Ecology & Evolution Department - Stony Brook University

Author: Akcakaya, H.R. and B.W. Brook. 2008.
Title: Methods for determining viability of wildlife populations in large landscapes. Pages 449-471 in: Models for Planning Wildlife Conservation in Large Landscapes.
Journal: J.J. Millspaugh and F.R. Thompson, III (editors). Elsevier/Academic Press, Burlington, MA.
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We review methods of population viability analysis (PVA) as applied to wildlife populations in large landscapes. For these populations, viability analysis requires careful consideration of the issues of spatial heterogeneity and scaling of ecological processes, habitat connectedness (including "permeability of the intervening matrix", and temporal dynamics of the landscape. Spatially structured models used for large-scale PVA include occupancy models, grid-based lattice models, demographically structured metapopulation models, and individual-based models. We discussed the assumptions and limitations of model types and the context within which each is more appropriate. Population viability analyses in large landscapes often require the definition of distinct subpopulations, which in turn depend critically on the spatial scale of, and barriers to, dispersal in relation to the distribution of suitable habitat. Another important factor is the effect of landscape dynamics on the temporal variability of the habitat, and hence on the dynamics of the wildlife populations. Viability of species in dynamic landscapes depends on the interaction between landscape change (the pattern, scale, rate, and direction of landscape changes in size, structure, and quality) and the species? ecology (its ability to disperse between and grow in the habitat patches or make use of the matrix). Spatial separation of populations can also provide the opportunity to validate the generality and applicability of model predictions in the absence of long-term monitoring data.

Author: Akcakaya, H.R., J. D. Stark, and T. S. Bridges (editors). 2008.
Title: Demographic Toxicity: Methods in Ecological Risk Assessment.
Journal: Oxford University Press, New York.
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Demographic toxicity is the ecological impact of a pollutant or toxicant on the population(s) of a plant or animal species. Such toxicity is measured in terms of population-level endpoints, such as risk of decline and population growth rate, rather than individual-level endpoints. In recent years, use of these methods has become increasingly popular in gauging the ecological consequences of various chemicals. Yet despite a growing emphasis on the study of living populations, there exist relatively few case studies or applications of models for such assessments, leaving less experienced researchers with no real guidelines with which to develop their own models. This contributed volume offers population and metapopulation models for a wide variety of species, focusing on the use of models to evaluate the risks faced by these species due to a variety of toxicants. Each chapter describes the application of a population model to one species, with the aim of demonstrating how various life history characteristics of that species are incorporated, how ecotoxicological impacts are modeled, and how the results have been or can be used in risk assessment. The accompanying CD-ROM includes data files for each species modeled in the book, along with a demo version of the RAMAS software used to create the models.

Author: Amaral, Ana R., M. Manuela Coelho, Jesús Marugán-Lobón and F. James Rohlf. 2008.
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, 112:38-47.
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The present study investigates the pattern of differentiation of cranial shape in three closely related delphinid cetacean species of the complex Delphinus-Stenella-Tursiops: Delphinus delphis, Stenella coeruleoalba and Tursiops 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: Arif, S., W. E. Aguirre, and M. A. Bell.
Title: Evolutionary diversification of operculum shape in Cook Inlet threespine stickleback.
Journal: Biol. J. Linn. Soc. In press.
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Author: Baillie, J.E.M., B. Collen, R. Amin, H.R. Akcakaya, S.H.M. Butchart, N. Brummitt, T.R. Meagher, M. Ram, C. Hilton-Taylor, and G.M. Mace. 2008.
Title: Towards monitoring global biodiversity.
Journal: Conservation Letters 1:18-26.
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The world's governments have identified reducing the rate of biodiversity loss as a global priority. However, we lack robust measures of progress toward this target. Developing indicators that are generally representative of trends in global biodiversity has presented the scientific community with a significant challenge. Here we discuss the development and implementation of the IUCN Red List Index with a new sampled approach, permitting the assessment of the conservation status and trends of large, speciose taxonomic groups. This approach is based on the IUCN Red List and measures trends in extinction risk through time. The challenges in developing this new approach are addressed, including determining the species groups to be included in the index, identifying the minimum adequate samples size, and aggregating and weighting the index. Implementing this approach will greatly increase understanding of the status of the world's biodiversity by 2010, enabling the first assessment of a number of key groups.

