Visualizing Monarch Migration Data in QGIS

It has been some time since I took GIS, but I have been relearning to make basic maps in Quantum GIS, a free, open-source version of geographic information system mapping software.

I found a website that is posting citizen-science data on Monarch butterfly sighting from this spring. I took data from April and May and edited it a little bit in OpenOffice Calc.

The data are posted using www.learner.org. The link for the past 14 days of Monarch sightings is here at: JourneyNorth. The table should look like this when you open it:

The chart can be copied and pasted into OpenOffice Calc. If you don't want the first column to show, be sure to paste using the "Paste Special" tool, which allows you to hide the first column and just paste the data you want. Also, you'll want to paste the non-html text, otherwise it will try to paste the photos. When the data were how I wanted them, I saved the spreadsheet as a CSV file. Since I knew that monarchs start their journey from their hibernation location in the Oyamel fir stands of Mexico, I took a few lat/long points from that location and added it to my spreadsheet.
The data on the website also include more information if you click on them, with descriptions from the people who uploaded their sightings.

For QGIS, I found a base map of countries and borders, which I used as the backdrop and basis for the Monarch sighting data that I wanted to show. I used the standard 1984 projection.

Brown to blue-green shows a progression in the spring migration

Most sightings are of just a few monarchs. But there are a couple darker green spots that signify a lot of butterflies at one site.

To add the Monarch data, I used the tool called "Create a shapefile from CSV file", which allows me to take pretty much any spreadsheet data and, as long as I have lat/long coordinates, I can project them in QGIS. It's very handy.

Once I could view the data in GIS, I could right click on them in the legend on the software and choose Properties. This brings me to a window where I can choose an attribute such as Date or Number to classify and change the colors of the points according to the different values for each attribute. Unfortunately I don't remember yet how to choose a scale on my own for this, and so for the Dates I have a rather unattractive Legend in my final PDF map. I'll work on this.

The Print Composer allows me to design a share-worthy map with a title, legend, or a number of other aspects if I need them. I created two maps with the data so far--one with the Dates that the monarchs were first spotted by a citizen scientist, and the other with the number of monarchs spotted by a citizen scientist on one outing. It seems that the citizen scientists uploaded their numbers according to their discretion. One citizen might have just seen one and posted it, while another was out riding a horse around for several hours and counted all of the butterflies along their route.

There are a few errors in the above maps. When I get a chance I will fix them, but for now you should get the gist of what they have to say. Monarchs are moving north. Most people just see a few monarchs at a time. The 0 data point(s) should have been taken out for the Number of Sightings map. The points located in Mexico should be black, because they just show where the monarchs started out and do not represent real citizen science data points.

One thing to note is how impressive it is that these data were obtained from citizen scientists. There is a lot of potential with such projects. A similar set of maps could be made for bird migrations. The places where the most of a species is seen should be studied to see if there is something at those sites that should be replicated at other sites to improve the species's chance at survival.

Fur: Ideas for further research

Much of what I will be writing about can also be said for the meat industry. I do not mean to stand on a higher ground since I do sometimes eat meat and I do own two clothing products that are accented with fur. I also wear leather. My bias against wearing fur for fashion will come through, but I hope that any readers that I get here will appreciate my effort to try to provide balanced information along with critical thoughts on industry information. Naturally, there are a few things to correct from my first post on this topic.

