Ecology & Evolution Department - Stony Brook University

Wherever wildlife management concerns the movement of individuals across structured habitat, its scale of operations will encompass metapopulation dynamics. The goal of this essay is to review the potential applications of metapopulation concepts and models in reserve design and conservation management. Our perspective is forward-looking. We show how some key problems of where to direct conservation effort and how to manage populations can be addressed in the context of regional habitat structure and the survival and renewal of habitat patches. We also mention several cases of successful metapopulation management and point out practical problems. We emphasize: 1. that the viability of a population may depend on surrounding populations, in which case metapopulation processes influence or determine reserve design and management options; 2. that understanding the dynamic processes of populations requires models, which make assumptions that need validating; 3. that the principle limitation of metapopulation models is their single-species focus.

Author: Akçakaya, H.R., S.H.M. Butchart, G.M. Mace, S.N. Stuart, and C. Hilton-Taylor. 2006.
Title: Use and misuse of the IUCN Red List Criteria in projecting climate change impacts on biodiversity.
Journal: Global Change Biology 12:2037-2043.
Abstract: <= click to show/hide

Recent attempts at projecting climate change impacts on biodiversity have used the IUCN Red List Criteria to obtain estimates of extinction rates based on projected range shifts. In these studies, the Criteria are often misapplied, potentially introducing substantial bias and uncertainty. These misapplications include arbitrary changes to temporal and spatial scales; confusion of the spatial variables; and assume a linear relationship between abundance and range area. Using the IUCN Red List Criteria to identify which species are threatened by climate change presents special problems and uncertainties, especially for shorter-lived species. Responses of most species to future climate change are not understood well enough to estimate extinction risks based solely on climate change scenarios and projections of shifts and/or reductions in range areas. One way to further such understanding would be to analyze the interactions among habitat shifts, landscape structure and demography for a number of species, using a combination of models. Evaluating the patterns in the results might allow the development of guidelines for assigning species to threat categories, based on a combination of life history parameters, characteristics of the landscapes in which they live, and projected range changes.

Author: Amaral, Ana R., M. Manuela Coelho, Jesús Marugán-Lobón and F. James Rohlf. 2008 (in press).
Title: Geometric morphometric analysis of cranial shape in closely related delphinid cetacean species: an evolutionary approach: Evolutionary morphology the skull in delphinids on the basis of geometric morphometric procedures.
Journal: Zoology.
Abstract: <= click to show/hide

The present study investigates the pattern of differentiation of cranial shape in three closely related delphinid cetacean species of the complex Delphinus-Stenella-Tursiops: D. delphis, S. coeruleoalba and T. truncatus. Dorsal and ventral aspects of the cranium were analysed using landmark-based geometric morphometric methods. While there was no evidence of sexual dimorphism for shape or size, multivariate statistical analyses showed that there were interspecific differences in skull morphology. Skull shape differences between the three studied species were related with cranial width and differences in the length of the rostrum relative to the cranial portion of the skull. D. delphis and S. coeruleoalba showed high cranial shape similarity, which is indicative of their evolutionary proximity when compared with T. truncatus. Phenetic clusters based on cranial shape similarities were found to be concordant with the molecular phylogenetic clades obtained from mitochondrial DNA genes. Geometric morphometric methods can thus be an exceptionally useful tool for the study of differentiation of delphinid cetacean species and therefore provide some insights into their evolutionary history.

Author: Antonyshyn , O. M., J. G. Mainprize, F. J. Rohlf, and M. A. Pahuta 2008 (in press).
Title: Biometric Morphing: a novel technique for the analysis of morphological outcomes following facial surgery.
Journal: Annals of Plastic Surgery.
Abstract: <= click to show/hide

The results of facial surgery are intuitively judged in terms of the visible changes in facial features or proportions. However, describing these morphological outcomes objectively remains a challenge. Biometric morphing addresses this issue by merging statistical shape analysis and image processing. This study describes the implementation of biometric morphing in describing the average morphological result of facial surgery. The biometric morphing protocol was applied to pre and postoperative images of (1) 40 dorsal hump reduction rhinoplasties and (2) 20 unilateral enophthalmos repairs. Preoperative and postoperative average images (average morphs) were generated. The average morphs provided an objective rendering of nasal and periorbital morphology, which summarized the average features and extent of deformity in a population of patients. Subtle alterations in morphology following surgery, that would otherwise be difficult to identify or demonstrate, were clearly illustrated. Biometric morphing is an effective instrument for describing average facial morphology in a population of patients.

