Tuesday, December 15, 2015

2015 caRd - A diveRsity of Santas

A keen observer will note that there are a number of similar taxa that are active this time of year.

Although well described in the literature, surprisingly little attention has been given to the ecology of these creatures. Observational data allows some traits to be compiled, however, and some simple exploratory analyses may allow us to better understand the 'Santa' assemblage.

                       heft transport first.appearance
Coca.cola.Santa         fat  reindeer             1900
Department.Store.Santa  fat  reindeer             1900
Salvation.Army.Santa    fat  reindeer             1890
Kriss.Kringle           fat  reindeer             1800
Santa.Claus             fat  reindeer             1700
Pere.Noel              thin    donkey             1400
Father.Christmas        fat      foot             1400
Sinterklaas            thin     horse              400
Saint.Nicholas         thin      foot              300
Ded.Moroz              thin      foot             1937

We are fortunate to also have sequence data (from DNA on milk glasses and lost beard hairs), so we can add additional information about relatedness amongst these species.

plot(xmas.tree, type = "c", FALSE, edge.color="darkgreen",  edge.lty=1, edge.width=18, label.offset = 1, direction="downward", font=3, tip.color="darkred")

The phylogeny shows that there seems to be an early divergence between European and North American santas. Indeed, there is a group of North American santas (Mall Santa, Coca-cola Santa, Salvation Army Santa) which are closely related (and also appear to share very similar traits, based on the table above). (Note that branch lengths in this phylogeny show nucleotide substitutions, and it is not time-calibrated, due to the absence of santa fossils).

One approach is to identify a few traits and plot them on the phylogeny to compare how traits vary among santas. Let's start with anatomical characteristics:

#Plot traits (fatness) against Santa
co1 = c("blue", "purple")
tiplabels(pch = 12, col = co1[as.factor(heft)], cex = 3.5, adj=c(0.5, 0), lwd=2)

#Let's see the transportation mode trait too:
co2 <- c("yellow", "gold", "darkorange", "red")
tiplabels(pch = 8, col = co2[as.factor(transport)], cex = 2, adj=c(0.5, 0), lwd=2)

legend("topleft", legend=c("reindeer", "donkey", "foot", "horse"), fill=rev(c("yellow", "gold", "darkorange", "red")))
legend("topright", legend=c("fat", "thin"), fill=c("blue", "purple"))
For a future study, we could ask whether the apparent correlation between fatness and reindeer usage is significant, once the underlying phylogenetic relationships were controlled for. 

We can also reconstruct santa traits (here, we look at the form of transportation) to explore what form of transportation ancestral santas likely used:

#reconstruct ancestral state
cc = ace(transport, xmas.tree, type="discrete")
co2 = c("yellow", "gold", "darkorange", "red")
nodelabels(pie = cc$lik.anc, piecol = co2, cex = c(1.5, rep(1, 8)))

The markers at each node show the probability that this ancestral taxa used each of the four possible types of transportation. It seems that the North American santas and their ancestors have long relied on a trusty reindeer mutualism.

Finally, we can look at the geography of all the various santas:

phylo.to.map(xmas.tree, locales)

To run this caRd yourself, follow the link to the R code: https://gist.github.com/cmtucker/8e5677bdd5c409d70738

Monday, December 14, 2015

A bird in the hand… Worth a bunch in the bush?

Guest post by University of Toronto-Scarborough Masters of Environmental Science Student Amica Ferras
     In less than a week, Christopher Filardi achieved a level of cyber-fame worthy of this digital age— but for all the wrong reasons. If you haven’t heard of him yet, that’s okay. Not all of us peruse biodiversity articles over our morning cereal. Here’s what you’ll need to know to hold your own around the water cooler.
Photo: University of Kansas