First, fur does not have to come from far away. Fur is still an important part of Canada's economy. If you live in Europe, northern countries farm fur. Second, the production of fur does not usually use a significant amount of toxic products. The only one of concern would be formaldehyde, but it is used in a small amount. Third, there is a sort of certification for "Origin Assured" products, that tells you that the fur came from a location that follows regulations on humane trapping, farming, and euthanasia (killing with the use of injection or carbon monoxide).
This blog post is still presenting very introductory information on fur. I gathered the information from a website, Fur Is Green, which is providing me with a good jumping-off point and helping me to identify potential research topics that I can look into more fully. This site tells its readers that fur is environmentally-friendly in a number of ways: (1)it is long-lasting; (2)processing it is earth-friendly;(3)it is biodegradable; (4)there is no waste from the animal*; (5)no endangered animals are killed in the fur industry✢; (6)there are more of many of the animals that are trapped for fur now than there were when settlers landed.✾The website also says that "local environmental protection controls ensure that there are no harmful result." The problem with this is that the treatment may depend on those environmental controls, which can be weakened by lobbying in an industry.
Another quote that runs along the same lines is: "Animal welfare is a top priority for the people working in the fur industry because when animals provide us with a wide range of products and services, we have a responsibility to ensure the highest standards of care and prevent unnecessary suffering." What I have to say to that is, if only our recognition of this were all that it took to prevent unnecessary suffering, then the world would be a much better place. For craft furriers and small-scale animal handlers, with sufficient resources in terms of money, space, and staffing, this recognition might be all that is needed. When people are well taken care-of, they tend to be better at treating others, including animals, with respect. However, there are some people who seem to have everything and still abuse others, so I do hope that the humane treatment laws in all of these places where fur is part of the economy have the rigor to stand up to any abuse.
As I had thought about in my previous post, it would appear that as long as the harvesting of fur is done humanely and sustainably, fur products are "better" for the environment than petroleum based polyester clothing. A quote from the website reads: "Up to one gallon of petroleum is needed to produce synthetic jackets. Production of synthetic fibers involves chemical reactions at high temperatures and using harmful substances." Going off of this, I have also read that the tiny fibers that come off our clothing when we do laundry can get into our waterways and have a negative impact. These fibers are now part of the microplastic problem−in which the oceans are filling up with tiny pieces of plastic−and fish and other organisms are ingesting them in place of food. Needless to say, the ramifications of this could be significant.
A final claim made on the Fur Is Green website that I would like to comment on is about the use of science as a matter of convenience versus inconvenience. The writers talk about the basic 'boom and bust' cycle in nature. Basically, left to their own devices, species' populations will rise and fall in a cycle due to such factors as predation, disease, and food abundance/scarcity. The fur industry is purportedly following conservation biologists' research on population dynamics and see themselves as helping to stabilize the population and end the lives of the "surplus" in a humane way. In terms of ethics, I find this to be a weak justification. Wild animals have a right to live out their lives in whatever way nature intended. Besides this, predation and disease generally serve a purpose in taking out the sick and dying. I would hazard a guess that the fur on these animals is not up to the industry's standards and that fur trappers aim to get healthier animals with better coats.
Overall, as long as they are not adversely affecting populations, then I suppose I cannot say too much against the industry, but they are not saviors for playing God. Besides this, in one Q&A panel on their website, where people are asking whether they are wearing cat or dog fur, the writers make an argument that "some animal rights groups are saying that raccoon dogs are dogs, because they are classified by biologists as in the canidae✧ family... but Nyctereutes procyonoides is really a completely distinct species that resembles a North American raccoon much more than it does a coyote, wolf or other members of the dog family." This is a sloppy argument since they say they follow what scientists say on the subject of population dynamics, which suits their industry, but not to other scientists whose classification of the raccoon dog as a member of the dog family might discourage buyers. This would be me. On my hat with the little tuft of fur, the label says "raccoon", and if it came from a raccoon dog, then in my opinion I am being misinformed.
So, I have a lot to read up on. We'll see how it goes. Thank you for your attention!*They specifically mention mink in this and so it is unclear whether this is the case for other animals. Mink oils are used in leather treatment and in cosmetics, and the rest is used in fertilizer.
✢ I have a very hard time believing this and it makes me suspicious of the rest of the claims from the Fur Is Green website. I had one friend on Facebook express excitement over the prospect of soon owning a snow leopard coat. Snow leopards are listed as Endangered.
✾ I have a hard time believing this as well. Also, what about the animals that have not recovered their pre-colonial populations?
✧ Coyotes, dogs, foxes, jackals, and wolves

Fur: environmental and ethical aspects

I have never wanted to know about fur. I see that it comes from animals that to humans have no other economic purpose. I have never thought about it past not wanting to wear it because it so obviously comes from an animal that had to die for it. However, recently one of my very good friends has worn it extensively for fashion purposes.

