About Rationally Speaking

Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Monday, September 02, 2013

My best papers: Biology, part II (2000-2009)

by Massimo Pigliucci

This is the second installment (you can find the first one here) of my favorite technical papers, selected among those I published during my first academic career, as an evolutionary biologist. The period covered below goes from 2000 to 2009 (though some papers were published afterwards), when I was a faculty at Stony Brook University. After that, I switched to full time philosophy, but I may need to wait a few years before having a sufficient publication record in that field to be able to pick favorites... If you’d like full e-reprint of any of the papers below (or those from the previous installment), just drop me an email. The full list of my publications is here.

The fall and rise of Dr Pangloss: adaptationism and the Spandrels paper 20 years later
(with J. Kaplan, Trends in Ecology and Evolution, 2000).

Twenty years have passed since Gould and Lewontin published their critique of ‘the adaptationist program’ – the tendency of some evolutionary biologists to assume, rather than demonstrate, the operation of natural selection. After the ‘Spandrels paper’, evolutionists were more careful about producing just-so stories based on selection, and paid more attention to a panoply of other processes. Then came reactions against the excesses of the anti-adaptationist movement, which ranged from a complete dismissal of Gould and Lewontin’s contribution to a positive call to overcome the problems. We now have an excellent opportunity for finally affirming a more balanced and pluralistic approach to the study of evolutionary biology.

Are ecology and evolutionary biology “soft” sciences?
(Annales Zoologici Finnici, 2002).

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten stuck on mathematically appealing but philosophically simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference.

Evolution of phenotypic integration in Brassica (Brassicaceae)
(with C.J. Murren and N. Pendleton, American Journal of Botany, 2002).

Phenotypic integration is a necessary characteristic of living organisms that results from genetic, developmental, and functional relationships among traits. The nature of these relationships can be influenced by the environment. We examined patterns of phenotypic integration of six species of rapid cycling Brassica and of Raphanus sativus within a phylogenetic context. Specifically, we tested the hypothesis that hybrid species show intermediate levels of integration in morphological and life-history characters compared to their putative parentals. We used matrix correlation tests to examine if cytogenetic relationships or ecological similarities among species partially explained the patterns of phenotypic integration. There was a significant negative relationship between the ecological and cytogenetic matrices, suggesting that more closely related species were ecologically dissimilar. However, neither ecological nor cyto- genetic matrices significantly explained differences among species in the pattern of their phenotypic correlations. Set correlation analysis indicated that important traits within the modules and the strength of the correlations within modules differed across species. We also found that there were a greater number of significant correlations between modules than within modules. Hybrid species were more integrated (had greater number of significant trait correlations) than either of their parents, both within and between modules. However, univariate analyses of character means of the hybrid species were not significantly different from the combined mean of their putative parents for 5, 6, or 7 of the 11 phenotypic characters (for Brassica napus, B. juncea and B. carinata, respectively); for the remaining characters, the hybrids were more similar to one of the parents.

Shade-induced plasticity and its ecological significance in wild populations of Arabidopsis thaliana
(with C. Callahan, Ecology, 2002).

In laboratory studies of Arabidopsis thaliana, plants shaded by neighboring vegetation (or subject to treatments mimicking shade) flower at a younger developmental stage, and sometimes earlier in time. We examined whether this shade avoidance response varies among and within natural populations of A. thaliana, and whether it corresponds to variable selection regimes at shaded and unshaded field sites, by conducting a two-year reciprocal transplant study and a parallel greenhouse study that manipulated the presence and timing of shade. In the field, shading had limited or inconsistent impacts on survivorship across several phases of the growing season. The date of bolting was earlier at the shadier site compared to the less shady site, but in the greenhouse there was no significant shade- induced plasticity for this trait. In both studies, we detected directional selection gradients favoring earlier bolting in shade, but gradients favoring earlier bolting were as strong in nonshaded conditions. The number of rosette leaves at bolting (i.e., the developmental stage of flowering) was significantly reduced by shade in both studies. However, there was either no directional selection on this trait, or selection to flower with more rather than fewer leaves. Despite the contrast in habitats, there was limited differentiation between populations for survivorship, reproductive fitness, size-related or flowering time traits, and no differ- entiation for trait plasticities. Some traits were variable among families within populations. A trade-off between age and developmental stage may limit the response to selection for flowering time, possibly explaining limited local adaptation. The adaptive significance of shade-induced flowering time plasticity remains equivocal. Future studies of the plasticity of flowering time in A. thaliana should investigate the effects of shading regimes together with other environmental variables on size- and timing-related traits.

