting excited about science. I’ve shared these ideas here as this was the type of biology which inspired me to pursue a degree and hopefully a career in zoology.

Sharks and the Media

I am becoming increasingly infuriated with the ignorance of tabloid journalists and the way that sharks are portrayed in media. I have a feeling this will probably be the first of many posts of a similar nature.

Do we really need things like this in our papers? Okay I do understand that stories like these do sell, but I do have many issue with the journalists and media writing stories like these. Unfortunately the people who write these stories have almost no education when it comes to sharks. I often see headlines along the lines of ‘KILLER SHARK SPOTTED OFF BRITISH COAST!’ or ‘ESCAPE FROM JAWS MAN ATTACKED BY KILLER SHARK’ and often is the case these headlines are accompanied by an image of a Great White (Carcharodon carcharias) or a Tiger Shark (Galeocerdo cuvier). However, when you read the article, the shark in question is very rarely a great white, and in some cases, for instance the story of the Benidorm there wasn’t even a shark involved. Luckily, the public could see straight through the fear mongering sensationalist idiocy which these papers perpetually spew across the front page. Although some may see these articles and think, ‘oh my sharks are pure evil’, ‘in never going in the water again unless all the sharks are gone’ or even ‘okay its a little over the top but what’s the harm in it?’ It must be stated these articles are reinforcing a negative archetype which intern, hinders the conservation efforts by disengaging public through misinformation which invokes fear and generates hate for these misunderstood animals. 

Unfortunately because these headlines do sell and they home in on our primal fears, spark excitement and make us think, (usually not for the right reasons) they will continue to misinform millions. So unless these papers start to employ people who actually know a thing or two about sharks, which, lets face it, they never will… we are stuck with these sensationalist stories. So, what should we do?

Throughout university, one thing is continuously drilled into you as a student, THINK CRITICALLY! When you see these headlines, opposed to seeing them and thinking ‘wow, how terrible, how terrifying, sharks are scary! we should get rid of them ect.’ We should look at these headlines with a degree of objectivity.  Of course, as long as we are swimming in seas and oceans, shark-human interactions will occur and on occasion there will be attacks resulting in injury and even fatalities, and of course these rare incidents are tragic and should be treated as such.

On the other hand, when a basking shark is spotted close to shore in Cornwall or Devon.  The ludicrous and unnecessary shouts begin. It is not uncommon to see lines like: ‘JAWS OF BRITISH COAST’ or ‘KILLER IN OUR WATERS’ sprawled in bold, full  capital letters, usually in front of a red back drop of the front page of popular a tabloid.

When you next see these sorts of headlines just take a minute to think about who is writing the article and why, how much do they know about sharks? why are they writing it? and of course what paper is it in. Adding to this point, all papers are guilty of writing sensationalist and usually hollow stories about sharks but some papers are much worse than others. The worst offenders tend to be the daily mail, the daily star and of course the abomination which is the sun. So next time you do see these slanderous headlines on these papers, just stop and think, is this the real story? is this worth my time or money? The answer is almost always going to be no.