Author: Banta, J. A., J. Dole, M. B. Cruzan, and M. Pigliucci. 2007.
Title: Evidence of local adaptation to coarse-grained environmental variation in Arabidopsis thaliana.
Journal: Evolution 61(10): 2419-2432.
Abstract: <= click to show/hide

Plants can achieve an appropriate phenotype in particular conditions either constitutively or plastically, depending in part on the grain size of the environmental conditions being considered. Coarse-grained environmental variation should result in selection for local adaptation and no selection on plasticity to novel levels of the coarse-grained environmental factors. We tested the hypotheses that natural populations of the well-studied model system Arabidopsis thaliana are locally adapted to spatially coarse- grained environmental variation, and that the photoperiodic regime per se is at least partially responsible for that local adaptation, by exposing natural populations to photoperiodic regimes characteristic of their native and foreign (novel) environments. We also tested the hypothesis that plasticity to novel photoperiodic regimes should appear random. We found that populations showed evidence of local adaptation at a spatially coarse grain, although not to photoperiodic regime per se. We also found that the plasticities to novel photoperiodic regimes appeared random and did not generally show evidence of adaptive divergence. Our study highlights the need for caution in extrapolating from the ?nding of local adaptation to the causes of local adaptation.

Author: Banta, J. A., S. C. Stark, M. H. H. Stevens, T. H. Pendergast, A. Baumert, and W. P. Carson. 2008.
Title: Light reduction predicts widespread patterns of dominance between asters and goldenrods.
Journal: Plant Ecology: DOI 10.1007/s11258-11008-19412-11253.
Abstract: <= click to show/hide

(Published early online. Volume and page numbers not yet assigned.)

Author: Bossdorf, O., C. Richards, et al. 2008.
Title: Epigenetics for ecologists.
Journal: Ecology Letters 11: 106-115.
Abstract: <= click to show/hide

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 ?ndings are potentially highly relevant to ecologists because they could signi?cantly improve our understanding of the mechanisms underlying natural and phenotypic variation and the responses of organisms to environmental change. To understand the full signi?cance 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.

Author: Butchart, S., H.R. Akçakaya, J. Chanson, J.E.M. Baillie, B. Collen, S. Quader, W. R. Turner, R. Amin, S.N. Stuart, C. Hilton-Taylor. 2007.
Title: Improvements to the Red List Index.
Journal: PLoS ONE 2(1): e140. doi:10.1371/journal.pone.0000140.
Abstract: <= click to show/hide

The Red List Index uses information from the IUCN Red List to track trends in the projected overall extinction risk of sets of species. It has been widely recognised as an important component of the suite of indicators needed to measure progress towards the international target of significantly reducing the rate of biodiversity loss by 2010. However, further application of the RLI (to non-avian taxa in particular) has revealed some shortcomings in the original formula and approach: It performs inappropriately when a value of zero is reached; RLI values are affected by the frequency of assessments; and newly evaluated species may introduce bias. Here we propose a revision to the formula, and recommend how it should be applied in order to overcome these shortcomings. Two additional advantages of the revisions are that assessment errors are not propagated through time, and the overall level extinction risk can be determined as well as trends in this over time.

Author: Butchart, S., H.R. Akçakaya, E. Kennedy, L. Master and C. Hilton-Taylor. 2006.
Title: Biodiversity indicators based on trends in conservation status: strengths of the IUCN Red List Index.
Journal: Conservation Biology 20:579–581.
Abstract: <= click to show/hide

Author: Byun-McKay, S. A. and Geeta, R. 2007.
Title: Protein subcellular relocalization: a new perspective on the origin of novel genes.
Journal: Trends Ecol. Evol. 22:338-344.
Abstract: <= click to show/hide

Author: Champagne, C.E.M., Goliber, T. E., Wojciechowski, M. F., Mei, R. W., Townsley, B. T., Wang, K., Paz M. W., Geeta, R., and Neelima R. Sinha. 2007.
Title: Compound Leaf Development and Evolution in the Legumes.
Journal: Plant Cell 19 3369-3378.
Abstract: <= click to show/hide

Author: Dávalos LM, Perkins SL. 2008.
Title: Saturation and base composition bias explain phylogenomic conflict in Plasmodium.
Journal: Genomics. 2008 May;91(5):433-42. Epub 2008 Mar 4.
Abstract: <= click to show/hide