When I mentioned my inability to ever decouple the thought of an animal dying with the sight of a fur accessory, she said she only wears vintage. She assumes that the label is correct. She assumes that it was done humanely. I would never assume this, but I am going to try my best to find out what practices are used, what extinctions are being caused, how common live skinning is. I will probably need to keep a bucket next to me for when I get sick, but fortunately I have experience with working closely with animals and even putting feral cats to sleep, so my skin has hardened quite a bit. I know about doing a job for a paycheck.

So far, besides the obvious PETA actions against fur, I also remember seeing a 60-Minutes type investigation on the fur used on Burlington Coat Factory's coats and how it came from dogs that were skinned alive. I don't see how I could ever be assured that fur was attained through humane practices, even if I was to be interested in buying it. Fur comes from far-away places like Russia and China, so I cannot casually drop in on the farm the way I feel I could do if I were buying meat from a farmer's market here and I wanted to visit the cattle.

I have never lived without synthetic materials like polyester fleece that could keep me warm without wearing fur. Because we live in an age of skepticism, my thoughts on the ethics of fur now must also take into account the environmental footprint. Polyester is plastic, made from oil. The clothing industry is very polluting. Maybe, in my investigation, I will find out that polyester producers deliberately funded smear campaigns against fur. Maybe fur is less harmful for the environment in the way that hunting for meat is less harmful than large-scale cattle ranches. Of course, there are still the tanning and other preparations of fur that I don't know about, so it may cause quite a bit of harm to the environment.

Maybe I will become the Temple Grandin of the fur trade, creating a set of best practices and a certification for businesses to stamp on their products and let buyers know where their fur is from and how it was harvested. My stomach is in knots at the thought of this. I don't want to research this topic, but I don't want to be ignorant about it, either.

I think the trouble will be finding unbiased information. I suppose if I read articles from the PETA types and from the fur trade businesses, I will be able to develop a middle ground story. I do not see myself being persuaded to ever buy fur, but at least I will be able to give fur fans information in case they want it and without the stomach-curling photos and videos. In the end, I think I will still prefer wool if I want a natural material. I may touch on down, which is another that I know will hurt to learn about.

There are more people in this world than the earth can sustain for a long period of time. The overarching issues is the fact that there are so many people and I think that if more people wanted to wear fur it would cause extinction for a lot of species.

I also came back to this issue after reading The Dodo's article about raccoon dogs being used for fur.

Monarchs: the basic research

Hi all, I've had this topic in the works for awhile. It's a complicated one and seems to be increasingly relevant.
Monarch butterflies (Danaus plexippus) are well-known to pretty much any American. They are brightly-colored and come with interesting qualities that are key to their survival. In their larval stage they feed almost exclusively on butterfly milkweed plants (Asclepias tuberosa) OR a climbing member of the milkweed family--sandvine/swallowvine/smooth swallow wort (Cynanchum laeve)  (USDA info here). This diet is what allows the monarch to be toxic to predators. Another important factor in the monarch species is their great migration which, being under threat for a number of reasons, means that the species itself is under threat.

Basics of monarch life cycle

Scientists began studying the monarch migration in the 1870s. With new technological developments in the 20th century they were able to get a good understanding of the nature of this phenomenon. Urquhart's work in the first half of the 20th century achieved the participation of thousands of people tagging monarchs for his study. In 1971, K. and C. Brugger discovered overwintering populations in the mountains of Mexico, specifically on Oyamel fir trees in the Sierra Pelon. During metamorphosis, monarchs synthesize magnetic particles into their thorax and it is presumed that this helps them with navigation. In the mountains in Mexico where they overwinter, magnetic readings are 100x higher than normal.

There is also an overwintering location in southern California, where the monarchs rest on eucalyptus and Monterey pine. The Monterey and Sierra Pelon sites seem to be preferable to the monarch because they protect them from extreme temperatures. When severe storms hit some of the overwintering peaks Mexico, the local monarch populations suffered (Brower, 1995).

