Tuesday, February 10, 2015

Charting Our Progress: Evolving Thoughts on Population Dynamics


By: Sarah Solomon

I have always been fascinated by the natural world – by the species that I encounter on a daily basis, and by those that exist on faraway lands. In thinking of how complicated and diverse human population dynamics can be, I’ve always sought to understand how other species’ populations are regulated. Why do some species go extinct, and what prevents others from meeting this same fate?
With ever-increasing human activity around the globe, some species are actually beginning to flourish beyond their natural ranges. From Asian carp to Dog-strangling Vine, the increased abundance and distribution of native and introduced species can be detrimental to the survival of others.
Louis Charles Birch, 1918-2009
University of Sydney

In the early 1940s, Australian insect ecologist Louis Charles Birch began to study how certain species of Dacinae fruit flies were becoming pests as a result of the expansion of cultivated fruit crops. Birch and his supervisor (and would-be lifelong colleague) Herbert Andrewartha were fascinated by the relationship of evolution to ecology, with a particular interest in how evolution can be charted in dynamic species of insects.

At the time of Birch and Andrewartha’s original research on the five most abundant species of fruit flies in eastern Australia, there was a prevailing hypothesis suggesting that all animal populations were self-regulating. This meant that populations of animals would increase under favourable conditions, and that eventually the population would grow so crowded that the birth rate would drop and the death rate would increase – hence the notion of self-regulation. It was believed that once a population reached a low enough density, the pressures on it would decrease and the population would be spared from extinction. Now in a laboratory setting, there was compelling evidence to support this hypothesis, but Birch had a different idea.

What actually happens to populations in nature? Why don’t they become extinct? How might we regulate populations of species that have extended beyond their natural ranges? Birch was part of a generation that started to wonder about these notions as they related to changes in natural environments due to human activities. He decided to look both within and outside of different fruit fly species in order to explore how external factors affect species density and changes in distribution.
In particular, D. tryoni had become a pest to fruit crops spanning the eastern coastal portion of Australia, with a significant increase in its range, adapting to cooler southern temperatures. He was also interested in charting this change – are species actively adapting to environmental changes, and are these changes observable? As it turns out, D. tryoni was even hybridizing with D. neohumeralis – another endemic fruit fly species of eastern Australia – to produce a population of flies with a 15 percent higher survival rate of immature eggs than D. tryoni. And all of this as a result of cultivating more fruit crops across the country!


Thus it seems that Birch was on to something – as it turns out, something very important indeed. It is unclear whether Birch could have anticipated just how much of an impact human activity would have on the environment, and in turn, just how much this change would affect species population dynamics. Today, conservation is at the forefront of science and policy, and the notion of studying the effects of abiotic factors on species population dynamics is imperative.

With scientists like Birch paving the way for thinking beyond the “self-regulating” hypothesis, research groups like that of Australian ecologist Euan Ritchie are committed to producing population models that can help inform conservation policies, and protect at-risk species from extinction.

In a 2009 study, Ritchie and colleagues uncovered how competition between the antilopine wallaroo and its wide-spreading counterpart, the Eastern grey kangaroo, is a threat to the survival of the former species. They also found that habitat – especially changes to landscape and the introduction of cattle ranching – contributed greatly to the viability of these species, and that of the common wallaroo (http://www.ncbi.nlm.nih.gov/pubmed/19175695). This type of modeling research is commonplace in the field of ecology today, as the notion of abiotic factors playing a significant role in species' survival is a widely accepted school of thought. With the growing impacts of climate change becoming more and more evident each day, it seems we have come a long way from the era when Birch’s ideas were considered a minority view.

More than fifty years later, the need to produce sound science with which to inform conservation policy is critical. Since Birch’s kick-start to understanding population dynamics, significant advancements have been made in genetics, and in the technologies for analyzing genetic diversity. Such techniques are helping to further highlight the types of genetic adaptations that Birch started to chart in the 1950s, producing fascinating insights into how populations are disappearing, appearing and adapting to external changes.

Overall, have we made all that much progress since Birch?

I would like to think that in many ways we have, but we still have yet to bridge the gap that exists between sound science and policy enforcement. It seems that despite strides being made on the scientific forefront, useful data are often not used or are discounted by policy decision-makers to suit the goals of various stakeholders. Research, like that of Birch and Andrewartha, and more currently Ritchie and colleagues, has major implications for conservation issues, and particularly for the growing concerns of harmful invasive species (see The Genetics of Colonizing Species).
Share your views, and leave a comment below!