Despite recent genome-based advances in understanding Plasmodium molecular evolution and its relationship to disease mechanisms and potential drug development, the phylogenetics of the group is currently limited to single-gene analyses. Here we develop and analyze a set of N100 putative orthologous genes derived from genome comparisons. We aimed to minimize systematic errors that arise when reconstructing the Plasmodium phylogeny with a genome-scale data set by evaluating the congruence of different genes, optimality criteria, and models of sequence evolution with previous studies encompassing fewer characters and more species. Saturation in substitutions and bias in base frequencies at third-codon positions characterized most Plasmodium genes. Molecular evolution models that partitioned rates of change by codon position were best at accounting for these sequence characteristics, as were analyses of amino acid alignments. These methods also ameliorated, but did not entirely avoid, the impact of reduced taxon sampling on phylogeny. The use of these models and expanded taxon sampling are necessary to maximize detection of multiple substitutions, overcome compositional biases, and, ultimately, resolve with confidence the phylogeny of Plasmodium.
PMID: 18313259 [PubMed - indexed for MEDLINE]

Author: Dunham, A.E., H.R. Akçakaya, T. S. Bridges. 2006.
Title: Using scalar models for precautionary assessments of threatened species.
Journal: Conservation Biology 20: 1499-1506.
Abstract: <= click to show/hide

Scalar population models, commonly referred to as count-based models, are based on time-series data of population sizes and may be useful for screening-level ecological risk assessments when data for more complex models are not available. Appropriate use of such models for management purposes, however, requires understanding inherent biases that may exist in these models. Through a series of simulations, which compared predictions of risk of decline of scalar and matrix-based models, we examined whether discrepancies may arise from different dynamics displayed due to age structure and generation time. We also examined scalar and matrix-based population models of 18 real populations for potential patterns of bias in population viability estimates. In the simulation study, precautionary bias (i.e., overestimating risks of decline) of scalar models increased as a function of generation time. Models of real populations showed poor fit between scalar and matrix-based models, with scalar models predicting significantly higher risks of decline on average. The strength of this bias was not correlated with generation time, suggesting that additional sources of bias may be masking this relationship. Scalar models can be useful for screening-level assessments, which should in general be precautionary, but the potential shortfalls of these models should be considered before using them as a basis for management decisions.

Author: Dustin Brisson, Daniel E. Dykhuizen and Richard S. Ostfeld. 2008.
Title: Conspicuous impacts of inconspicuous hosts on the Lyme disease epidemic.
Journal: Proc. R. Soc. B (2008) 275, 227–235, doi:10.1098/rspb.2007.1208.
Abstract: <= click to show/hide

Emerging zoonotic pathogens are a constant threat to human health throughout the world. Control strategies to protect public health regularly fail, due in part to the tendency to focus on a single host species assumed to be the primary reservoir for a pathogen. Here, we present evidence that a diverse set of species can play an important role in determining disease risk to humans using Lyme disease as a model. Hosttargeted public health strategies to control the Lyme disease epidemic in North America have focused on interrupting Borrelia burgdorferi sensu stricto (ss) transmission between blacklegged ticks and the putative dominant reservoir species, white-footed mice. However, B. burgdorferi ss infects more than a dozen vertebrate species, any of which could transmit the pathogen to feeding ticks and increase the density of infected ticks and Lyme disease risk. Using genetic and ecological data, we demonstrate that mice are neither the primary host for ticks nor the primary reservoir for B. burgdorferi ss, feeding 10% of all ticks and 25% of B. burgdorferi-infected ticks. Inconspicuous shrews feed 35% of all ticks and 55% of infected ticks. Because several important host species influence Lyme disease risk, interventions directed at a multiple host species will be required to control this epidemic.

Author: Evgeni V. Sokurenko, Richard Gomulkiewicz and Daniel E. Dykhuizen. 2006.
Title: Source–sink dynamics of virulence evolution.
Journal: NATURE REVIEWS, MICROBIOLOGY, 548-555, Vol.4, July 2006.
Abstract: <= click to show/hide

To understand the evolution of genetic diversity within species — bacterial and others — we must dissect the first steps of genetic adaptation to novel habitats, particularly habitats that are suboptimal for sustained growth where there is strong selection for adaptive changes. Here, we present the view that bacterial human pathogens represent an excellent model for understanding the molecular mechanisms of the adaptation of a species to alternative habitats. In particular, bacterial pathogens allow us to develop analytical methods to detect genetic adaptation using an evolutionary ‘source–sink’ model, with which the evolution of bacterial pathogens can be seen from the angle of continuous switching between permanent (source) and transient (sink) habitats. The source–sink model provides a conceptual framework for understanding the population dynamics and molecular mechanisms of virulence evolution.