Christopher Filardi is the director of Pacific Programs at the American Museum of Natural History’s Center for Biodiversity and Conservation. This past September he and his team were part of an international expedition to the mountains of Guadalcanal, one of the islands in the Solomon Archipelago. Lead by native islanders, the team was on a mission to assess the biodiversity and habitat constraints of this unique region in order to develop a tailored conservation strategy. It was there on those mysterious island mountains that Filardi happened upon a true legend by any biology geek’s standards — the Guadalcanal Moustached Kingfisher. Even if you have zero interest in species biology, the stats on this bird are impressive. Only three sightings of the Kingfisher have been documented in all of history: a single female captured in the 1920’s, and another two in the 1950’s. No male specimen had ever been recorded and no live animal had ever been photographed. This bird can play a mean game of Hide-and-Go-Seek.
Upon discovery of the Kingfisher colony, Filardi and his team set to work. Calls were recorded, habitat was meticulously documented, behavior and motion patterns were scrutinized and population dynamics were assessed. And then, they killed one. (Cue the angry villagers with pitchforks and hippies with signs).
The collection was purely scientific. Filardi and his team stuck to a field biology motto of collect, dissect, but ultimately respect. Filardi hoped that the Kingfisher specimen would open the door to discovering more about the elusive species and their ultra-specific habitat. But the road to media-hell is paved with good intentions, and as the story spread like wildfire Filardi’s actions fell under attack. His ‘collection’ was deemed “perverse, cruel” by a representative from PETA to the Daily News, and the UK online Daily Mail described it as “slaughter”. The story exploded, appearing in the Huffington Post, Washington Post, Nature World News and Audubon, just to name a few. For those links and more I suggest checking the wonderful world of Google, but I will personally recommend that you read Fildari’s self-defense in Audubon https://www.audubon.org/news/why-i-collected-moustached-kingfisher, and the Toronto Star’s coverage of the controversy http://www.thestar.com/news/insight/2015/10/17/why-a-scientist-killed-a-bird-that-hadnt-been-seen-in-50-years.html. The Star does a fabulous job of presenting both sides of the story, and also goes into detail about the rather dubious past of field biology.
In the 1700’s and 1800’s specimen collection was more sport than science. It was a my-stuffed-animal-carcass-is-bigger-than-your-stuffed-carcass race, and rare species paid the ultimate price. Great Auks, for example, upon classification as endangered in 1775, were hunted at an alarming rate by naturalists attracted to its rareness. In 1884 a final pair of Auks was caught by fishermen, and no Auk has ever been sighted since. Specimen collection has come a long way since then though, and field biology has contributed to some groundbreaking scientific discoveries. Consider eggs— comparisons of eggshell thickness from samples collected across decades was used to identify the detrimental effects of DDT and other pesticides to natural ecosystems.
So, those are the facts. And my opinion about it? I’m siding with Filardi. Science has come a long way from naturalist trophy hunting in the 1800’s. Nowadays, before even setting foot outside of the lab scientists must undergo a rigorous evaluation process to determine if collection permits will be granted. Cost-benefit analyses, potential outcomes, and fragility of a species and ecosystem are all heavily weighted in before a decision is reached. Filardi’s expedition was no exception to this rule. (And for anyone questioning the usefulness of collections at all, I suggest you read the following article http://biology.unm.edu/Witt/pub_files/Science-2014-Rocha-814-5.pdf. I’d be happy to argue with you on that front another day).
It wasn’t as if Filardi saw the Kingfisher, pulled a net out of his pack and started swinging. After discovering the Kingfisher colony, the bird was carefully observed over several days. Input from the native islanders, assessments of habitat resilience and population robustness were all carefully analyzed before deciding to humanely collect the single male specimen. The unwilling sacrifice of the Kingfisher was honorably recognized, and the collection will be worthwhile if Filardi has anything to do with it. Scientists now have access to a complete set of genetic information for the Kingfisher. It will now be possible to undertake full molecular, toxicological and evolutionary diagnostics. Scientists may discover disease and pollutant susceptibilities that will guide Kingfisher protection efforts, or identify a direct evolutionary pressure to explain the appearance or behavior of the birds. At a more macro level, the specimen could reveal a shared trait between all high-elevation avian species or allow for an assessment of the particular environmental pressures the island ecosystem exerts over its inhabitants.  
Remember though, the point of the Guadalcanal expedition was not a Kingfisher hunt, but an internationally commissioned excursion to study the biodiversity and ecosystem threats in the Solomon Archipelago. Working with native islanders and Solomon government officials, Filardi’s team was working to establish a conservation strategy to protect the unique island system. The Pacific Island tribes have tended to their mountainous lands for decades, but recent international development has threatened the natural state of the ecosystem. Intensive mining and logging ventures have already begun transforming the lowlands of the islands, and climate change at large is effecting the delicate balance of ocean and forest features that unique species like the Kingfisher rely on. For species limited to a single isolated habitat, even minor changes in soil pH, precipitation or fluid motility can have astronomical effects on species survival. These are not the resilient squirrels and raccoons we in North America watch thrive everywhere from lush forests to derelict urban alleyways. Filardi’s collection will go a long way in identifying what needs to be done to protect these habitat-specific island species.
In fact, it already has. Discovery of the Kingfisher led Filardi to talks with local tribes and the Solomon government which culminated in formal agreements to protect the island mountain region under the recently passed Protected Areas Act. Filardi has already booked a return flight to Guadalcanal to help negotiate the next steps in this exciting conservation effort.

So, what do you think? 

Sunday, December 6, 2015

The hurdles and hardships of science in China

In my last post on China I discussed why China is becoming a scientific juggernaut. I focussed on all the things that seem to be working in its favour (funding, high expectations on scientists, etc.). While I do think that science in China is good and getting better, it is also important to point out some of the hurdles and limitations that hold back some aspects of scientific advance here.