Author: Bell, M. A., J. D. Stewart and P. J. Park.
Title: The world’s oldest fossil threespine stickleback.
Journal: Copeia. In press.
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Author: Bossdorf, O., C. Richards and M. Pigliucci. 2008.
Title: Epigenetics for ecologists.
Journal: Ecology Letters 11: 106-115.
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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.

Author: Bossdorf, O. and M. Pigliucci.
Title: Plasticity to wind is modular and genetically variable in Arabidopsis thaliana.
Journal: Evolutionary Ecology. In press.
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Thigmomorphogenesis, the characteristic phenotypic changes by which plants react to mechanical stress, is a widespread and probably adaptive type of phenotypic plasticity. However, little is known about its genetic basis and population variation. Here, we examine genetic variation for thigmomorphogenesis within and among natural populations of the model system Arabidopsis thaliana. Offspring from 17 field-collected European populations was subjected to three levels of mechanical stress exerted by wind. Overall, plants were remarkably tolerant to mechanical stress. Even high wind speed did not significantly alter the correlation structure among phenotypic traits. However, wind significantly affected plant growth and phenology, and there was genetic variation for some aspects of plasticity to wind among A. thaliana populations. Our most interesting finding was that phenotypic traits were organized into three distinct and to a large degree statistically independent covariance modules associated with plant size, phenology, and growth form, respectively. These phenotypic modules differed in their responsiveness to wind, in the degree of genetic variability for plasticity, and in the extent to which plasticity affected fitness. It is likely, therefore, that thigmomorphogenesis in this species evolves quasi-independently in different phenotypic modules.

Author: M.E. Bradley, J.S. Rest, W.H. Li, and N.B. Schwartz.
Title: Sulfate Activation Enzymes: Phylogeny and Association with Pyrophosphatase.
Journal: J. Mol. Evol. (2008).
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The enzymes catalyzing the first two reactions in the sulfate activation pathway, ATP-sulfurylase (S) and APS-kinase (K), are fused as 'KS' in animals but are fused as 'SK' in select bacteria and fungi. We have discovered a novel triple fusion protein of K, S, and pyrophosphatase (P) in several protozoan genomes within the Stramenopile lineage. These triple domain fusion proteins led us to hypothesize that pyrophosphatase enzymes and sulfate activation enzymes physically interact to impact the thermodynamics of the sulfate activation pathway. In support of this hypothesis, we demonstrate through biochemical assays that separately encoded KS and P proteins physically interact and that KS/P complexes activate more sulfate than KS alone. We also conclude on the basis of phylogenetic analyses that all known KS fusions originate from a single fusion event early in the eukaryotic lineage. Strikingly, our analyses support the same conclusion for all known SK fusions. These observations indicate that the patchwork of fused and nonfused S and K genes observed in modern-day eukaryotes and prokaryotes are the result of the two ancestral fusion genes evolving by an assortment of gene fissions, duplications, deletions, and horizontal transfers in different lineages. Our integrative use of genomics, phylogenetics, and biochemistry to characterize pyrophosphatase as a new member of the sulfate activation pathway should be effective at identifying new protein members and connections in other molecular pathways.

Author: Dávalos, L.M., A. C. Bejarano, and H. L. Correa. 2008.
Title: Disabusing cocaine: Pervasive myths and enduring realities of a globalised commodity.
Journal: International Journal of Drug Policy.
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For more than 30 years Colombia has waged an internal War on Drugs with the support of the international community. During this time, the illegal economy has evolved toward integrating cultivation with processing and trafficking, making Colombia the largest grower of coca in the world. The environmental impact of coca production and processing is vast, accounting for large quantities of toxic chemicals directly dumped onto the soil and watersheds, as well as most deforestation since the 1990s. The policies pursued to stem the coca economy, however, are based on unfounded assumptions about the behaviour of coca growers in the context of international markets. Despite their unfounded premises, these assumptions have acquired a mythical stature. In this article we review the most persistent myths about coca production with a view to understanding its links to environmental degradation. To this end, we present data on the economic and demographic background of coca growers, their impact on the environment, and their behaviour in the larger context of international markets and current eradication policies.