Comparative Studies of Evolutionary Responses to Light Environments in Arabidopsis
(with H. Pollard and M.B. Cruzan, American Naturalist, 2003).

In this article, we compare the reaction norms to foliage shade (changes in light quality, spatially fine-grained environmental variation) and photoperiod (day length, spatially coarse-grained environmental variation) in several haplotypes of Arabidopsis thaliana from Scandinavia. We found that both across-environment means and phenotypic plasticities evolved continuously and very rapidly within this group. Both character means and trait plasticities were highly integrated, in part as predicted by the adaptive plasticity hypothesis for response to foliage shade (the so-called shade-avoidance syndrome). We found that a significant but small fraction of the variance in across-treatment trait means and plasticities in response to one environmental factor is explained by variation of the same traits in response to the other factor. Genetic relatedness based on chloroplast DNA sequence variation among haplotypes was not associated with variation in across-treatment character means or their plasticities, suggesting that evolution of these characters has occurred on a local geographic scale via reticulation (outcrossing) among maternal lines rather than by the differential survival of selfing lineages.

Genetic assimilation and a possible evolutionary paradox: can macroevolution sometimes be so fast as to pass us by?
(with C.J. Murren, Evolution, 2003).

The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the ‘‘hardening’’ of the neo-Darwinian synthesis and was relegated to a secondary role for decades. Recently, several papers have appeared, mostly independently of each other, to explore the likelihood of genetic assimilation as a biological phenomenon and its potential importance to our understanding of evolution. In this article we briefly trace the history of the concept and then discuss theoretical models that have newly employed genetic assimilation in a variety of contexts. We propose a typical scenario of evolution of genetic assimilation via an intermediate stage of phenotypic plasticity and present potential examples of the same. We also discuss a conceptual map of current and future lines of research aimed at exploring the actual relevance of genetic assimilation for evolutionary biology.

Phenotypic integration: studying the ecology and evolution of complex phenotypes
(Ecology Letters, 2003).

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science.

Selection in a model system: ecological genetics of flowering time in Arabidopsis thaliana
(Ecology, 2003).

Arabidopsis thaliana and some of its close allies have been a model system for genetics, developmental biology, and molecular biology for some time. More recently, they have been adopted by an increasing number of laboratories involved in evolutionary ecological research. In this paper, I illustrate some of the methods and advantages concerning the use of Arabidopsis to study selection and the constraints imposed on it by the genetic architecture underlying morphological and life history traits. Populations of A. thaliana and closely related species show a wider ecological variance than had been suspected, and it is increasingly clear that even such a relatively simple organism presents endless challenges to ecologists and evolutionary biologists. The study of the evolution of life history traits in this group also provides us with an invaluable opportunity to advance our search for ways to integrate biological knowledge at the organismal and molecular levels. At the same time, these efforts also yield a better understanding of the type of research that can be carried out independently at these two levels of the biological hierarchy.

Species as family resemblance concepts: the (dis-)solution of the species problem?
(BioEssays, 2003).

The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical literatures on the species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is conceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion presented here is Templeton’s cohesion idea.

Evolution of phenotypic plasticity: where are we going now?
(Trends in Ecology & Evolution, 2005).

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development.

Jack of all trades, master of some? On the role of phenotypic plasticity in plant invasions
(with C.L. Richards, O. Bossdorf, N.Z. Muth and J. Gurevitch, Ecology Letters, 2006).

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives.

Do we need an extended evolutionary synthesis?
(Evolution, 2007).