Author: Geeta, R. and Gharaibeh, W. 2007.
Title: Historical evidence for a pre-Columbian presence of Datura in the Old World and implications for a first millenium transfer from the New World.
Journal: J. Biosci. 32: 1227-1244.
Abstract: <= click to show/hide

Author: Ginzburg, L.R and Damuth, J. 2008.
Title: The space-lifetime hypothesis: viewing organisms in four dimension, literally.
Journal: American Naturalist 171:125-131.
Abstract: <= click to show/hide

Much of the debate about alternative scaling exponents may result from unawareness of the dimensionality appropriate for different data and questions; in some cases, analysis has to include a fourth temporal dimension, and in others, it does not. Proportional scaling simultaneously applied to an organism and its generation time, treating the latter as a natural fourth dimension, produces a simple explanation for the 3/4 power in large-scale interspecies comparisons. Analysis of data sets of reduced dimensionality (e.g., data sets constructed such that one or more of the four dimensions are fixed), results in predictably lower metabolic exponents of 2/3 and 1/2 under one and two constraints, respectively. Our space-lifetime view offers a predictive framework that may be useful in developing a more complete mechanistic theory of metabolic scaling.

Author: Ginzburg, L.R., and Jensen, C.XJ. 2008.
Title: From controversy to consensus: the indirect interference functional response.
Journal: SIL Biology 30/2, April 2008.
Abstract: <= click to show/hide

Theoretical debate between advocates of the prey-dependent (H2) and ratio- dependent (AG) functional responses has given way to an understanding that most functional responses exhibit some form of predator dependence (ABRAMS & GINZBURG 2000). The intermediate models of Beddington-DeAngelis (1975) (BD) and Hassell-Varley (1969) (HVH) capture some of the properties of ratio dependence without the extreme assumption of total prey sharing. When and how to use these intermediates remains a mystery; this uncertainty prevents prediction of: (i) the equilibrial response of trophic systems to enrichment; (ii) the length of trophic chains; and (iii) the stability of trophic systems. Whether the goal of an applied project is to keep population densities low (e.g. when managing a pest or counteracting an algal bloom) or to maintain sufficient population densities (e.g. when conservation is the goal), functional response assumptions directly impact the decision-making process. With the eventual goal of using predator-prey equations to aid in management and conservation efforts, some guidance in choosing an appropriate functional response needs to be provided. In this paper we will delineate the strengths and weaknesses of the prey- and ratio-dependent forms and suggest a novel predator-dependent form that preserves the viable attributes of both extremes.

Author: Ginzburg, L.R. Jensen, CX. J. and Yule, J.V. 2007.
Title: Aiming the "unreasonable effectiveness of mathematics" at ecological theory.
Journal: Ecological Modeling 207, pp. 356-362.
Abstract: <= click to show/hide

A good theory is focused without being blurred by extraneous detail or overgenerality. Yet ecological theories frequently fail to achieve this desirable middle ground. Here, we review the reasons for the mismatch between what theorists seek to achieve and what they actually accomplish. In doing so, we argue on pragmatic grounds against mathematical literalism as an appropriate constraint to mathematical constructions: such literalism would allow mathematics to constrain biology when the biology ought to be constraining mathematics. We also suggest a method for differentiating theories with the potential to be "unreasonably effective" from those that are simply overgeneral. Simple axiomatic assumptions about an ecological system should lead to theoretical predictions that can then be compared with existing data. If the theory is so general that data cannot be used to test it, the theory must be made more specific.

Author: Ginzburg, L.R. and Colyvan, M. 2004.
Title: Ecological Orbits: how planets move and populations grow.
Journal: Oxford University Press, New York, NY.
Abstract: <= click to show/hide

Author: Harcourt-Smith, W. H. E., M. Tallman, S. R. Frost, D. F. Wiley, F. J. Rohlf, E. Delson. 2008 (In press).
Title: Analysis of selected hominoid joint surfaces using laser scanning and geometric morphometrics: a preliminary report.
Journal: Pp. 000-000 in E. J. Sargis and M. Dagosto (eds.) Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay. Springer: Dordrecht.
Abstract: <= click to show/hide

