Monday, March 11, 2013

Ecology in everyday life: Monday links

To start, it’s reassuring to know that honeybees like caffeine too. So as you sip your coffee, know that you aren’t the only species who benefits from a little something to start the day.

Citizen science success. iNaturalist.org provides a platform for interested citizens to collect and submit observational data for a huge variety of taxa. This creates an expanding database of species IDs and geographical locations across the US. At present, they have 200,000 observations, which is pretty amazing.

Beautiful wildlife gifs, a reminder that nature is an astonishing place.

Predator/Prey. For some ecologists, work and creative undertakings overlap. So with this in mind, I wanted to point out a band that has taken this marriage of art and ecology to the extreme. Predator/Prey is a Canadian band headed by Dak de Kerhove and Adam Phipps that has released an album built around the concept of species interactions. Dak de Kerkhove is a PhD student studying predator-prey interactions between fish with Peter Abrams and Brian Shuter, so in this case art imitates life.

Most of the songs take inspiration from a combination of emotional subtext and ecological theory. For example, “A Run of Rabbits” focuses on prey dynamics and red queen, with the prey ever running to stay in one place. “Plump of Grouse” is inspired by death and predator prey cycles and written from the perspective of a predator. Because de Kerkhove's work has taken him to the far North, the band can't tour, and instead decided to release a web game that allows you to experience predator-prey interactions from the perspective of a fox. Pretty cool.

**The ecological connections are sometimes subtle, so here is the cheat sheet I was given**
Unkindness of Ravens (INTELLIGENCE / MUTUALISM)
Bed of Mussels (ENDURANCE / PASSIVE FORAGING)
Sounder of Boar (REVENGE / LOSS OF TRAITS UNDER DOMESTICATION)
Knot of Snakes (DESIRE / MATE COMPETITION)
Skulk of Foxes (LOSS / MONOGAMY)
Rout of Wolves (POWER / SOCIAL HIERARCHY)
Priory of Panthers (COOPERATION / GAME THEORY)
Plump of Grouse (DEATH / PREDATOR PREY CYCLES)
Mischief of Mice (OVERWHELMED / COMPETITION)
Shoal of Fish (DEDUCTION / CREPUSCULAR FORAGING)
Run of Rabbits (FEAR / RED QUEEN)
Gang of Elk (ACCEPTANCE / SELFISH HERD)
Piteousness of Doves (LOSS / GAME THEORY) 
                           ****

Wednesday, March 6, 2013

Can you lecture through Twitter?

The question is intriguing, and recently David Shiffman taught a marine bycatch lecture entirely on Twitter. It seems like an excellent way to reach a broad audience and a novel use of social media. I would be interested to know how the participants felt about the content detail. Universities have been diminishing the classroom experience, in favor of online courses, but this Twitter exercise maintains contact with the instructor (as opposed to pre-recorded videocasts with discussion boards monitored by a TA).

Tuesday, March 5, 2013

Evolution of conservation – what counts?

Winter, M., Devictor, V. and Schweiger, O.. 2013. Evolutionary diversity and nature conservation: where are we? Trends in Ecology and Evolution. http://dx.doi.org/10.1016/j.tree.2012.10.015

and the response:

Rosauer, D.F. and Mooers, A.O. 2013. Nurturing the use of evolutionary diversity in nature conservation. Trends in Ecology and Evolution. http://dx.doi.org/10.1016/j.tree.2013.01.014

The problem has been called the agony of choice – available resources for conservation are dwarfed by need. And as a result, we are forced to prioritize, to save some species and lose others. Much of the attention given to phylogenetics in ecology lately is on its use, questionable or otherwise, in ecophylogenetic metrics. However the important and useful research being done relating evolutionary information to conservation decisions deserves more attention.

This work has created a recurrent and sometimes contradictory discussion about whether evolutionary relationships contribute complementary information to traditional conservation targets (e.g. biodiversity, habitat types) and whether such information can easily be incorporated into conservation activities (e.g. Rodrigues et al. 2005; Faith 2008; Rodrigues et al. 2011; Tucker et al. 2012 etc.). A couple of papers recently in TREE are continuing this discussion and together do a nice job of summarizing the state of evolutionarily informed conservation practices. Most interesting about the article and the response is that even the opposing sides of the discussion appear to be converging on the same conclusion—that evolutionary diversity should be incorporated into conservation decisions—and differ primarily in how they justify this and the extent to which they feel it will be useful.

Phylogenetic diversity (PD) can be defined specifically as a measure of evolutionary diversity, however here it is more generally defined as the evolutionary information (e.g. phylogenetic relatedness) represented in a community and a common measure of evolutionary information. A community with high PD might include many distantly related species and hence represent many branches in a phylogenetic tree. The simplest argument for why PD might inform conservation is that maximizing PD will maximize the range of species’ ecologies and function that is conserved. In contrast, species richness targets have no relation to a community’s functionality.

