Thursday, 23 August 2012

EMS Project: Mapping bird distribution.

I feel like I have completely abandoned this blog - I haven't, I've just had my mind in other places (i.e. stuck in ArcGIS, my old pal) and having a little bit of me time with my other blog. I've had a lot of things on my mind and, without wanting to clog up this blog or my main Twitter account (RachLinaker) with personal-rubbish, I put it onto my other. Now, everything is all right in the world - woohoo.

So, of late I have been inputting the reams and reams of data collected by those lovely people of the EMS management team (massive thanks to you!) and looking at the survey sheets that go alongside them to gauge where abouts on the shore the birds were recorded from. It has been one heck of a task and one that took much longer than anticipated, as such I am now crying out for 'the fear' to hit me. Come on... Please! Anyway, I'm finally done - hurrah.

Messy messy.
Things were looking a little messy (trust me, when you're playing around with hundreds of points, the little colourful balls on the page do resemble a child's birthday party... I've said that one before) so I wanted to play around with the shapefiles and have them represent high and low tide, great, except some sides were only sampled and high or low. I scrapped that idea and hopefully, once I've done the statistics, this will back it up (I've saved the new layers just in case there is a significant difference between either numbers or activity patterns - probably a little difficult to do with a relatively small sample size). Instead, I opted to divide the counts up as to whether they were feeding or roosting - this should give an idea of what areas of each site are used more readily by each species and give an idea of these little hotspots so to speak. Looking back, this is exactly why the mapping was done in the first place so that's good. I've come across a few bumps along the way unfortunately, one being that for some sites, activity just was not recorded. Others, for example with Bran Sands in particular, multiple birds were noted on the survey sheets but numbers hadn't been noted beside them so it may be a little skewed. Also, I've had to scrap the "end count" data with regards to the mapping - there were just too many that either weren't counted or activity was accounted for or anything like that. Not like anybody cares about this but it's a nice note for me at least! 

I still need to sort out the legend somewhat. I've probably made things very difficult for myself, but essentially the legend is only showing the size classes used for the map - fine - except I've made two separate layer files so that I can show both Feeding and Roosting birds, and then only select one or the other - now GIS is creating duplicate birds on the legend... I think I may have to manually manipulate it since my brain is officially dead tonight.

What I need you to do is imagine that the legend looks awfully pretty. I think I'm going to have another play around and set it out on portrait paper, not landscape, and then at least the legend can go down vertically on the right. At least you can see that certain species do prefer certain areas of the habitat... 

I'm going to have a google around and see about placing two different maps on the same page. There must be a way of doing it and I'm just being a little bit blind.

More to come! 

Rachel, xo

Wednesday, 8 August 2012

EMS Project: Maps galore

As I mentioned in my last post, I've been working ridiculously hard with my old pal GIS trying to formulate some maps and whatnot for the EMS project I am currently working on. Thus far I have created a few maps with general species abundances (it looks very messy and almost looked like a child's birthday party, i.e. with a lot of brightly coloured 'balloons' all over the shop).

AVERAGE bird abundances and distribution per site, there are six.
N.B. Legend not present due to crazy amount of data. It needed messing with.
Pushing that aside (for now), I decided to have a look at recreational activities both from the Excel spreadsheet and the photocopied annotated survey sheets so I could gauge approximate distribution of activity per site. Again, I've done this using the large 1:50,000 OS map to look at the generalised picture rather than each localised site...

That's better with a legend.
I can use these shapefiles for the localised maps since they're pretty much in the right locations anyway. I may have to have a fiddle around with some mind. I was also thinking of splitting up the EMS activity maps into two - shore-based recreational activities and water-based recreational activities. Then there would have to be one for fishing/harvesting/collecting since there are a few sea coal collectors, bait diggers, anglers [well, one] etc.

We'll see.