2B-PLS analysis of GPA aligned and slid (semi)landmark data from laser scans of Homo, Pan and Gorilla tibiae and tali was undertaken in order to test a new approach for distinguishing between taxa and individuals. When centroid size is restored to the data, the preliminary results of our joint congruence study are encouraging. Thus it appears clear that both size and shape, rather than shape alone, are critical in determining the statistical degree of congruence between the tibial and talar joint surfaces. This may seem intuitive, since when trying to match joints using visual estimation alone, one naturally would discard elements incompatible due to size differences. Shape alone, at least for the surfaces used here, is not a sufficient factor in estimating joint congruence.
In a comparison of all three genera using tibial and talar PLS axis 1 scores, there was reasonably good visual separation (~75%, see Figure 17.3) of intrageneric matches from intergeneric mismatches. Within Homo, individual matches were not distinguished from individual mismatches when the apes were included. However, in a second analysis where apes were not included, 73% of individual mismatches within Homo were separated from individual matches (Figure 17.4). It is likely that intergeneric differences swamp the subtler distinctions expected within a genus (or species). Therefore, when considering potential hominin fossil material in an analysis such as this one, the important factor is whether the values for that pair of fossils fall far away from the band of matched individuals, or are closer to (or even within) that band.
The DF analysis of the first 10 pairs of singular warp scores yielded good reclassification results, with 101 of 106 pairs correctly identified (over 95%, as per Table 17.2). Given that DFA considers variation across all variables and compares differences between groups relative to variation within groups, it is not surprising that discrimination is better in Figure 17.5 than in Figure 17.3. However, the basic pattern of group distribution is similar.
This statistical treatment of the PLS scores could therefore be useful for discriminating between matched and unmatched isolated fossil elements (where reciprocal joint surfaces are present). This is particularly true given that the tibial malleolar surface was not included in this analysis, and that the results were nonetheless positive; its inclusion should improve the results. This technique, therefore, has considerable potential for sorting isolated elements recovered from paleontological or archeological sites, in particular, where it is hypothesized that two or more closely related taxa may co-occur. The results from this study are preliminary, and a number of different directions are currently being explored to further refine our techniques. In particular, we are evaluating different ways of sliding the semilandmarks, so that more complex surfaces such as the malleolar facets can be used in future analyses. Further analyses will also benefit from larger sample sizes, which are currently being collected. Most importantly, our next phase of research will incorporate fossil elements into the analysis for the first time.

Author: Hoch, JM. 2008.
Title: Variation in penis morphology and mating ability in the barnacle, Semibalanus balanoides.
Journal: Journal of Experimental Marine Biology and Ecology, 359 pp. 126-130. 9 May 2008.
Abstract: <= click to show/hide

Author: Jensen, C, Jeschke, J.M. and Ginzburg, L.R. 2007.
Title: A direct, experimental test of resource vs. consumer dependence: comment.
Journal: Ecology 88(6), pp.1600-1602.
Abstract: <= click to show/hide

Author: Jensen, C. X., and Ginzburg, L. R. 2005.
Title: Paradoxes or theoretical failures? The jury is still out.
Journal: Ecological Modeling. 118 (2005):3-14.
Abstract: <= click to show/hide

Author: Natalia Korotkova, Sujay Chattopadhyay, Tami A. Tabata, Viktoria Beskhlebnaya, Vladimir Vigdorovich, Brett K. Kaiser, Roland K. Strong, Daniel E. Dykhuizen, Evgeni V. Sokurenko and Steve L. Moseley. 2007.
Title: Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli.
Journal: Molecular Microbiology (2007) 64(1), 180–194 doi:10.1111/j.1365-2958.2007.05648.x.
Abstract: <= click to show/hide

Immune escape is considered to be the driving force behind structural variability of major antigens on the surface of bacterial pathogens, such as fimbriae. In the Dr family of Escherichia coli adhesins, structural and adhesive functions are carried out by the same subunit. Dr adhesins have been shown to bind decayaccelerating factor (DAF), collagen IV, and carcinoembryonic antigen-related cell adhesion molecules (CEACAMs). We show that genes encoding Dr adhesins from 100 E. coli strains form eight structural groups with a high level of amino acid sequence diversity between them. However, genes comprising each group differ from each other by only a small number of point mutations. Out of 66 polymorphisms identified within the groups, only three were synonymous mutations, indicating strong positive selection for amino acid replacements. Functional analysis of intragroup variants comprising the Dr haemagglutinin (DraE) group revealed that the point mutations result in distinctly different binding phenotypes, with a tendency of increased affinity to DAF, decreased sensitivity of DAF binding to inhibition by chloramphenicol, and loss of binding capability to collagen, CEACAM3 and CEACAM6. Thus, variability by point mutation of major antigenic proteins on the bacterial surface can be a signature of selection for functional modification.