A couple of technical methods for analyzing the monarch migration were found in the literature. Isotopic studies seemed to be the most current. Cardenolide is the toxin that larvae sequester from milkweed. Scientists were able to do cardenolide 'fingerprinting' on monarchs and determine the geographic region where the larvae had fed (Brower, 1995). The map below shows a rough sketch of the migration as described in the articles.

Monarch migrations. Trees show reserves where monarchs overwinter.

The eastern migration takes place in stages. The first generation migrates up to Louisiana, Texas, and sometimes Florida. Some make it further. The monarchs may breed for one or two more generations during the summer as they move overall in a clockwise pattern and return to the Oyamel fir trees in Mexico.

References:

Brower, L. (1996). Monarch butterfly orientation: missing pieces of a magnificent puzzle. The Journal of Experimental Biology, 199:93-103. http://jeb.biologists.org/content/199/1/93.full.pdf .

USDA (2014). Invasive Species Alert. Monarch Joint Venture. http://www.fs.fed.us/wildflowers/pollinators/Monarch_Butterfly/documents/Swallow-wort_flyer_MJV.pdf .

Wassenaar, L. I. & Hobson, K. A. (1998). Natal origins of migratory monarch butterflies at overwintering colonies in Mexico: New isotopic evidence. PNAS, 95(26): 15436-15439. http://www.pnas.org/content/95/26/15436.long .

CORRECTION NOTE: Previously I wrote that the caterpillars feed on Common Milkweed, or Asclepias syriaca. I was mistaken. They prefer Butterfly Milkweed, or Asclepias tuberosa.

Conserving the critically endangered "river pig"

Poyang Lake--finless porpoise habitat

As I wrote previously, the Yangtze finless porpoise has been moved from Second Class to First Class Protection Status in China. In some ways, this is very good. It means that higher government offices will be responsible for the species' protection. It also means that the work carried out by citizens, environmental organizations, and research institutes has fortunately caught the government's attention and drawn it towards this charismatic and valuable animal.

However, the law does not in and of itself address the issues that are actually impacting the porpoise's population. It seems to focus on direct impacts, in particular poaching or killing for other reasons. Unfortunately, because the porpoise is at the top of its food chain, there are a multitude of direct and indirect factors that threaten its survival. By simply living in and along the Yangtze River, the porpoise continually comes face-to-face with the environmental externalities that accompany economic development. These include pollution, constant sand-dredging, irresponsible fishing practices, boat accidents, and dam-building. Each one of these problems will require a policy to address it along with the monetary and human resources needed to enforce new rules or laws. China has a record of passing laws quickly, but it also has problems with corruption, particularly with environmental regulations.

If officials decide to take control of the situation, they will probably relocate chemical plants rather than try to enforce upgrades. This is one of the actions that they have taken in other cases of extreme pollution problems. (Not my favorite solution, since it is just outsourcing pollution to another poor area or even another country, possibly. This also doesn't address non point-source pollution, which is significant in China.)

Constant sand-dredging, irresponsible fishing accidents, and dam-building are other impacts that are closely tied to economic development. Sand is used in making cement for construction purposes. Anyone who has visited China recently knows that the building is not going to stop any time soon... not with China's goals to urbanize its population. The dredging occurs on a 24-hour basis, disrupting fish beds and eggs in the sediment and leading to a decline in the porpoises' prey. This likely has an impact on the local fishermen as well, leading them to use increasingly extreme methods to keep their catches high for the market. For example, apparently Dongting Lake (one of the key habitats for the porpoise) is a maze of finely woven fishnets--a haven turned deathtrap for porpoises. At this lake, a few local activists--the Yueyang Finless Porpoise Protection Association--have been working to educate fisherman and even succeeded in getting the sand-dredging to stop during nighttime hours. According to them, their actions have led to a slight increase in the population of porpoises at that lake. If that is true, then education and compromises with economic interests might what we need to keep the Yangtze finless porpoise from going extinct.