Author: Dávalos, L.M., and A. Corthals. 2008.
Title: A new species of Lonchophylla (Chiroptera: Phyllostomidae) from the eastern Andes of northwestern South America.
Journal: American Museum Novitates 3635, 1-16.
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Since 2004 five new species have been described in the nectar-feeding phyllostomid bat genus Lonchophylla. All the new species are endemic to one Neotropical ecoregion, suggesting that more species remain to be discovered among collected specimens currently referred to several widespread taxa. Herein we describe a new species, Lonchophylla orienticollina, endemic to the middle elevations of the eastern Andes of Venezuela, Colombia, and Ecuador. The new species superficially resembles its sympatric congener L. robusta, but its cranial morphology and combination of measurements are distinctive. Throughout its range, L. orienticollina is sympatric with L. robusta, and it also overlaps with L. handleyi in the Cordillera Oriental of Ecuador. The evolutionary processes leading to the divergence among Lonchophylla species, as well as the ecological mechanisms that enable multiple, subtly different species to coexist will remain obscure without new field and phylogenetic studies.

Author: Doall, M.H., Padilla, D.K., Lobue, C.P., Clapp, C., Webb, A.R., Hornstein, J. 2008.
Title: Evaluating northern quahog (= hard clam, Mercenaria mercenaria L.) restoration: are transplanted clams spawning and reconditioning?
Journal: Journal of Shellfish Research 27(5):1069-1080.
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Author: Dykhuizen, D. E., D. Brisson, S. Sandigursky, G. P. Wormser, J. Nowakowski, R. B. Nadelman, and I. Schwartz. 2008.
Title: The propensity of different Borrelia burgdorferi sensu stricto genotypes to cause disseminated infections in humans.
Journal: Am. J. Tropical Med Hygiene 78:806-810.
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Author: Catherine H. Graham and Paul V. A. Fine. 2008.
Title: Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time.
Journal: Ecology Lteers, 11:1265-1277.
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A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.

Author: J. Gurevitch, T.G. Howard, I.W. Ashton, E.A. Leger, K.M. Howe, E. Woo and M. Lerdau. 2008.
Title: Effects of experimental manipulation of light and nutrients on establishment of seedlings of native and invasive woody species in Long Island, NY forests.
Journal: Biological Invasions 10: 821-831.
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While earlier studies on the process of invasion often focused on single factors or on the general explanation of 'disturbance,' recent work has attempted to move towards a more mechanistic understanding of the factors that promote plant community invasion. Manipulative experiments provide a means for discerning causal relationships and interactive effects of environmental factors in promoting invasion; such experiments have been conducted in a number of grassland and shrub ecosystems. This study extends multifactor manipulative experiments into forest communities to compare factors influencing early seedling establishment for native and invasive woody plants. In Long Island, NY, invasion patterns are correlated with forest community type (pine barrens or hardwood), light availability, and soil N and Ca. We conducted manipulative field experiments in two different years to determine the relative importance and interaction of experimental gaps and N and Ca addition in pine barrens and hardwood forests in promoting invasion. We used seedlings of seven common native and invasive species in the first experiment, and 16 native and invasive species paired phylogenetically in the second experiment. Light had the strongest effect on plant growth; all plants grew more in gaps. We found no difference in the average growth rates of native and invasive species. Invasives responded more to high resources than did natives, with highest relative growth rates in gaps in the more fertile soils of the hardwood forests. Opportunities for invasion may differ from year to year, with differential success of invaders only in some years and under some environmental conditions. Clearly, to understand the complex interactions between resources and invasion in forests will require many manipulative experiments across a range of environments and using suites of invasive and native species.