References:
Baker, H. G., and Stebbins, G. L. (1965). The genetics of colonizing species: proceedings. Academic Press Inc.


Ritchie, E. G., Martin, J. K., Johnson, C. N., and Fox, B. J. (2009). Separating the    influences of environment and species interactions on patterns of distribution and abundance: competition between large herbivores. Journal of Animal Ecology, 78,    724-731. doi: 10.1111/j.1365-2656.2008.01520.x



Monday, February 9, 2015

Can an algorithm tell you where to submit your next paper?


Choosing where to submit a manuscript is a difficult proposition. For a strong manuscript, you might hope for a high profile, high impact journal, but also to be considered is the hope (or need) for rapid publication, preferably without too many cycles of rejection, revision, and resubmission.

Maybe you saw this around twitter, but a little over a week ago, one paper offered a solution to the “where to publish?” puzzle. Published in PLoSONE (the journal chosen using their algorithm), authors Salinas and Munch provided one answer to "Optimizing the Submission Decision Process".

Surveys usually show that journal impact factor is the highest priority for authors, and a typical measure of paper success. Recognizing the importance of citations--and journal impact factors as an indirect predictor of them--the authors use Markov decision processes to determine the optimal submission process to maximize citation total. This model is a race against time, where delays reduce the total citations and worse, increase the probability that a paper will be scooped (and therefore have minimal citation value). They also considered a more complex model which maximizes citations, while minimizing delays due to rejection, resubmission and revisions.

The top choice of journals for the first model (maximize citations), were Ecology Letters, Science, and Molecular Ecology Resources. For the second model, the top journals to balance citations and time loss, were Molecular Ecology Resources, PLoSONE, and Ecology Letters.

Finally, if you know your willingness to tradeoff the number of times you submit your paper until acceptance and the number of citations it will receive, you can choose between several strategies. One option is a path that involves submission to a high impact journal (Ecology Letters in particular, possibly Ecological Monographs), accepting that you may actually need to resubmit your paper several times but will gain high citations. Alternately, you could choose a journal such as PLoSONE where resubmission is low and citation rate is moderate. Finally, many specialized journals may be faster, but provide relatively low citations. (Fig 3 below).
From Salinas and Munch 2015.
So what the authors get right is that choosing where to submit is a difficult task. Choosing journals is a skill that a scientist hones over a career. Graduate students have the hardest time, I think, not having experience with the underlying complexities (e.g. this journal is slow, this journal prefers experimental work rather than simulation approaches, Science will probably reject you, but at least it will be very fast...). Students usually have to rely on supervisors and more experienced collaborators precisely because they lack informed priors. That being said, the approach from this paper strikes me as a silly (and just bad) way of choosing journals.

The biggest reason is that even though everyone chooses "impact factor" as their primary criteria for choosing a journal in a survey, in practice impact factor is innately balanced against manuscript quality. Sure, there's the odd soul who always starts at Science and works their way down, but most researchers have a reasonably unbiased view of their manuscript's quality, and journal choice is conditioned by that estimate of manuscript quality. (More commentary on this from Marcel Holyoak and others, here). So it's really about maximizing citations, given the quality of a particular work. This implies authors must have knowledge of the journals in their field, not a simplistic algorithm.

Scooping doesn't strike me as the biggest concern for most ecologists either. There is a cost of declining novelty, perhaps, but it would be a rare ecological paper that lost all citation value because something similar had been published slightly earlier. (Or so I think. Is scooping a big issue in ecology?) 

Additionally, citations simply aren't the only thing concern for researchers, especially early-career people. The quality of journals that you publish in has important implications. Sending all of your papers to PLoSONE to reduce the time to publication while maximizing citations, while apparently a viable strategy, won't do a lot for a career application (not to pick on PLoSONE, which I think has an important role, but isn't usually the first choice journal for ecological research). Publishing in prestigious journals is usually considered an indicator of research quality. 

Journal choice will probably always be a subjective, imperfect behaviour. Even if a more complicated algorithm could be constructed, there are too much subjective inputs--paper quality, subject importance and novelty, journal quality--for the choice to be so simplistic.

