Thursday, May 31, 2012

Putting ecological niche models to good use

I won’t be the first or the last person to state that I find ecological niche models (ENMs) a bit problematic. In their simplest form, ENMs are statistical models correlating species presences or presences and absences with climatic factors. These models can then be used to predict the location of suitable habitat either elsewhere in space or later in time. They can be used to examine how species’ ranges may shift with climate change, to predict where invasive species’ ranges will expand, or to suggest appropriate locations for new reserves. Over the last while, they’ve faced a fair amount of criticism. For example, most fail to incorporate biotic interactions and so they capture a species’ realized niche: this means that it might not be accurate to extrapolate the model to areas where the biotic environment is different. There are also questions of what is the appropriate spatial scale for environmental data; the problem that many populations’ dynamics (especially invasive species) are not at equilibrium with the environment, so their observed relationship with climatic factors may not represent their niche; statistical and data-quality issues; and the difficulties of validating predictions that may be made for changes in habitat 50+ years in the future. Like many new techniques, ENMs became popular quickly, before they developed an appropriate foundation, and so they were subject to misuse and inappropriate conclusions. But this is a typical pattern – the development of ecophylogenetic tools has followed a similar path.

While this period of early growth has tarnished some people’s view of ENMs, it would be a shame to disregard them altogether when there are people still using them in interesting and inventive ways. A great example is Banta et al. (2012), which combines a model organism, intraspecific phenotypic variation, and spatial structure of genetic variation with ecological niche modelling. Banta et al. focus on the problematic assumption of such models that intraspecific variation in climatic tolerances is minimal or unimportant. One approach to exploring this issue more is to develop intraspecific ENMs using genotypes, rather than species, as the unit of analysis.

Banta et al. take advantage of the fact that the model organism Arabidopsis thaliana is genetically well understood, allowing them to identify ecologically different genotypes, and is widely distributed across highly varied habitats. The authors looked at genotypes of Arabidopsis that varied in flowering time and asked whether these ecologically differentiated genotypes had different niche breadths and potential range sizes. They also looked at the classic macroecological question of whether niche breadth and range size are correlated (in this case, intraspecifically). To answer these questions, they identified 15 single locus genotypes for flowering time (henceforth “genotypes”), and developed ENMs for each, looking at the climatic conditions associated with each genotype. Using the output from these models, Banta et al. calculated the niche breadth (measured based on how much suitability varies among habitat types) and the size of potential habitat (the sum of units of suitable habitat) for each genotype.

The authors could then look at how intraspecific variation in flowering time related to differences in niche breadth and range size among the different Arabidopsis genotypes. They found that genotypes tended to differ from each other in both niche breadth and range size. This is important because ENMs assume that small amounts of genetic variation among populations shouldn’t affect the accuracy of their results. In fact, even differences in a single gene between genotypes could be associated with differences in niche breadth and potential range. In general, late flowering genotypes tended to have smaller potential ranges. The authors suggest a few explanations for this, including that late flowering genotypes may be adapted to harsher conditions, where flowering late is beneficial, but unable to compete in less stressful habitat. Regardless of the particular explanation, it shows that single locus differences can drive phenotypic differences among individuals, which in turn have notable macroecological effects.
From Banta et al. 2012. Relationship between potential range size and flowering time/niche breadth

Similar to the pattern found in a number of interspecific studies, the authors found a strong correlation between potential range size and niche breadth. This matches the oft-quoted statement by Brown (1984) that generalist species should have large potential ranges compared to specialist species, which should have small potential ranges since they only tolerate a narrow range of environments. It should be noted that this explanation is based on the assumption that habitat types are equally common: should a specialist species be adapted (only) to a widespread habitat type, the correlation between niche breadth and potential habitat size would be weakened. Because this study didn’t incorporate competition or other biotic interactions, it is not possible to conclude that there are differences in climatic tolerances among genotypes rather than differences in competitive abilities, for example. Inferior competitors may be exclude from ideal habitats and so appear to be specialized to harsh conditions (and the authors note this). This is always the difficulty with interpreting observational patterns, and further, the ongoing difficulty with defining a species’ niche based on observational data. In any case, this study does a nice job of exploring the underpinnings of macroecological variation and uses EMNs in an informative way, and suggests many interesting extensions.

Monday, May 14, 2012

Writing about writing about research.

I suppose it was inevitable that someone would publish a scientific paper about blogs that write about scientific publications. That’s either very meta, or a little myopic, or both. Appropriately then, the paper “Research Blogs and the Discussion of Scholarly Information” is published in PLoS ONE, the most prominent open access journal. The internet has expanded scientific discourse beyond the traditional forms of published media, and blogs tend to provide a less formal, more accessible form of communication. The authors were particularly interested in how discussion of published works on research blogs related to the citation of published works in the traditional published literature. When we discuss and cite papers in blogs, those citations are meaningless in the traditional sense, in that they aren’t incorporated into citation analyses.

The authors used the blog aggregator to identify well-established science blogs. They surveyed 126 blogs, recording the names and fields of journals of the 10 most recently reviewed articles on each blog. They also recorded general information about the blog author(s). Life sciences were by far the most common area blogged about (39% of blogs), although life sciences account for only 21% of all publications. Given the fact that women now receive similar numbers of life science degrees, it is perhaps surprising that the vast majority of blogs have male authors (~67% have a single male author, and ~9% have multiple authors, at least one of which is male).

Regardless of who authors the blogs, the papers that are cited in blogs are predominantly from the highest profile journals – Science, Nature, and PNAS. These journals all have expensive paywalls for non-subscribers. The fourth most cited journal, by contrast, is PLoS ONE. It’s hard to say what this means. It may just be that Science, Nature, and PNAS are well represented in their sample because they are interdisciplinary, and so many blogs will cite them. Or, it may be that bloggers are attracted to the same types of papers that Science and Nature are – high profile, “important”, maybe controversial. Further, bloggers may write about high profile papers, but they do so with greater depth and knowledge than most mainstream media.

There’s only so much that you can draw from a relatively small, simple survey, but some of the trends seem contrary to the supposed openness and accessibility of web-based science communication. Research blogs are written primarily by men, and focus on high-profile, non-open access papers. Does the open-access nature of a blog overcome the non-open access nature of the papers they write about? Does writing about a Science paper make the information within it accessible to more people, or does it decrease the number of people who can fully appreciate your post? Ultimately research blogging is complex, like any form of online media; it can improve on traditional communication while still showing some of the same limitations. It does bode well though that, given the number of blogs commenting on this paper, research bloggers tend to be informed and pretty self-aware.

Thursday, May 3, 2012

Robert Sokal: Statistical giant in ecologists' boots

Robert Sokal (1960):
from Wikipedia

No student of my generation, trained in ecology and evolutionary biology, will not have heard of Sokal and Rholf’s Biometry textbook. Most would have used it in a class or to inform their analyses. Sadly, Robert Sokal passed away last month at the age of 86. He had a tremendous career, mostly at Stony Brook University in New York, and contributing to statistics and science for over half a century. As a testament to his impact, the third edition of Biometry has been cited over 14000 times! It is the canon for experimental design and analysis in the biological sciences.

He had extraordinary and tumultuous experiences as a youth -fleeing Nazi Germany and being raised in China. Whether, such experiences give rise to greatness, or whether his innate intellectual abilities sealed his destiny is an interesting question. Regardless, his impact and legacy will be deservedly long lasting.

47th Carnival of Evolution: catch the news.

The latest edition of the Carnival of Evolution is up at Evolving Thoughts. Read it, enjoy it, pass it along.