Author: Harcourt-Smith, W. H. E., M. Tallman, S. R. Frost, D. F. Wiley, F. J. Rohlf, E. Delson. 2008.
Title: Analysis of selected hominoid joint surfaces using laser scanning and geometric morphometrics: a preliminary report.
Journal: Pp. 373-383 in E. J. Sargis and M. Dagosto (eds.) Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay. Springer: Dordrecht.
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Author: Hunt, G., M. A. Bell, and M.P. Travis. 2008.
Title: Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage.
Journal: Evolution 62:700-710. (doi:10:1111/j.1558-5646.2007.00310.x)
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Natural selection has almost certainly shaped many evolutionary trajectories documented in fossil lineages, but it has proven difficult to demonstrate this claim by analyzing sequences of evolutionary changes.In a recently published and particularly promising test case, an evolutionary time series of populations displaying armor reduction in a fossil stickleback lineage could not be consistently distinguished from a null model of neutral drift, despite excellent temporal resolution and an abundance of indirect evidence implicating natural selection. Here, we revisit this case study, applying analyses that differ from standard approaches in that: (1) we do not treat genetic drift as a null model, and instead assess neutral and adaptive explanations on equal footing using the Akaike Information Criterion; and (2) rather than constant directional selection, the adaptive scenario we consider is that of a population ascending a peak on the adaptive landscape, modeled as an Orstein-Uhlenbeck process. For all three skeletal features measured in the stickleback lineage, the adaptive model decisively outperforms neutral evolution, supporting a role for natural selection in the evolution of these traits. These results demonstrate that, at least under favorable circumstances, it is possible to infer in fossil lineages the relationship between evolutionary change and features of the adaptive landscape.

Author: Jeong, S., Rebeiz. M., Andolfatto, P., Werner, T., True, J.R., and Carroll, S.B. 2008.
Title: The evolution of gene regulation underlies the morphological divergence of two closely related Drosophila species.
Journal: Cell 132: 783-703.
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Understanding the mechanisms underlying the morphological divergence of species is one of the central goals of evolutionary biology. Here, we analyze the genetic and molecular bases of the divergence of body pigmentation patterns between Drosophila yakuba and its sister species Drosophila santomea. We found that loss of pigmentation in D. santomea involved the selective loss of expression of the tan and yellow pigmentation genes. We demonstrate that tan gene expression was eliminated through the mutational inactivation of one specific tan cis-regulatory element (CRE) whereas the Tan protein sequence remained unchanged. Surprisingly, we identify three independent loss-of-function alleles of the tan CRE in the young D. santomea lineage. We submit that there is sufficient empirical evidence to support the general prediction that functional evolutionary changes at pleiotropic loci will most often involve mutations in their discrete, modular cis-regulatory elements.

Author: Keith, D.A, H.R. Akcakaya, W. Thuiller, G.F. Midgley, R.G. Pearson, S.J. Phillips, H.M. Regan, M.B. Araujo, T.G. Rebelo. 2008.
Title: Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models.
Journal: Biology Letters 4:560-563.
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Species responses to climate change may be influenced by changes in available habitat, as well as population processes, species interactions and interactions between demographic and landscape dynamics. Current methods for assessing these responses fail to provide an integrated view of these influences because they deal with habitat change or population dynamics, but rarely both. In this study, we linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations under stable and changing climate scenarios in South African fynbos, a global biodiversity hot spot. Results indicate that complex interactions between life history, disturbance regime and distribution pattern mediate species extinction risks under climate change. Our novel mechanistic approach allows more complete and direct appraisal of future biotic responses than do static bioclimatic habitat modelling approaches, and will ultimately support development of more effective conservation strategies to mitigate biodiversity losses due to climate change.