Tuesday, February 3, 2015

Predatory open access journals: still keep'n it classy

As most academics are aware, there are hundreds of predatory open access journals that try to trick authors into submitting to their journals, charge exorbitant fees, and do not ensure that articles are peer reviewed or live up to basic scientific standards. The most celebrated cases are journals that embarrassingly publish non-sensical fake papers. I don't know why, but I sometimes go to the journal websites to see what they publish or who is on their editorial boards. I received such an e-mail this morning from SOJ Genetic Science published by Symbiosis, a recognized predatory publisher. This journal, unlike others, actually has a single published issue with an editorial! I thought: "wow, are they trying to be legitimate?"; then I read the editorial. The editorial is probably best described as a nonsensical diatribe about genetics, which lacks any real connection to modern genetic theory. Here is my favourite paragraph:



Predatory open access journals: still keep'n it classy.

Monday, February 2, 2015

Reproductive Character Displacement or Alternative Explanations?

*Guest post by Santiago J. Sánchez-Pacheco

Closely related animal species are often so similar that it is hard to distinguish them. This immediately leads to the question of how the individuals of such species, when in sympatry, can recognize their conspecifics. Usually, the species differ in traits (i.e., species recognition signals; e.g., visual and sound signals) that are detectable by sensory mechanisms. Less is known, however, about how these phenotypic differences evolve. A common view is that hybrids suffer reduced fitness or cannot be produced whatsoever, and therefore selection should favor individuals with traits that avoid interspecific matings. By diverging in such traits, females and males of closely related species are less likely to waste energy in failed matings. This widely accepted assumption is usually referred to as “reproductive character displacement” (Losos, 2013).  

From Evolution (Third edition; Futuyma, 2013).

When Brown and Wilson (1956) described character displacement, they proposed the following process: populations of two closely related species, after first coming into contact with each other, interact “in such a way as to diverge further from one another where they occur together”. Such divergence minimizes the chances of both competition and hybridization between the species, and therefore favors coexistence over exclusion.


While it is generally accepted that natural selection is the force increasing the frequency of the divergent traits, whether or not the resulting divergence is driven by the interaction between the two species (e.g., competition) remains uncertain. If a pattern of differences is consistently detected between populations of two closely related species when they are compared in allopatry versus sympatry, it seems reasonable to attribute this pattern to the interaction of both species. However, a number of processes other than a response to interspecific interaction may result in a “displacement-like” patternsubstantial differences of the environments between allopatry and sympatry, phenotypic plasticity or even random processes can all trigger differentiation (Kamath, 2014).   

Based on six criteria (Box 1) established by Schluter & McPhail (1992) as general indicators to rule out alternative processes that might lead to a displacement-like pattern, recently Stuart & Losos (2013) pointed out that only a small portion (9 of 144 cases) of recent studies claiming evidence for ecological character displacement can conclude with a high degree of certainty that the interspecific interaction led to the observed divergence. According to Stuart & Losos, falsification of only one of these six criteria is enough evidence to determine that such divergence did not result from character displacement. Consequently, their findings suggest that most documented cases of ecological character displacement are equally consistent with other evolutionary and ecological phenomena. Although these two studies focus only on ecological character displacement, it is worth noting that the same eco-evolutionary principles underlie reproductive character displacement, so that alternative processes could also explain phenotypic differentiation presumably derived from interspecific interaction.

Despite the concept of character displacement having remained in the evolutionary literature for decades, this assumption has seldom been subjected to critical scrutiny. Indeed, it was not until recently that significant progress in designing thorough studies to rigorously test this adaptive hypothesis was achieved (e.g., Stuart et al. [2014]).

Box 1: Modified from Stuart and Losos (2013). The six criteria for Ecological Character Displacement (ECD).


References

Brown Jr., W. L. and E. O. Wilson. 1956. Character displacement. Systematic Zoology 5(2): 49–64.


 
Schluter, D. and J. D. McPhail. 1992. Ecological character displacement and speciation in sticklebacks. The American Naturalist 140: 85–108.

Stuart Y. E. and J. B. Losos. 2013. Ecological character displacement: glass half full or half empty. Trends in Ecology and Evolution 28(7): 402–408.

Stuart Y. E., Campbell T. S., Hohenlohe, P. A., Reynolds, R. G., Revell, L. J. and J. B. Losos. 2014. Rapid evolution of a native species following invasion by a congener. Science 346: 463–466.

A blog post reviewing Stuart and Losos (2013) from a different perspective: