Measuring the Pacific extinction spasm

It is a fact that humans have caused numerous extinctions around the globe. Almost all of the large bodied mammals of North America disappeared after the arrival of humans sometime around 20,000 years ago –likely due to compounding effects of hunting and climate change.  This North American example has been controversial, largely because it constitutes a single observation. However, humans colonized the Pacific islands over a span of a couple of thousand years, between 3,500 to 700 years ago. Species extinctions followed these colonizations on each island, confirming the link between humans and extinctions. Yet how many species went extinct? This question may be relatively easily answered for large organisms since evidence of their existence is well recorded, but for small-bodied organisms like birds, this is a difficult question to answer.

In a recent paper in the Proceedings of the National Academy of Sciences, Richard Duncan, Alison Boyer and Tim Blackburn use sophisticated methods to estimate the true magnitude of bird (specifically nonpasserines –i.e., not perching or songbirds) extinctions on 41 Pacific islands (including islands from Hawaii, Melanesia, Micronesia and Polynesia). Estimating the number of extinctions prior to recorded history is an extremely difficult exercise, but Duncan and colleagues use a set of statistical methods (Bayesian mark-recapture) to produce reliable estimates. The data available include a spotty fossil record, and so the researchers needed an appropriate estimate of the number of species present on islands in the past. To do this they examined the fossil record and compared it to species that are found there today. Only a subset was found in the fossil record. From this, they determined how the number of fossils found, body size of the organisms and island size affected detection probability. With these informative detection probabilities, they were able to estimate past richness and compare that to today’s richness – and the difference is the number of extinctions.

Across these 41 islands, Duncan et al. estimate that human colonization resulted in at least 983 extinctions. Nine-hundred and eighty-three species are no longer with us because of the presence of humans. Coupled with human activities elsewhere, from over-hunting, habitat destruction and the introduction of non-native species, we responsible for thousands of extinctions. For the first time in Earth’s history, a single species (us) is the direct cause for thousands of other species going extinct. A paper such as this is an important analysis, but it certainly doesn’t make us feel good about ourselves.

Duncan, R., Boyer, A., & Blackburn, T. (2013). Magnitude and variation of prehistoric bird extinctions in the Pacific Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1216511110

Gendered assumptions and science: still a problem

Sometimes I feel like covering sexism and science has the potential to trigger a weary response, a feeling that this is well-travelled territory. And generally, academia is fairly self-aware about the causes and consequences of its current gender gap (see the special issue in Nature). But then I hear or read something that disappointingly reminds me that society as a whole still has a ways to go.

The first was a minor story. The curator of “I f--king love science”, a widely-followed Facebook page on things scientific and otherwise, happened to reveal that they were Elise Andrew--a female. While this seemed to be a non-event, apparently young men everywhere (i.e. on the internet) were shocked that their mental picture of a male scientist was untrue. Many comments fell along the lines of “you’re a girl?!” and “all that time picturing a man!”. Even more frustrating was that commenters also mentioned Elise’s appearance – attractive and female and a scientist--apparently this was so surprising as to be worthy of comment. And while I wanted to dismiss this as being limited to problems with Internet culture and hardly indicative of larger societal trends, something else happened – Yvonne Brill, a brilliant American rocket scientist passed away. Her work on propulsion systems now helps keep communications satellites in orbit, and she was a successful engineer with an interesting career. She clearly deserved a national obituary, and she got one in the New York Times. It started:

“She made a mean beef stroganoff, followed her husband from job to job and took eight years off from work to raise three children. “The world’s best mom,” her son Matthew said.

But Yvonne Brill, who died on Wednesday at 88 in Princeton, N.J., was also a brilliant rocket scientist, who in the early 1970s invented a propulsion system to help keep communications satellites from slipping out of their orbits.”

By way of comparison, not one of Steve Jobs’ obituaries started with a mention of his hobbies or personal accomplishments, or his status as a father. The only other recently (2012) deceased female scientist I could think of, astronaut Sally Ride, similarly received an obituary in the NYT that emphasized her gender - "American Woman Who Shattered Space Ceiling".

The need of society, reporters, and popular culture to reconcile a female scientist’s gender with their occupation appears to still be common. So much so that the one science writer came up with the Finkbeiner Test (Columbia Journalism Review) to point out articles which rely on the “she’s a woman AND a scientist” trope. Such articles tend to mention:

• The fact that she’s a woman 
• Her husband’s job 
• Her child-care arrangements 
• How she nurtures her underlings 
• How she was taken aback by the competitiveness in her field 
• How she’s such a role model for other women 
• How she’s the “first woman to…” 

The point is not that it is always unacceptable to include such things in articles, but that unless the article is about sexism or balancing work-life balance, these facts are irrelevant when reporting on a scientist's professional accomplishments. Gender shouldn't be the default position when we consider scientists who happen to be women. And apparently this message still needs to be repeated. Some people have suggested that one equalizer is to simply to also ask male scientists about their personal lives more often. However writer Finkbeiner notes that these questions rarely improve science journalism: "They’re [scientists] all normal human beings and the thing that makes them so interesting is the science. So, if you want to humanize them, talk about their motivations. Talk about how they got interested in their field. Talk about the part of their life that led them to become such an interesting scientist—because childcare is not interesting."

Note: while problems with gendered assumptions is a very general societal issue, academia isn't totally blameless. Having served on a number of lecture organizing committees, I've noticed that if the email for speaker nominations doesn't explicitly say that we wish to nominate male and female scientists at the top of their careers, female scientists are rarely nominated. Students' mental image of a top scientist tends to skew male. If that simple note is included though, nominations begin to approach gender ratios for professors at that career stage.

Carbon sequestration in boreal forests: below-ground interactions matter

K. E. Clemmensen, A. Bahr, O. Ovaskainen, A. Dahlberg, A. Ekblad, H. Wallander, J. Stenlid, R. D. Finlay, D. A. Wardle, B. D. Lindahl. Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest. 2013. Science. Vol. 339 no. 6127 pp. 1615-1618. DOI:10.1126/science.1231923 

One of the most important developments in plant ecology over the last 20 or so years is the inclusion of belowground interactions with fungi into traditional studies of plant diversity, productivity, and ecosystem functions. Results like those from van der Heijden (1998)--which showed experimentally that the assumed link between ecosystem function and plant diversity was actually driven by arbuscular mycorrhizal fungal diversity (through their effects on plant communities)—must alter how we see plant community dynamics. Not only does this reinforce the importance of complexity in ecology, but more specifically it suggests that if fungi are a necessary component of plant community identity and function, they must be explicitly considered in management and conservation plans.

For example, an important current issue is the question of which ecosystems will be carbon sinks as part of a focus on atmospheric CO2 levels. Understanding the mechanisms by which carbon is stored is therefore an important topic. Boreal forests sequester net amounts of carbon in soil and it is generally assumed that this is as a result of plant litter and organic matter accumulating in soil. Clemmensen et al. (2013) examined soil chronosequences for forested islands in Sweden to test whether this hypothesis held. These islands differed in the frequency of fire occurrences, between large and frequently burnt islands and smaller, infrequently burnt islands.

The authors identified the age since fixation of C found in the chronosequences and used models of C source to look at the relative contribution of the two possible processes: either fixation of C through aboveground plant litter or below-ground inputs through root-associated fungi. Carbon input tended to be higher on the small islands that were burnt less often, and this was associated entirely with root-derived input. Further, DNA barcoding showed that on these small islands, there were mycorrhizal fungi associated with the soil depths where the root-derived inputs were occurring. On islands which burned more frequently, and had lower carbon input, fungi were absent at these depths (figure below). This difference in fungal profile was related to the fact that infrequently burnt islands had older mycelium with low turnover, hence greater carbon sequestration.

From Clemmensen et al (2013). A) Fungal functional groups associated with soil depths on large, frequently burnt islands (panel 1) and small, infrequently burnt islands (panel 2).

The authors convincingly show that, at least in some ecosystems, the view that decomposition of litter primarily drives humus accumulation (and the accompanying carbon sequestration) must be tempered with the knowledge that organic layers also accumulate from below by roots and root-associated fungi. This suggests that there is a need to consider fungal communities as well as plant communities for when managing forests and making inventories of global carbon stores. And probably a need to consider fungi much more often in general.

A map for defending your PhD

*

Evolution on an ecological scale

Andrew Gonzalez, Ophélie Ronce, Regis Ferriere, and Michael E. Hochberg. 2013. Evolutionary rescue: an emerging focus at the intersection between ecology and evolution. Philos Trans R Soc Lond B Biol Sci. 368 (1610).doi: 10.1098/rstb.2012.0404 (Intro to special issue).

David A. Vasseur, Priyanga Amarasekare, Volker H. W. Rudolf, Jonathan M. Levine. 2011. Eco-Evolutionary Dynamics Enable Coexistence via Neighbor-Dependent Selection. The American Naturalist, Vol. 178, No. 5, pp.E96-E109.

Ecology and evolution are often treated as connected but ultimately discrete areas of study. Ecological processes are usually the main source of explanation for ecological patterns and  ecologists may ignore evolutionary processes under the assumption that these are most important over longer time scales than are of interest (e.g. speciation). However, there is also an increasing recognition that rapid evolutionary dynamics can contribute to ecological observations. In a time where rapid changes to climate and habitat are the greatest threats to most species, the suggestion that rapid evolution might play a role in extinction prevention and diversity maintenance is an important one.

Increasingly researchers are exploring this concept. The concept of evolutionary rescue (ER), has been particularly championed by Andy Gonzalez and Graham Bell of McGill University. ER results when evolution occurs fast enough to arrest population declines and allow populations to avoid extinction in the face of changing conditions. Changing conditions resulting in maladapted populations should result in population declines followed by extinction. However, if selection for resistant types (which are present in the population, or result from mutations) occurs, population declines can be countered. The result is a characteristic u-shape curve, showing the initial geometric decline, followed by a geometric increase – escape from extinction is then a balance between rates of evolution and success of resistant types compared to rates of population decline.

From Bell & Gonzalez 2009.

The question of whether evolution may have relevance to population declines is not precisely new, but it is especially relevant given we are in a period of habitat changes and extinction. A special issue of Proc B is focused only ER, on the question of its importance, prevalence, and predictability. Many of the articles extend theory, exploring assumptions about the type of environmental change, type and extent of the threat, presence of dispersal, spatial gradients, etc. A few articles attempt the more difficult task of testing for ER in natural systems and assessing its likely prevalence and value to conservation activities. It is an interesting journal issue and a great example of the importance of context in determining when an idea takes off. The theoretical background for evolutionary rescue has existed for many years, but it took the context of climate change (and perhaps the collaboration of an ecologist and evolutionary biologist?) for it to gain ground as an area of ecological research.

Another interesting paper, this one linking evolutionary dynamics with community coexistence, is from Vasseur et al. (2011). In this case, the authors suggest an evolutionary mechanism that could augment coexistence when ecological conditions allow for niche partitioning and that could allow coexistence when ecological conditions lead to competitive exclusion. If species exhibit tradeoffs between traits that are optimal for intraspecific interactions and traits that are optimal for interspecific interactions, evo-ecological dynamics can produce coexistence. Such tradeoff means that a species will be a superior interspecific competitor when rare and a poor interspecific competitor when common. Such a tradeoff creates neatly alternately selective pressures depending on whether a species is common (fitness declines) or rare (fitness increases). This is presented as a theoretical model, but it seems like in a tractable system one could easily test for changes in ecological and evolutionary pressures as predicted by the model.

No one would argue with the conclusion that a closer relationship between ecology and evolutionary biology would be beneficial for both. But in practice this seems to be the exception rather than the rule. "Evolutionary ecology" as it exists is fairly restricted, and if complaints about seminar topics is to provide a hint, most ecologists feel disconnected from evolutionary topics and vice versa. If evolutionary dynamics are relevant on an ecological scale, it seems that we should at least attempt to understand their prevalence and importance in natural systems.

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) 
                           ****

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).

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.

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.

Academic ambivalence, part 2: poor prospects

The topic of Caroline's excellent post on why we choose grad school and an academic career seems to be hitting an on-line crescendo. A number of blogs and numerous posts to the ECOLOG listserve have been arguing and lamenting the state of job prospects and the grad school experience in general. What has been lacking is an analysis of the job numbers. In a case of perfect timing, Jordan Weissmann, and The Atlantic, has posted an excellent analysis of the numbers of recent PhDs employed across fields. The general message is: the number of fulltime, permanent jobs waiting for PhDs has been declining. However, the proportion of PhDs taking up post-doctoral postions has not declined (and in fact has increased for many disciplines).

From PhD comics

People in graduate school need to be cognizant of the available options, but it seems that if there is an emerging bottleneck, it certainly is not at the postdoc stage (the proportion of postdocs has not changed recently). Of course, the academic stream is but one option for recent PhDs, and the loss of other opportunities is a serious concern. The graphs in the Weissmann post enumerate full-time jobs, and I wonder how many people are taking up part-time, sessional positions as a way to move forward? Regardless, employment opportunities are changing.

My feeling is that academic institutions should be doing a better job of researching, and presenting viable career options to their graduate students. There are a number of industry, governmental and non-governmental postions out there, but people in academia often have a very limited understanding of these types of positions -where they are, how many are available and what kind of training they are looking for.

Perhaps it is time for graduate programs institute real career training.