Author: Lachance, J. 2008.
Title: A Fundamental Relationship Between Genotype Frequencies and Fitnesses
Journal: Genetics 180:1087-93
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The set of possible postselection genotype frequencies in an infinite, randomly mating population is found. Geometric mean heterozygote frequency divided by geometric mean homozygote frequency equals two times the geometric mean heterozygote fitness divided by geometric mean homozygote fitness. The ratio of genotype frequencies provides a measure of genetic variation that is independent of allele frequencies. When this ratio does not equal two, either selection or population structure is present. Within-population HapMap data show population-specific patterns, while pooled data show an excess of homozygotes.

Author: Levinton, J.S. 2008.
Title: The Cambrian Explosion: How Do We Use the Evidence?
Journal: BioScience 58: 855-864
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The Cambrian explosion is an excellent example of a grand idea that has been tempered by the steady collection of data to test hypotheses. Historically, the idea of an “explosion” developed from an apparent lack of bilaterian animal fossils before a certain point in the fossil record, in contrast with a great diversity of life that seemed to appear in the Cambrian period. DNA molecular clock estimates contradict this story, however, with most dates for the divergence of major phyla predating the Cambrian by 100 million to 400 million years. The contradiction might be rectified by corrections to the clock or by discoveries of Precambrian bilaterian fossils. Although many candidates exist, no single environmental or biological explanation for the Cambrian explosion satisfactorily explains the apparent sudden appearance of much of the diversity of bilaterian animal life. Scientists’ understanding of this phenomenon has been greatly amplified in recent years by better geological dating and environmental characterization, new fossil discoveries, and by a great expansion of our knowledge of developmental mechanisms and their evolutionary meaning.

Author: Levinton, J.S., Pochron, S.T. 2008.
Title: Temporal and geographic trends in mercury concentrations in muscle tissue in five species of Hudson Rive, USA, fish.
Journal: Envrionmental Toxicology and Chemistry. 27: 1691-97.
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We analyzed a New York (USA) state database of mercury concentrations in muscle tissue for five species of fish (striped bass, yellow perch, largemouth bass, smallmouth bass, and carp) over a range of locations in the Hudson River (USA) between 1970 and 2004. We used regression models to discern temporal andgeographic change in the fish while controlling for a positive correlation between mercury concentration and body mass. Mercury concentrations significantly increased in fish from New York Harbor waters to the mid–Hudson River. Striped bass and yellow perch showed a shallower increase in mercury concentration with river mile than did carp, largemouth bass, and smallmouth bass. Mercury concentrations declined over the 34-year period. These results imply that a geographically restricted source of mercur y may be spread throughout the watershed by toxin-laden dispersing species. The increase of mercury toward the north may relate to a point source in the mid–Hudson River, or it may indicate mercury released from the Adirondack watershed. The decline of mercury over three decades corresponds to a reduction of various inputs in the region. The temporal and geographic pattern of mercury in sediments corresponds to the geographic trend of mercury in fish.

Author: Mace, G.M., N. Collar, K.J. Gaston, C. Hilton-Taylor, H.R. Akcakaya, N. Leader-Williams, E.J. Milner-Gulland and S.N. Stuart. 2008.
Title: Quantification of extinction risk: IUCN's system for classifying threatened species.
Journal: Conservation Biology 22:1424-1442.
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The IUCN (International Union for Conservation of Nature) Red List of Threatened Species was increasingly used during the 1980s for assessing the conservation status of species for policy and planning purposes. This use stimulated the development of a new set of quantitative criteria for listing species in the categories of threat: Critically Endangered, Endangered, and Vulnerable. These criteria, which were intended to be applicable to all species except microorganisms, were part of a broader system for classifying threatened species, fully implemented by IUCN in 2000. The system and the criteria have been widely used by conservation practitioners and scientists and now underpin one indicator being used to assess the Convention on Biological Diversity 2010 biodiversity target. We describe the process and the technical background to the IUCN Red List system. The criteria refer to fundamental biological processes underlying population decline and extinction. But given major differences between species, the threatening processes affecting them, and the paucity of knowledge relating to most species, the IUCN system had to be both broad and flexible to be applicable to the majority of described species. The system was designed to measure the symptoms of extinction risk, and uses 5 independent criteria relating to aspects of population loss and range size decline. A species is assigned to a threat category if it meets the quantitative threshold for at least one criterion. The criteria and the accompanying rules and guidelines used by IUCN are intended to increase the consistency, transparency, and validity of its categorization system, but it necessitates some compromises that affect the applicability of the system and the species lists that result. In particular, choices were made over the assessment of uncertainty, poorly known species, depleted species, population decline, restricted ranges, and rarity; all of these affect the way that red lists should be viewed and used. Processes related to priority setting and the development of national red lists need to take account of some assumptions in the formulation of the criteria.

Author: Nomakuchi, S., P. J. Park, and M. A. Bell.
Title: Correlation between exploration activity and use of social information in threespine sticklebacks.
Journal: Behavioral Ecology. In press.
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Author: Perino L.L., Padilla D.K., Doall M.H. 2008.
Title: Testing the accuracy of morphological identification of northern quahog larvae.
Journal: Journal of Shellfish Research 27:1081-1085.
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Author: Pigliucci, M. 2008.
Title: The borderlands between science and philosophy: an introduction.
Journal: Quarterly Review of Biology 83(1): 7-15.
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Science and philosophy have a very long history, dating back at least to the 16th and 17th centuries, when the first 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.
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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.
Title: Okasha's Evolution and the Levels of Selection: toward a broader conception of evolutionary biology.
Journal: Biology & Philosophy. In press.
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The debate about the levels of selection has been one of the most controversial both in evolutionary biology and in philosophy of science. Okasha’s book makes the sort of contribution that simply will not be able to be ignored by anyone interested in this field for many years to come. However, my interest here is in highlighting some examples of how Okasha goes about discussing his material to suggest that his book is part of an increas- ingly interesting trend that sees scientists and philosophers coming together to build a broadened concept of "theory" through a combination of standard mathematical treat- ments and conceptual analyses. Given the often contentious history of the relationship between philosophy and science, such trend cannot but be welcome.

Author: Pigliucci, M.
Title: Sewall Wright's adaptive landscapes: 1932 vs. 1988.
Journal: Biology & Philosophy. In press.
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Sewall Wright introduced the metaphor of evolution on "adaptive landscapes" in a pair of papers published in 1931 and 1932. The metaphor has been one of the most influential in modern evolutionary biology, although recent theoretical advancements show that it is deeply flawed and may have actually created research questions that are not, in fact, fecund. In this paper I examine in detail what Wright actually said in the 1932 paper, as well as what he thought of the matter at the very end of his career, in 1988. While the metaphor is flawed, some of the problems which Wright was attempting to address are still with us today, and are in the process of being reformulated as part of a forthcoming Extended Evolutionary Synthesis.

Author: Pigliucci, M.
Title: What, if anything, is an evolutionary novelty?
Journal: Philosophy of Science. In press.
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The idea of phenotypic novelty appears throughout the evolutionary literature, usually in the context of some attack (or defense) of the modern synthesis of the 1940s. Novelties have been defined so broadly as to make the term meaningless, as well as so narrowly as to apply only to a limited number of spectacular structures, such as wings and eyes. In this essay I briefly examine some of the available definitions of phenotypic novelty and construct an argument leading to the conclusion that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that these frameworks should be considered in addition to, and not as potential substitutes of, the modern synthesis.