In my previous post I noted that the expectations placed on students and researchers (i.e., to produce a minimum number of papers in journals with high impact factors, IFs) provided motivation to do good science. This is undoubtedly true, however, these strict expectations also reinforce a strategy of ‘paper-chasing’ where students are encourage to figure out how to get a paper. This is because the reward structure is so quantitative. While this type of evaluation systems has pros and cons, it does create a different sense of urgency than I’ve experienced elsewhere.

Pragmatic factors
The Great Fire Wall of China from "Cracks appear in the Great Fire Wall of China" posted by the China Daily Mail, Sep. 25th 2013.
I have never yelled at my computer or cursed the internet as much as I have in China. In the west we often hear about the ‘Great Firewall of China’ and probably do not think much about what this actually means. It sucks. The internet barely functions for significant proportions of the working day. I thought that this might have to do with the number of people and lack of infrastructure, but I no longer believe this to be true. Other countries in the region have great internet, and China has very advanced infrastructure. I’m pretty sure that when there is high traffic, the national security protocols and activity monitoring servers are the bottleneck.

Because the government policy is to block certain websites, most of the scientific internet websites and data sharing portals are not accessible here, but this may change at any given time. For example: Google Drive, Dropbox, Facebook, Blog sites, Twitter, Google Maps, and Google Scholar are all services routinely used by scientists and which are blocked in China. The reason for these to be blocked, as far as I understand it, is that they do not share users’ activities and the government cannot monitor what individuals share and download (which reinforces the value of these services to me). I also suspect that they are blocked to give local companies a chance to succeed without competition from global corporations, or perhaps simply because of disagreements with the companies.

I have had immense trouble trying to share files with my lab back in Canada (and to post this blog entry –which is why I’m doing it from Cambodia!). I am not currently engaging in social media –something that I saw as a legitimate activity for communicating science. I am having a very hard time searching for articles without Google Scholar. I also have trouble with other websites that should not be blocked, but that use third party encryption. For example, I can’t log in to my University library in Toronto, and I couldn’t connect my Canadian grant application to the Canadian Common CV (which we are required to do in Canada) because the CCV web interface was blocked (I had to get my post doc in Canada to do it for me). I have tried to go to researchers’ websites to find that they are blocked because they use a blogging site (e.g., Wordpress). The amount of time I spend doing basic online professional activities has increased 3 to 4-fold.

This is important because Chinese scientists are at a disadvantage when it comes to international collaboration and participating in online initiatives. I would encourage scientists outside of China to consider these imposed limitations to ensure that information and collaboration is barrier-free. Here are some tips:

  1. Don’t link to your Google scholar publications on the publications page of your website
  2. Don’t use a blog site to host your website (e.g., Wordpress)
  3. Don’t use Dropbox or Google drive to collaborate on papers
  4. Don’t use gmail as your work e-mail, Air China, for example, won’t send e-mails to gmail.
  5. Social media has emerged as a great way to communicate with broader communities, it is important to recognize that these dialogues exclude Chinese scientists.
  6. Ironically, as I write in this blog, blogs are blocked and while blogs provide a great platform to discuss ideas and issues, they are not available to Chinese scientists. 

These last two are interesting as journals increasingly require or request tweets or blog posts to help maximize exposure, but these forms of communication are not on scientists’ radar here.

Chinese science has been increasing by leaps and bounds despite these limitations. This is a testament to the hard work and dedication by Chinese scientists. I have no doubts that basic scientific research in China will continue to increase its stature and impact.

One thing that is interesting to me is that many of the graduate students here use VPNs (Virtual Private Networks) to mask their IP addresses. They are able to access blogs, Google Scholar, etc. In conversations with people, VPN use is extremely widespread and successful at circumventing government filters, most of the time (there seems to be an arms race between the government and VPNs). It really makes me wonder how much longer these governmental controls can be realistically maintained.

Wednesday, December 2, 2015

Paper of the lustrum*

(*lustrum = five years)

I’m co-teaching (with Kendi Davies and Julian Resasco) a graduate seminar focused on current trends and advances in community ecology. It’s been great, and having a small group with varied backgrounds (disease ecology, microbial ecology, restoration, community ecology theory, etc) allows for flexible and interesting discussions. Somehow the topic last week drifted to favourite papers, and we ended up with a plan to choose and defend the paper that was—in our opinion—the best one published in ecology in the last 5 years.

Today we described and defended our choices and tried to decide what the ‘best’ actually means, anyways. I don’t think anyone quite realised just how difficult this exercise would be. First, 5 years isn’t actually a very long time when measured in academic publishing years. That’s only the time of the average PhD, or less than the entire tenure-track period. I immediately thought of several papers I love, only to realize that sadly, they were from before 2010 (e.g. papers like these). 

Nearly everyone started their search the same way: with a Google Scholar search, looking at the most cited papers between 2010-2015. Some people looked at the most popular papers from high impact journals (Ecology Letters, Science, Nature, PNAS, etc); others looked at the output of eminent ecologists during that time period. At least one used his committee members for advice, and for the new grad students this was a nice crash course in the recent literature. Citations, quality journals, or eminent names might have been starting points for finding these papers, but it was interesting how little these actually seemed to matter. When defending their choice of paper, absolutely no one mentioned citations or journal as deciding factors. 

The papers we chose, and why: 
Conceptual synthesis in community ecology. (The Quarterly Review of Biology) Vellend 2010  
This was my choice, although I went back and forth between a short list of papers. For me, the ‘best’ paper had to either change how we do ecology, or how we think about ecology. I think Vellend 2010 has a lot of value as a pedagogical tool, and a device for organizing ecological knowledge. It has the potential to aggregate the varied, context dependent data that ecologists have been collecting for generations. Further, rather than the disjointed approach my undergraduate texts took for community ecology (productivity here, lynx-hare plot there), a single framework should help students understand community ecology as a cohesive set of ideas. And I admire papers that have big ideas.

 This was a cool choice, because it turns out to be a massively important development that many of the less molecularly-inclined knew little about. This paper introduced the use of CRISPR/Cas for gene editing. The CRISPR system is been found in archaea and bacteria, and provides a form of adaptive immunity against viruses. Importantly, it has been developed for use in incredibly precise genome editing that is heritable. It has massive implications for the study of evolution, microbial ecology, disease, population genetics, and everything in between. It is also the source of ethical concerns because it can (and has) be used to modify human embryos. 

Biodiversity loss and its impact on humanity. (Nature) Cardinale et al. 2012 
This was the choice of two students, so it may have been the de facto winner. It is a massively cited paper (>1000), and both students chose it in part because it makes a clear contribution to human welfare and society. It represents a massive undertaking (they analysed more than 1000 papers) reviewing research on how biodiversity relates to a large number of relevant ecosystem services. In particular, Table 1 (below) can be used for applied and basic research, and shows where research and data agree, disagree, or are lacking. This is certainly a must read for ecologists.

This paper helped to concentrate and inspire research on intraspecific variation and to highlight the areas of research that are still poorly studied (and it actually made my short list too). There is obvious variation within species (long acknowledged as important to evolution, starting with Darwin) but this is often ignored in community ecology. Bolnick et al. point out the many possible and important implications that arise from such variation. The writing is clear and highlights extremely well the general mechanisms that might interact with intraspecific variation. For the student who chose it, it was inspiring enough when it first came out, that they changed their research direction. 
Table 1: Bolnick et al. 
This paper was chosen in an opposite fashion: it is brand new, and rather than having inspired current research, the student thought it would inspire future approaches. The paper integrates community ecology and disease ecology in a novel and sophisticated way, advancing an area of research currently receiving a lot of attention. In this paper, mice are ‘mesocosms’ in which the importance of bottom-up versus top-down control of infection (by malaria and a nematode) could be tested. (Quote: "It's a real page-turner"). 

This was another paper chosen because it inspired the student's current studies. Ladau et al. brought together a massive data set for marine bacterial biodiversity, allowing them to map it on a global scale and develop predictive distribution models. Interestingly, they found that diversity patterns were lower at the equator, contrary to typical findings in other organisms. The student cited the careful methodology, extensive data, and comparison of results to those in macro-scale systems as the paper’s strengths. 
From Ladau et al. "Maps of predicted global marine bacterial diversity. Color scale shows relative richness of marine surface waters as predicted by SDM. Samples were rarefied to 4266 rDNA sequences to enable accurate estimation of relative richness patterns on a global scale from data sets with different sequencing depths. True richness is expected to exceed estimated values. (a) In December, OTU richness peaks in temperate and higher latitudes in the Northern Hemisphere. (b) In June, OTU richness peaks in temperate latitudes in the Southern Hemisphere..."

The final paper was Kendi’s choice. Community ecology has struggled with weak connections between pattern and process. The experimental and quantitative work coming from this research group has provided multiple examples for how to connect theory, statistics, and experimental results in a very rigourous fashion. In this paper, the focus is particularly on functional/trait approaches to community assembly and coexistence, and the authors manage to connect careful experimental data with Chessonian coexistence theory, using trait data to estimate species’ fitness and niche differences, and then using these to predict species coexistence.

After the fact, of course, lots of other great papers came to mind. It isn't really possible to choose one best paper, either. But the characteristics people looked for in a great paper were pretty similar - inspiring, providing novel approaches to particular questions, focused on big questions or ideas, and making contributions that go beyond academic ecology.