Author: Levinton, J.S., Pochron, S. 2008.
Title: Temporal and geographic trends in mercury concentrations in muscle tissue in five species of Hudson River, USA, fish.
Journal: Environmental Toxicology and Chemistry. 27: 1691-1697.
Abstract: <= click to show/hide

Author: N. Mouquet, T. Daufresne, S. M. Gray and T. E. Miller. 2008.
Title: Modelling the relationship between a pitcher plant (Sarracenia purpurea) and its phytotelma community: mutualism or parasitism?
Journal: Functional Ecology 22:728-737.
Abstract: <= click to show/hide

1. To improve our understanding of the relationship between the pitcher plant (Sarracenia purpurea) and the phytotelma community inhabiting its leaves we built an exploratory, mechanistic model based on stochiometric constraints on carbon and nitrogen associated with prey decomposition.
2. Our theoretical results suggest that the phytotelma community is acting as a mineralizing system producing nitrogen for the plant. This is confirmed by data collected in the field and in the literature, that show the amount of nitrogen produced by the decomposition of prey is sufficiently high to be considered as a major source of nitrogen for the plant.
3. In our model, nitrogen yield is higher if the phytotelma community is restricted to bacteria alone than when the full food web is present. Nitrogen availability is negatively affected by bacterivores (rotifers and protozoa mostly) and positively affected by a cascading effect of mosquito larvae.
4. When sedimentation rate is high, mosquitoes have a global positive effect on nitrogen production because they indirectly reduce the amount of nitrogen lost through sedimentation more than they export nitrogen through pupation. On the other hand, when sedimentation rate is low there is a hump-shaped relationship between the uptake rate of bacterivores by mosquito larvae and the nitrogen yield in the plant.
5. We conclude that plant–bacteria and plant–mosquito interactions are predominantly mutualistic, whereas plant–bacterivore interactions are predominantly parasitic. Our work also illustrates how ecosystem properties (here nitrogen production by the phytotelma community) can be understood as a function of trophic complexity and can be seen as a product of selection at the scale of a community.

Author: Norris Z. Muth and Massimo Pigliucci, 2007.
Title: Implementation of a novel framework for assessing species plasticity in biological invasions: responses of Centaurea and Crepis to phosphorus and water availability.
Journal: Journal of Ecology 95:1001-1013.
Abstract: <= click to show/hide

It is widely considered that phenotypic plasticity is important to species invasiveness. However, few empirical studies have expressly assessed the relationship between species invasiveness and their responses to environmental variability. Thoughtfully incorporating phenotypic plasticity into studies of invasiveness requires explicit links among appropriate environmental variables, traits relevant to invasion success, and comparison groups of species, populations or genotypes (competitors or close relatives) that place focal species in context. We examine trait responsiveness in introduced species of Crepis and Centaurea (Asteraceae) that have been characterized by different degrees of success. Speci?cally, we assess the extent to which species are robust in the face of harsh environments and opportunistically responsive to favourable conditions.We exposed all species to water and phosphorus availability treatments in a common glasshouse experiment and report the responses of phenological, architectural, size and ?tness traits. We predicted that, compared with less invasive congeners, invasive species would more often display robust ?tness in harsh environments (here, drought and no phosphorus addition) and would also be more responsive to favourable conditions (no drought and phosphorus additions). In both Crepis and Centaurea we found evidence of greater stress tolerance to low phosphorous among the more invasive congeners, albeit for different components of ?tness. Contrary to expectations, we observed no relationship between invasiveness and opportunism. Overall, trait responses were highly variable and largely idiosyncratic with respect to invasive categorization. Consistent with basic expectations, across-environment species performance largely corresponded to degree of invasiveness. Our results suggest that, even among closely related species, relationships between invasiveness and phenotypic plasticity do not necessarily reveal consistent patterns, nor do they conform to simple theoretical expectations. We suspect that phenotypic plasticity may indeed play an important role in many species invasions, but the breadth of relevant factors (which genotypes, which populations, which traits, which environments) reduces the likelihood of detecting robust general patterns.

Author: Pigliucci, M. 2008.
Title: The borderlands between science and philosophy: an introduction.
Journal: Quarterly Review of Biology 83(1): 7-15.
Abstract: <= click to show/hide

Science and philosophy have a very long history, dating back at least to the 16th and 17th centuries, when the ?rst scientist-philosophers, such as Bacon, Galilei, and Newton, were beginning the process of turning natural philosophy into science. Contemporary relationships between the two fields are still to some extent marked by the distrust that maintains the divide between the so-called "two cultures." An increasing number of philosophers, however, are making conceptual contributions to sciences ranging from quantum mechanics to evolutionary biology, and a few scientists are conducting research relevant to classically philosophical fields of inquiry, such as consciousness and moral decision-making. This article will introduce readers to the borderlands between science and philosophy, beginning with a brief description of what philosophy of science is about, and including a discussion of how the two disciplines can fruitfully interact not only at the level of scholarship, but also when it comes to controversies surrounding public understanding of science.