The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

Finding the way in phenotypic space: the origin and maintenance of constraints on organismal form
(American Journal of Botany, 2007).

One of the all-time questions in evolutionary biology regards the evolution of organismal shapes, and in particular why certain forms appear repeatedly in the history of life, others only seldom and still others not at all. Recent research in this field has deployed the conceptual framework of constraints and natural selection as measured by quantitative genetic methods. In this paper I argue that quantitative genetics can by necessity only provide us with useful statistical summaries that may lead researchers to formulate testable causal hypotheses, but that any inferential attempt beyond this is unreasonable. Instead, I suggest that thinking in terms of coordinates in phenotypic spaces, and approaching the problem using a variety of empirical methods (seeking a consilience of evidence), is more likely to lead to solid inferences regarding the causal basis of the historical patterns that make up most of the data available on phenotypic evolution.

Epigenetics for ecologists
(with O. Bossdorf and C.L. Richards, Ecology Letters, 2008).

There is now mounting evidence that heritable variation in ecologically relevant traits can be generated through a suite of epigenetic mechanisms, even in the absence of genetic variation. Moreover, recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations. These novel findings are potentially highly relevant to ecologists because they could significantly improve our understanding of the mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change. To understand the full significance of epigenetic processes, however, it is imperative to study them in an ecological context. Ecologists should therefore start using a combination of experimental approaches borrowed from ecological genetics, novel techniques to analyse and manipulate epigenetic variation, and genomic tools, to investigate the extent and structure of epigenetic variation within and among natural populations, as well as the interrelations between epigenetic variation, phenotypic variation and ecological interactions.

Is evolvability evolvable?
(Nature Reviews Genetics, 2008).

In recent years, biologists have increasingly been asking whether the ability to evolve — the evolvability — of biological systems, itself evolves, and whether this phenomenon is the result of natural selection or a by-product of other evolutionary processes. The concept of evolvability, and the increasing theoretical and empirical literature that refers to it, may constitute one of several pillars on which an extended evolutionary synthesis will take shape during the next few years, although much work remains to be done on how evolvability comes about.

The proper role of population genetics in modern evolutionary theory
(Biological Theory, 2008).

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthesis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics.

A comprehensive test of the ‘limiting resources’ framework applied to plant tolerance to apical meristem damage
(with J.A. Banta and M.H.H. Stevens, Oikos, 2010).

Tolerance to apical meristem damage (AMD) is a form of plant defense against herbivory. Theoretical models come to different conclusions about the effects of inorganic soil nutrient levels on tolerance to AMD, and different plants have shown different relationships between these variables. To assign some order to these disparate patterns and to resolve conflicts among the models, the ‘limiting resources model’ (LRM) was developed. However, we believe that the LRM is actually comprised of several different models, which we describe. Our study marks the first comprehensive and simultaneous test of the entire LRM framework, treating it explicitly as separate models, which also evaluates the models’ underlying assumptions. We studied tolerance to AMD in laboratory-reared natural populations of Arabidopsis thaliana from three different regions of Europe, spanning a wide latitudinal gradient. We show that, in different populations of this species, basic responses to nutrients and damage are best described by different models, which are based on different assumptions and make different predictions. This demonstrates the need for complexity in our explanations, and suggests that no one existing model can account for all relationships between tolerance to AMD and nutrients. Our results also demonstrate that fruit production can provide a misleading approximation of fitness in A. thaliana, contrary to the common assumption in the literature.

Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana
(with O. Bossdorf, D. Arcuri and C.L. Richards, Evolutionary Ecology, 2010).

Heritable phenotypic variation in plants can be caused not only by underlying genetic differences, but also by variation in epigenetic modifications such as DNA methylation. However, we still know very little about how relevant such epigenetic variation is to the ecology and evolution of natural populations. We conducted a greenhouse experiment in which we treated a set of natural genotypes of Arabidopsis thaliana with the demethylating agent 5-azacytidine and examined the consequences of this treatment for plant traits and their phenotypic plasticity. Experimental demethylation strongly reduced the growth and fitness of plants and delayed their flowering, but the degree of this response varied significantly among genotypes. Differences in genotypes’ responses to demethylation were only weakly related to their genetic relatedness, which is consistent with the idea that natural epigenetic variation is independent of genetic variation. Demethylation also altered patterns of phenotypic plasticity, as well as the amount of phenotypic variation observed among plant individuals and genotype means. We have demonstrated that epigenetic variation can have a dramatic impact on ecologically important plant traits and their variability, as well as on the fitness of plants and their ecological interactions. Epigenetic variation may thus be an overlooked factor in the evolutionary ecology of plant populations.