A nation's waterways are critical economically. By cleaning them up and taking care of them, the governments could help to ensure economic prosperity in the long term while also benefiting people who depend on it for their livelihood. The fact that China has already lost the baiji and stands to lose another intelligent mammal serves as a warning that public health is also at risk. People are living next to those factories, drinking that water, and eating that fish. If the resources are not sufficient to maintain a population of more than 1000 finless porpoises, what does that mean for people down the road?

Scientific facts on the Yangtze river porpoise

When I tell other people about the Yangtze finless porpoise, their first reaction is nearly always: “But how does it swim?” I'm sure they're picturing something that resembles a dolphin just rolling and floating around in the water, because they are also usually laughing when they try to picture it. In fact, the Yangtze river dolphin lacks a dorsal fin, yes, but it still has everything else in place that it needs to swim. Some researchers suggest that the lack of a dorsal fin is an adaptation to their environment. It might have something to do with the relatively calmer, shallower waters that they inhabit as compared with their sea-dwelling relatives.

The Yangtze finless porpoise is actually a sub-species of finless porpoises. The other populations are found along the coasts of Japan and China. There is also a similar species that is attempting to survive in the upper reaches of the Ganges River. The freshwater sub-species survive by means similar to other porpoises and dolphins. They use echolocation to navigate underwater and feed on fish. They also live in pods or small groups and communicate with each other through clicks and squeaks. Studies on their communication habits suggest that, perhaps because of the higher sediment load of the Yangtze River, these porpoises produce clicks at higher frequencies than saltwater porpoises.

A number of population studies have been carried out over the past few decades, and none of the trends are good. One carefully conducted population survey of Yangtze finless porpoises was conducted using two boats and field observations from the upper Yangtze River by Yichang down to the lower Yangtze River by Shanghai in November and December 2006.

Zhao, W., Barlow, J., Taylor, B. L., Pitman, R. L., Wang, K., Wei, Z., Stewart, B., Turvey, S.T., Akamatsu, T., Reeves, R.R., Wang, D. (2008). Abundance and conservation status of the Yangtze finless porpoise in the Yangtze River, China. Biological Conservation, 141:3008-3018.

The greatest amount of porpoises were found in the middle reaches of the river, around Wuhan and down to Poyang Lake. The smallest, and also most separated, population was at the upper reaches by Yichang. Both Dongting Lake and Poyang Lake existed as important habitats for this animal in the past, but now the porpoises face severe threats in these places as well as throughout the rest of their range. Depending on the statistical measures used, estimates of the porpoises from older studies (late 1980s to early 1990s) tell us that populations went from between 1450 and 1650 individuals down to about 800 individuals in 2006. (These are the numbers I kept reading that made me stop and want to just hide my head under a blanket instead of continuing with the blog.)

At the Baiji Dolphinarium in Wuhan, captive breeding programs have been carried out successfully. Judging from their publications, the authors from this research station do not appear confident in the porpoise's survival prospects in its natural environment and they stress the need for more captive breeding in order to understand the reproductive behaviors of the animal. The females can breed at around six years of age. The first freshwater finless porpoise born in captivity was a male at the Baiji Dolphinarium in 2005. These researchers also stress the the need for more and better reserves. So far, the most successful and encouraging reserve is the Tian'e-Zhou Oxbow Nature Reserve, formed by the Yangtze River near Shishou and now serving as the protected home of at least thirty porpoises that have been allowed to live and breed there.

As I mentioned briefly in my previous post, the Yangtze river porpoise's protection status has been upgraded. In my next post I will discuss what this means along with what it means in terms of conservation protocol.

Good news, to be followed by science, finally

I started this blog imagining that I would write three neat articles about the Yangtze finless porpoise and then move on to a next topic. What ended up happening is that I got so depressed from reading about the low survival prospects for this animal that I couldn't even write about it.
Fortunately, as of October 28 of this year, China's Ministry of Agriculture declared the Yangtze finless porpoise "first glass protected species," putting it in the same category as the great panda. It will now get real attention and the Chinese government will be able to put in place stricter protection measures.
Thank you, The WaterHub, for the good news.
Now I can write about the science.