Author: Pigliucci, M. 2008.
Title: Is evolvability evolvable?
Journal: Nature Reviews Genetics 9: 75-82.
Abstract: <= click to show/hide

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.

Author: Pigliucci, M. 2007.
Title: Do we need an extended evolutionary synthesis?
Journal: Evolution 61(12): 2743-2749.
Abstract: <= click to show/hide

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 uni?cation 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.

Author: Pigliucci, M. 2007.
Title: Finding the way in phenotypic space: the origin and maintenance of constraints on organismal form.
Journal: Annals of Botany 100: 433-438.
Abstract: <= click to show/hide

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.

Author: Radeloff, V.C., D.J. Mladenoff, E.J. Gustafson, R.M. Scheller, H.S. He, P.A. Zollner, H.S He, and H.R. Akçakaya. 2006.
Title: Modeling forest harvesting effects on landscape pattern in the Northwest Wisconsin Pine Barrens.
Journal: Forest Ecology and Management 236: 113-126.
Abstract: <= click to show/hide

Forest management shapes landscape patterns, and these patterns often differ significantly from those typical for natural disturbance regimes. This may affect wildlife habitat and other aspects of ecosystem function. Our objective was to examine the effects of different forest management decisions on landscape pattern in a fire adapted ecosystem. We used a factorial design experiment in LANDIS (a forest landscape simulation model) to test the effects of: (a) cut unit size, (b) minimum harvest age and (c) target species for management. Our study area was the Pine Barrens of northwest Wisconsin, an area where fire suppression has caused a lack of large open areas important for wildlife. Our results show that all three management choices under investigation (cut unit size, minimum harvest age and target species for management) have strong effects on forest composition and landscape patterns. Cut unit size is the most important factor influencing landscape pattern, followed by target species for management (either jack pine or red pine) and then minimum harvest age. Open areas are more abundant, and their average size is larger, when cut units are larger, target species is jack pine, and minimum harvest age is lower. Such information can assist forest managers to relate stand level management decision to landscape patterns.

Author: Reed, J.M.. H.R. Akçakaya, M. Burgman, D. Bender, S.R. Beissinger, and J.M. Scott. 2006.
Title: Critical habitat.
Journal: Pages 164-177 in The Endangered Species Act at Thirty: Conserving Biodiversity in Human-dominated Landscapes (volume 2). J.M. Scott, D.D. Goble, and F.W. Davis, editors. Island Press, Washington.
Abstract: <= click to show/hide

Author: Sujay Chattopadhyay, Michael Feldgarden, Scott J. Weissman, Daniel E. Dykhuizen, Gerald van Belle, Evgeni V. Sokurenko. 2007.
Title: Haplotype Diversity in "Source-Sink" Dynamics of Escherichia coli Urovirulence.
Journal: J. Mol. Evol. (2007) 64:204–214, DOI: 10.1007/s00239-006-0063-5.
Abstract: <= click to show/hide

FimH, the mannose-specific, type 1 fimbrial adhesin of Escherichia coli, acquires amino acid replacements adaptive in extraintestinal niches (the genitourinary tract) but detrimental in the main habitat (the large intestine). This microevolutionary dynamics is reminiscent of an ecological "sourcesink" model of continuous species spread from a stable primary habitat (source) into transient secondary niches (sink), with eventual extinction of the sink-evolved populations. Here, we have adapted two ecological analytical tools—diversity indexes DS and a—to compare size and frequency distributions of fimH haplotypes between evolutionarily conserved FimH variants ("source" haplotypes) and FimH variants with adaptive mutations (putative "sink" haplotypes). Both indexes show two- to threefold increased diversity of the sink fimH haplotypes relative to the source haplotypes, a pattern that ran opposite to those seen with nonstructural fimbrial genes (fimC and fimI) and housekeeping loci (adk and fumC) but similar to that seen with another fimbrial adhesin of E. coli, papG-II, also implicated in extraintestinal infections. The increased diversity of the sink pool of adhesin genes is due to the increased richness of the haplotypes (the number of unique haplotypes), rather than their evenness (the extent of similarity in relative abundances). Taken together, this pattern supports a continuous emergence and extinction of the gene alleles adaptive to virulence sink habitats of E. coli, rather than a one-time change in the habitat conditions. Thus, ecological methods of species diversity analysis can be successfully adapted to characterize the emergence of microbial virulence in bacterial pathogens subject to source-sink dynamics.

Author: Sujay Chattopadhyay, Daniel E. Dykhuizen, Evgeni V. Sokurenko. 2007.
Title: ZPS: visualization of recent adaptive evolution of proteins.
Journal: BMC Bioinformatics 2007, 8:187 doi:10.1186/1471-2105-8-187.
Abstract: <= click to show/hide

Background: Detection of adaptive amino acid changes in proteins under recent shortterm selection is of great interest for researchers studying microevolutionary processes in microbial pathogens or any other biological species. However, independent occurrence of such point mutations within genetically diverse haplotypes makes it difficult to detect the selection footprint by using traditional molecular evolutionary analyses. The recently developed Zonal Phylogeny (ZP) has been shown to be a useful analytic tool for identifying the footprints of short-term positive selection. ZP separates protein-encoding genes into evolutionarily long-term (with silent diversity) and short-term (without silent diversity) categories, or zones, followed by statistical analysis to detect signs of positive selection in the short-term zone. However, successful broad application of ZP for analysis of large haplotype datasets requires automation of the relatively labor-intensive computational process. Results: Here we present Zonal Phylogeny Software (ZPS), an application that describes he distribution of single nucleotide polymorphisms (SNPs) of synonymous (silent) and non-synonymous (replacement) nature along branches of the DNA tree for any given protein-coding gene locus. Based on this information, ZPS separates the protein variant haplotypes with silent variability (Primary zone) from those that have recently evolved from the Primary zone variants by amino acid changes (External zone). Further comparative analysis of mutational hot-spot frequencies and haplotype diversity between the two zones allows determination of whether the External zone haplotypes emerged under positive selection. Conclusions: As a visualization tool, ZPS depicts the protein tree in a DNA tree, indicating the most parsimonious numbers of synonymous and non-synonymous changes along the branches of a maximum-likelihood based DNA tree, along with information on homoplasy, reversion and structural mutation hot-spots. Through zonal differentiation, ZPS allows detection of recent adaptive evolution via selection of advantageous structural mutations, even when the advantage conferred by such mutations is relatively short-term (as in the case of “source-sink” evolutionary dynamics, which may represent a major mode of virulence evolution in microbes).

Author: Tellez, V.O. and Geeta, R. (in press).
Title: Dioscorea howardiana, a new species in section Trigonobasis (Dioscoreaceae).
Journal: Brittonia.
Abstract: <= click to show/hide

Author: Tellez, V.O. and Geeta, R. (accepted).
Title: Sinopsis taxonómica de la sección Apodostemon (Dioscorea; Dioscoreaceae).
Journal: Revista Mexicana de Biodiversidad.
Abstract: <= click to show/hide

Author: J. Khai Tran, Tiina Ylioja, Ronald F. Billings, Jacques Régnière, and Matthew P. Ayres. 2007.
Title: IMPACT OF MINIMUM WINTER TEMPERATURES ON THE POPULATION DYNAMICS OF DENDROCTONUS FRONTALIS.
Journal: Ecological Applications, 17(3), 2007, pp. 882–899.
Abstract: <= click to show/hide

Predicting population dynamics is a fundamental problem in applied ecology. Temperature is a potential driver of short-term population dynamics, and temperature data are widely available, but we generally lack validated models to predict dynamics based upon temperatures. A generalized approach involves estimating the temperatures experienced by a population, characterizing the demographic consequences of physiological responses to temperature, and testing for predicted effects on abundance. We employed this approach to test whether minimum winter temperatures are a meaningful driver of pestilence from Dendroctonus frontalis (the southern pine beetle) across the southeastern United States. A distance-weighted interpolation model provided good, spatially explicit, predictions of minimum winter air temperatures (a putative driver of beetle survival). A Newtonian heat transfer model with empirical cooling constants indicated that beetles within host trees are buffered from the lowest air temperatures by ;1–48C (depending on tree diameter and duration of cold bout). The life stage structure of beetles in the most northerly outbreak in recent times (New Jersey) were dominated by prepupae, which were more cold tolerant (by .38C) than other life stages. Analyses of beetle abundance data from 1987 to 2005 showed that minimum winter air temperature only explained 1.5% of the variance in interannual growth rates of beetle populations, indicating that it is but a weak driver of population dynamics in the southeastern United States as a whole. However, average population growth rate matched theoretical predictions of a process-based model of winter mortality from low temperatures; apparently our knowledge of population effects from winter temperatures is satisfactory, and may help to predict dynamics of northern populations, even while adding little to population predictions in southern forests. Recent episodes of D. frontalis outbreaks in northern forests may have been allowed by a warming trend from 1960 to 2004 of 3.38C in minimum winter air temperatures in the southeastern United States. Studies that combine climatic analyses, physiological experiments, and spatially replicated time series of population abundance can improve population predictions, contribute to a synthesis of population and physiological ecology, and aid in assessing the ecological consequences of climatic trends.