Although the conservation literature includes many studies of phylogenetic diversity that are oriented towards real-world applications, in practice, conservation activities rarely incorporate PD. Winters et al. seem lukewarm about the value of phylogenetically informed approaches (one header is “A promising but yet ambiguous additional biodiversity component for conservation”). They suggest that there are a number of ways in which phylogenetic diversity can be informative: it can act as a measure of rarity and facilitate decision-making if rarity is a priority (and perhaps other measures of rarity not available) (e.g. http://www.edgeofexistence.org/). It may act as additional information to be incorporated with measures of species richness – areas with similar richness may have very different amounts of PD. However, the authors question “But what would the added value of conserving areas or communities of unexpectedly high phylogenetic diversity, or spending money on phylogenetically eroded areas, actually be?” The most common arguments, they suggest, are that phylogenetic diversity is a proxy for functional diversity and/or a measure of the evolutionary potential of a community. However, since ecological/functional similarity is not always correlated with PD, and evolutionary potential is not related to PD in a predictable manner, these are inadequate.

Winters et al. seem to suggest that PD is valuable because it can (but not always) act as a proxy for things we actually want to account for (rarity, etc). This is the point that the response from Rosauer and Mooers has the hardest time with. Why does evolutionary diversity not have intrinsic value if, say, species diversity does? Further, species richness is objectively a poor measure of diversity, since it treats all species as having equal value. In contrast, phylogenetic measures of diversity already account for one difference (evolutionary distinctiveness) between species, and hence should already be more effective in capturing total diversity in an assemblage. Rosauer and Mooers state “In an era of triage, difficult decisions are being made, and we know that inclusion of [evolutionary diversity] could make a substantial difference to the outcome for biodiversity, suggesting that it should be considered as one among many criteria”.

Regardless of differences in motivation, both authors agree that the greatest barrier is actually in bringing these ideas into practice. There are many ways of measuring evolutionary diversity (and species diversity, if we’re being fair) and choosing the correct metric can be a minefield. Calculating measures of evolutionary relationship requires specialized knowledge. On the other hand, it is easier and faster than ever to generate phylogenetic trees using DNA sequence databases and available software. Further, evolutionary information lacks the attractiveness that taxonomic-focused conservation has (it is more exciting to save the tigers than the genes). So what remains is to make the jump from theory and case studies to practice, and to find ways to explain why an echidna should receive more protection than all the other rodents. But if evolutionary information makes the agony of choice a little less, it is a worthy goal.
The power of phylogenies?
(Lanna Jin)
Cited
Faith D.P. (2008). Threatened species and the potential loss of evolutionary diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conservation Biology, 22, 1461-1470.
Rodrigues A.S.L., Brooks T.M. & Gaston K.J. (2005). Integrating evolutionary diversity in the selection of priority areas for conservation: does it make a difference? In: Phylogeny and conservation (eds. Purvis A, Gittleman JL & Brooks TM). Cambridge University Press Cambridge, UK, pp. 101-199.
Rodrigues A.S.L., Grenyer R., Baillie J.E.M., Bininda-Emonds O.R.P., Gittleman J.L., Hoffmann M., Safi K. & al. e. (2011). Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philosophical Transactions of the Royal Society, London, B, 1579, 2652-2660.
Tucker C.M., Cadotte M.W., Davies T.J. & Rebelo A.G. (2012). The distribution of biodiversity: linking richness to geographical and evolutionary rarity in a biodiversity hotspot. Conservation Biology, 25:2.
Vane-Wright (1991). What to protect - systematics and the agony of choice. Biological conservation, 55, 235-254.


Monday, February 25, 2013

Assorted links: predictable evolution, why the US government maybe the best thing for open access, and the lab junk drawer

A few interesting places to start the week. Probably these are worthy of full blog posts, if only I had the time.

A recently published paper in PLOS Biology shows that in multiple experiments, independent  populations of E. coli showed similar processes driving adaptive diversification. That is, similar ecotypes of E. coli arose from different populations, sometimes as a result of the exact same mutations at the same nucleotide position. A really cool result.

Good news on the open access front - the US government revealed a new policy stating that publications from taxpayer-funded research should be made free to read after a year’s embargo. It will remain to be seen how this plays out for most researchers, but it appears to be an important step, and one inline with European policies. It seems like steps made by big governments and universities will ultimately be what will create a new normal in publishing.

Why do biology labs tend to have hoarder-esque tendencies? Even newish labs seem to have a junk drawer of equipment that may or may not work inherited from past tenants, half used primers, ancient samples in a freezer somewhere, and more sharpies that don't work than do. An amusing list of the usual suspects was complied in this comment thread.