Selection dynamics in native and introduced Persicaria species
(with K.L. O’Donnell, International Journal of Plant Science, 2010).

Plant invasions represent natural experiments that allow us to both explore the dynamics of natural selection in the wild and examine the evolution of an invader on contemporary timescales. We conducted a study of 10 natural populations of two invasive species (Persicaria lapathifolia and Persicaria cespitosa) and one native species (Persicaria pensylvanica) to quantify the amount of natural selection acting on these species to compare the selection dynamics to which each is exposed. We also conducted a germination trial to compare the potential for invasion determined by germination rate. A Lande-Arnold-style multiple regression selection analysis was performed on five morphological traits (height, stem diameter, leaf number, leaf shape, and leaf area) using flower number as our fitness proxy. Most selection was indirect and caused by correlations with other traits under selection. However, there was significant direct selection for increased leaf number in both natives and invasives and for thicker stems in just the invasives. The germination test showed that not only do the invasive plants have a significantly higher germination rate (>60% compared with 3% for the noninvasives) but they also germinate significantly faster; both findings have large implications for the ability of these two invasive species to spread.

Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation
(with C.L. Richards and A.W. Schrey, Ecology Letters, 2012).

The expansion of invasive species challenges our understanding of the process of adaptation. Given that the invasion process often entails population bottlenecks, it is surprising that many invasives appear to thrive even with low levels of sequence-based genetic variation. Using Amplified Fragment Length Poly- morphism (AFLP) and methylation sensitive-AFLP (MS-AFLP) markers, we tested the hypothesis that differentiation of invasive Japanese knotweed in response to new habitats is more correlated with epigenetic variation than DNA sequence variation. We found that the relatively little genetic variation present was differentiated among species, with less differentiation among sites within species. In contrast, we found a great deal of epigenetic differentiation among sites within each species and evidence that some epigenetic loci may respond to local microhabitat conditions. Our findings indicate that epigenetic effects could con- tribute to phenotypic variation in genetically depauperate invasive populations. Deciphering whether differences in methylation patterns are the cause or effect of habitat differentiation will require manipulative studies.

On the different ways of ‘‘doing theory’’ in biology
(Biological Theory, 2012).

‘‘Theoretical biology’’ is a surprisingly heterogeneous field, partly because it encompasses ‘‘doing theory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer simulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the allegedly much more restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shaping biological theorizing.


  1. This inspires me to (re)collect the lists of my publications and patents. I wrote most in a corporate research lab after brief bits in two university research labs. I think the most famous person I knew was John Tukey (at Princeton). He invented the word 'bit'.

  2. In my humble opinion (and of course my taste), evolutionary biologists "ought to read" these masterpieces:

    Genetic assimilation and a possible evolutionary paradox: can macroevolution sometimes be so fast as to pass us by? (with C.J. Murren, Evolution, 2003).

    Species as family resemblance concepts: the (dis-)solution of the species problem? (BioEssays, 2003).

    Jack of all trades, master of some? On the role of phenotypic plasticity in plant invasions (with C.L. Richards, O. Bossdorf, N.Z. Muth and J. Gurevitch, Ecology Letters, 2006).

    Do we need an extended evolutionary synthesis? (Evolution, 2007).

    Finding the way in phenotypic space: the origin and maintenance of constraints on organismal form (American Journal of Botany, 2007).

    Is evolvability evolvable? (Nature Reviews Genetics, 2008).

    The proper role of population genetics in modern evolutionary theory (Biological Theory, 2008).


Note: Only a member of this blog may post a comment.