I need to create the shapefiles now for bird counts at the start and the end of each survey and to locate these on the localised maps. Then, somehow, I need to map on recreational disturbance. I'm sure I can fathom this out... There's a clever person hiding somewhere inside...

Saturday, 4 August 2012

EMS project: Becoming reacquainted with my friend GIS.

I can't tell you how long I've been wanting to start a little 'diary' of my analytical project that is currently underway. Many moons ago [it seems!] I stated that I had to do a research project as required by my MSc and this was to be done with an external organisation. As I've mentioned a fair few times, I chose to do mine with the EMS management team, specifically working with INCA, Natural England, and the RSPB. I've been officially working on the project for a month now though, unfortunately, have been getting nowhere. I had to wait for data to be sent, I had issues installing my good friend ArcGIS onto my laptop (I even bought myself a new laptop for this purpose), and then there was the issue of me actually becoming reacquainted with the programme. Phew!

My main point of contact for the project has been Maeve, the current EMS project officer and she's brilliant. I think she's received many e-mails/texts/rambles fuelled by frustration, coffee, and on one occasion beer, asking for advice on how to get the data into GIS. I was just not having a good time with it. Essentially I need to create separate shapefiles for each species, both at the start and the end of the bird count surveys. This way I can map abundances. I'm not sure what I'm going to do with the end counts just yet, I think that'll be another "please give me some advice" e-mail, but at present I was just using the 'average' values to get a general idea of the prevalence of bird species at each of the six sites (Hartlepool North Sands, North Gare, South Gare, Redcar Rocks, Seaton Snook, and Bran Sands). Then, alongside this, I'm going to display their likely activity (either feeding or roosting) based on the sum of averages. It gets a little complicated so it's just going to be as a % representation (I think, I'll see how it goes).

The other wall that I hit was to do with getting this data actually into GIS. Those who know me, I'm always trying to better what I've done. I'm never happy with it - perfectionism, it's a blessing and a curse at the same time. Anyway, the way that the previous EMS officer, Katherine, had input the data was manually, inserting each value into each field one by one. Given that I am playing with what, about 600 points per species (if you consider that there are about 10 fields per value as well) I wasn't too happy with manually inputting this data, one by one. Cue a lot of googling and e-mailing GIS 'experts' to try and see whether I could do this. The only solution I could think of was saving a spreadsheet as a database (thank goodness for Open Office, Microsoft Office doesn't do the database extension anymore) and importing this into GIS via the XY (coordinates). The data I had been given didn't have coordinates, and that is why the data had previously been input manually so that each record could be placed where it needed to be on the map. 

A few days of wanting to throw my laptop out of the window, I had a solution. I grabbed the XY coordinates off GIS for each of the six sites, assigned them to the appropriate values, and then imported the data in and just smushed around the values myself. Looking back I probably should have done this first off but clearly my noggin didn't want to cooperate. 


As a little bit of GIS-practice, I wanted to recreate the European Marine Site (EMS)/ Special Protection Area (SPA)  boundary map that I had found. I gathered the SPA data from the JNCC website, opened up my two 1:50,000 OS maps downloaded off Digimap and had a play around. I couldn't find any EMS GIS data and I didn't fancy recreating the polygon shapes myself so I made a duplicate SPA-boundary file and edited the vertices to delete any that weren't part of the EMS. It all sounds very complicated but I knew what I was doing. Threw on a title, a legend, a North arrow, and a scale bar and voila. My first little map produced for a while. 

Simple, but it made me very happy.
So, now that I've had a really good play around with this and that (pressing far too many buttons for my liking and probably wrecking havoc to the data - only messing, I know what I'm doing!) I feel like I at least have a little bit of knowledge and confidence that I can work with the data. It just took a little while to get going, that's all.

I guess this kind of reiterates that old mantra, "never give up". It's true, you'll get there in the end. 

Friday, 3 August 2012

Marine Litter: The time has come to clean up our act.

Earlier this year, the Marine Conservation Society (alongside retailer Marks & Spencers) organised their first ever Big Beach Clean Up. Over 6,000 volunteers got involved and lent a helping hand in cleaning up 100 beaches and waterways across the UK. The amount of effort and cooperation was fantastic and everyone should be so proud of themselves. I was supposed to be one of those volunteers at the Bridlington Beach Clean but I had far too much on (with regards to university work) and, after taking a weekend out already, I just couldn't afford the time off. Shockingly, over 3,200 bin bags of rubbish were collected in total. This amounted to in excess of 11,500kg! That's an absolutely disgusting amount of waste found. The final report devised by the MCS can be seen here (with some lovely photos, too!)

One of the bags from Cramond clean up - Image from
From the report, the MCS identified a few main key components of the rubbish, these included:
  • Plastic parts
  • Glass
  • Consumer rubbish (i.e. crisp packets, lolly sticks)
  • Caps and lids
  • String, cord, cloth, and string.
  • Polystyrene
  • Fishing line
  • Cigarette butts
What they found hasn't surprised me in the slightest - I've wandered along beaches before, frequently kicking at old beer cans (obviously picking them up afterwards), bottle tops, and the amount of cigarette butts I've seen is just repulsive... Smokers, the beach is not your ashtray. In fact, there are numerous campaigns about by the MCS or Surfers Against Sewage that are trying to stop this... I came across one of the SAS campaigns and it did make me giggle. Very effective if I might add!

No butts on the beach!
As human population and waste levels explode, the oceans which cover 71% of the Earth's surface are in grave danger of becoming what can only be described as 'plastic soup' . Plastics have been part of our everyday lives for over 50 years now. Compared to glass or metals they are much cheaper to produced in the masses and tend to be more durable. As such, plastics have replaced much of these materials and, unfortunately, constitute a large proportion of the marine litter problem. Scientists have revealed that up to 80% of the waste found on the coast, ocean surface or seabed is plastic. That's a shocking amount, however considering that the annual plastic production (globally) has been estimated to be in excess of 250 million tonnes (!!) this figure does not seem so shocking - especially when Greenpeace suggested than up to 10% of these end up on our oceans. Whilst it is near impossible for plastics to be eliminated entirely, there are a series of methods that can help mitigate this problem.
Image by Lindsey Hoshaw              
As I am sure you are all aware, the oceans are not closed systems and are all connected by currents; they just do not represent a static environment in the slightest. This means that point sources of marine debris often result in the mass movement elsewhere, carried by these currents. Where several currents meet, their convergence zone, marine debris often accumulates in large patches, the largest of which known as the "Great Pacific Garbage Patch" (see image above). The collision of four ocean currents creates a vortex that draws in the litter and keeps it contained in these gyres. There's a lot more information about these gyres on the 5Gyres website, a non-governmental organisation pledging to help clean up this problem!
As shown by the list posted above, the common culprit of the marine debris problem is that of the macroplastic (e.g. plastic bags!), however plastics that appear naked to the human eye are also a huge problem. Small plastics less than 5mm in diameter are referred to as microplastics and are becoming a bit of an issue within the marine realm. I've been meaning to post this blog post for sometime now after such good feedback from one on my other 'project' - LiveFoodLove. Earlier in the month I wrote up a little piece  ("To scrub, or not to scrub") about the issues of plastics present in cosmetic products, namely facial and body scrubs. A lot of people seemed quite unaware of their potential danger and I guess, from their point of view, it's very easy to forget about those little things we just cannot see.
Of course, the cosmetic industry is not to blame entirely for microplastics can have various other entry routes. One interesting example that I noted an article I wrote (on this subject, actually) was to do with the release of microplastics from our clothes. A group of researchers (Browne et al. 2011) tested waters from shoreline habitats around the world, noting that the most common polymers consisted of polyester, arcylic, and nylon (polyamides) fibres - this links them back to synthetic clothes. Shockingly, in excess of 1,900 of these microplastic fibres can be released into wastewater from the laundering of a single synthetic item. Considering that some people do two loads a day (of course family-size dependent) this is an alarming amount. Living in a house of six (granted, poor students who need to pay the bills) the washing machine is on at least once or twice a day. Imagine that we have, say, 4 items per wash that are synthetic (figure plucked out of my head, completely inaccurate) and every day we are doing two loads. Per week we have (in theory) released 106,400 fibres into the environment. That is one household.

Compared to their larger older brothers, the macroplastics, microplastics are a bit like the evil unknown at the moment because no one really understands what direct effect they can have on the marine environment, particularly at ecosystem level. Baseline data is often difficult to collect as you can imagine - most of these little plastics are less than 1mm in length and, as such, cannot be tallied in a survey from a boat. There persistence in the marine environment has therefore been assessed by other means, such as via CPRs. Continuous Plankton Recorders (not cardiopulmonary resuscitation...) can be deployed from merchant vessels and towed during a normal day-to-day sail. Via this method, collaborative work between SAHFOS (Sir Alistair Hardy Foundation for Ocean Science) and the University of Plymouth (where I did my undergraduate - hurrah) has shown that there has been a significant increase in the amount of microplastics present over the last 40 years.

Marine litter has the potential to cause a myriad of problems for marine ecosystems. Plastics are likely to cause problems associated with:
  • Facilitating the movement of alien species, or
  • Entanglement of marine species, or
  • Ingestion of the plastics.

Non-indigenous species
In July 2009, Murray Gregory from the University of Auckland published a study in the Philosophical Transactions of The Royal Society B assessing the environmental implications and dangers posed from marine litter in our oceans. One of the main concerns that he highlighted was the potential for individuals to ‘hitch-hike’ on floating marine debris therefore moving them elsewhere into areas previously inaccessible. This movement of ‘alien species’ can have serious detrimental effects of resident populations and may drive species’ extinctions. In remote areas such as the tropical islands of Oceania or the sub-Antarctic islands, resident species may be unique to that area and as such warrant serious consideration for their protection.

Image source: Greenpeace
Over 100,000 of marine mammals die annually due to either ingestion or entanglement of marine debris, and considering that this figure only applied to the North Pacific Ocean, it is expected that the global marine mammal mortalities associated with marine litter is to substantially exceed this figure. Entanglement is a serious problem for species living amongst areas of high marine litter, particularly when composed of derelict fishing gear (such as long-lines or drift nets), synthetic ropes or packing bands.

Image source: NOAA
Although there are a number of marine species affected marine mammals, who, being naturally curious and playful, are attracted to floating debris and so are most at risk. Fur seal pups, for example, are highly vulnerable, resulting in a drawn-out death sentence. The collar of marine debris tightens as the seal grows, constricting arteries and strangling the animal. The death of marine mammals at such a young age can have long-term effects on population stability and, as such, may hinder population recoveries. It is expected that with an increase in plastic pollution there will be a quickening in population decline of the northern sea lion, northern fur seal, and endangered Hawaiian monk seal.

The hard truth; Albatross chicks are fed plastic particles
mistaken for food and as a result die from starvation, suffocation
or toxicity. (Image source: Chris Jordan).
  Marine litter can be small and easily mistaken for food and so ingestion of marine litter is quite a common problem amongst marine species. Ingestion causes a magnitude of problems ranging from:
  • Sub-lethal: Decline in feeding resulting in starvation and stunted growth rate due to malnutrition.
  • Lethal: intestinal or oesophageal obstruction.

The relative abundance of plastic and plankton in the North Pacific Ocean reveals shocking results. In a study in 2001, on average 330,000 pieces were found per square kilometre with a max count of nearly one million. This is likely to affect a number of organisms based on their feeding habits. Seabirds, filter-feeders, and other species that feed within the ocean’s surface layers are likely to be affected. Laysan albatross chicks of the Midway Atoll (Northern Hawaiian Islands) are severely affected; of the 500,000 individuals born annually 200,000 die as a result of the debris accumulation from the Great Pacific Garbage Patch.

This issue is hardly undocumented with various campaigns flying around to try and educate the plastic user about the problems of inappropriate plastic disposal. My favourite (in a morbid way, I mean it is more effective) is that by the Mediterranean Association to Save the Sea Turtles (MEDASSET). I remember posting this up on Facebook a fair few months ago and a fair few of my friends did not even notice the plastic bag, If they can't even notice it then how do you expect a turtle to? In fact, a study published in 2010 revealed that one in three sea turtles found stranded or dead in the Adriatic Sea had debris (ropes, plastic and long-lines) present in their gastrointestinal tract.

As well as the ingestion of macroplastics, the ingestion of microplastics is a growing concern given their tendency to absorb Persistent Organic Pollutants or POPs. The most common POPs include PCBs (Polychlorinated biphenyls), DDT (Dichlorodiphenyltrichlorethane), and BPA (Bisphenol A). Various adverse health effects have been documented with regards to these, ranging from effects on the immune system, reproductive system, nervous system, and the endocrine (hormone) system. DDT, for example, can induce what is referred to as imposex (development of male sex characteristics) in dogwhelks, whilst BPA mimics oestrogen causing problems to both fish and humans. POPs accumulate in the animal's fatty tissue and, with this in mind, apex predators of the ocean food chain tend to show the highest levels.

You are what you eat.
In the UK alone we are estimated to consume over 380,000 tonnes of seafood per year. Given what I have just told you about POP accummulation and such, seafood consumption includes toxic and plastics remains too. The Nephrops (Scampi) fishery, a commerically important fishery within UK waters (bringing in about £95.8 million per year), was studied in 2011 for plastic remains. Over 83% of Nephrops caught contained little indigestible plastic fibres.

The image on the right (source: is a fantastic pictorial of the marine debris problem, relating it back to human consumption. Just to highlight some key points from it:
  • Humans consume, on average, 36lbs of seafood per person per year.
  • The Great Pacific Garbage Patch contains an estimated 3.5 million tonnes of rubbish.  
  • 51 billion bottles are used (yearly) in the U.S. alone, only 1 in 5 are recycled. 
  • 260 known species eat non-biodegradable plastic materials (of course not out of choice, it is mistaken for food!)
  • Some of these fish are eaten by other fish, the contamination is therefore biomagnified up the food web.

I understand that telling the ever-increasing population that they all have to ditch their synthetic clothes and reduce their weekly washing amounts is an unlikely scenario (and would most likely result in me being a very unpopular person). Being a little more careful about what we buy - cosmetics especially - will help substantially with the microplastic issue. Reducing macroplastic prevalence is much easier (easier said than done mind you), but make a few simple changes and you're on your way to helping the environment.

Reduce, Reuse, and Recycle.
It is imperative that there is a continuation in these 'three Rs'. This should reduce the amount of waste discarded within the environment, a lot of which ends up in our oceans. The UK effort for the recycling programme has improved substantially over the years, so let’s continue our efforts. Reducing the amount of waste discarded is easy, opt for a re-usable cloth bag for groceries and only drink beverages in glass bottles or buy items with very limited packaging.  If you DO use a shopping bag for whatever reason, do reuse it. We actually have a drawer in the kitchen stuffed full of shopping bags. They will always be used for for rubbish and never thrown away AS rubbish.
For marine debris that has washed up on our coasts, the solution is simple and requires very little physical effort. Beachwatch, MCS' coastal environmental initiative, aims to involve local people and communities that want to help clean up the shore. They organise various big beach clean ups (as aforementioned) so check out when the next one is and get involved. Even if you are not part of a formal clean-up programme, next time you’re at the beach take a bag and pick up some of the rubbish yourself.
Every little helps!