Author: Przeslawski R., Bourdeau P.E., Doall M.H.,, Pan J., Perino L., Padilla D.K. 2008.
Title: The effects of a harmful alga on bivalve larval lipid stores.
Journal: Harmful Algae 7:802-807.
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Author: Richards, C., R. L. Walls, J. P. Bailey, R. Parameswaran, T. George and M. Pigliucci. 2008.
Title: Plasticity in salt tolerance traits allows for invasion of novel habitat by Japanese Knotweed s.l. (Fallopia japonica and F. x bohemica, Polygonaceae).
Journal: American Journal of Botany 95(8): 931-942.
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Japanese knotweeds are among the most invasive organisms in the world. Their recent expansion into salt marsh habitat provides a unique opportunity to investigate how invasives establish in new environments. We used morphology, cytology, and AFLP genotyping to identify taxa and clonal diversity in roadside and salt marsh populations. We conducted a greenhouse study to determine the ability to tolerate salt and whether salt marsh populations are more salt tolerant than roadside populations as measured by the efficiency of PSII, leaf area, succulence, height, root-to-shoot ratio, and total biomass. Clonal diversity was extremely low with one F. japonica clone and five F. bohemica genotypes. The two taxa were significantly different in several traits, but did not vary in biomass or plasticity of any trait. All traits were highly plastic in response to salinity, but differed significantly among genets. Despite this variation, plants from the salt marsh habitats did not perform better in the salt treatment, suggesting that they are not better adapted to tolerate salt. Instead, our data support the hypothesis that plasticity in salt tolerance traits may allow these taxa to live in saline habitats without specific adaptation to tolerate salt.

Author: Stoebel, D. M., A. M.Dean, D.E. Dykhuizen. 2008.
Title: The cost of expression of Escherichia coli lac operon proteins is in the process, not the products.
Journal: Genetics 178:1653-1660.
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Author: True, J.R. 2008.
Title: Combing evolution.
Journal: Evol Dev. 10:400-402.
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Author: Valentin, A. E., X. Penin, J.-P. Chanut, J.-M. Sévigny, and F. J. Rohlf. 2008.
Title: Arching effect on fish body shape in geometric morphometric studies.
Journal: J. of Fish Biology, 73:623-638.
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Upward and downward arching of the body was observed during a study on redfishes Sebastes sp. population structure in the north-west Atlantic Ocean. The present study investigated the potential causes of this arching artefact. The results suggested that it is not related to biological factors (size or species) or to the preservation technique (freezing), but is rather due to slight posture differences between fishes during landmark capture. The consequences of the arching artefact on data analysis are discussed. An approach coupling a PCA-based model of the arching with Burnaby's orthogonal projection is proposed for removing the artefact from the data.

Author: Yukilevich, R. and J.R. True. 2008.
Title: African morphology, behavior and phermones underline incipient sexual isolation between US and Caribbean Drosophila melanogaster.
Journal: Evolution 62: 2807-2828.
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Understanding incipient sexual isolation and speciation is an important pursuit in evolutionary biology. The fruit fly Drosophila melanogaster is a useful model to address questions about the early stages of sexual isolation occurring within widespread species. This species exhibits sexual isolation between cosmopolitan and African flies, especially from Zimbabwe populations. In addition, we have recently described another example of partial sexual isolation between some US and Caribbean populations. This and other phenotypic data suggests that Caribbean flies might be segregating African traits. In the present work we study the geographical variation at the pheromone locus desaturase-2, as well as morphology and courtship behavior across the US-Caribbean region. We find that US and Caribbean populations show sharp geographical clines in all traits and demonstrate that Caribbean traits are more similar to those of Africa than to US populations. Further, African traits in the Caribbean are associated with sexual isolation and best explain variation in sexual isolation when all traits are considered together. These results imply that Caribbean mating preferences are likely to be based on African traits and that even at such early stages of sexual isolation, individuals may already cue in on several traits simultaneously during mate choice.

Author: Yukilevich, R., Lachance, J., Aoki, F., True, J. R. 2008
Title: Long-term evolution of epistatic genetic networks.
Journal: Evolution 62:2215-2235.
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Gene networks are likely to govern most traits in nature. Mutations at these genes often show functional epistatic interactions that lead to complex genetic architectures and variable fitness effects in different genetic backgrounds. Understanding how epistatic genetic systems evolve in nature remains one of the great challenges in evolutionary biology. Here we combine an analytical framework with individual-based simulations to generate novel predictions about long-term adaptation of epistatic networks. We find that relative to traits governed by independently evolving genes, adaptation with epistatic gene networks is often characterized by longer waiting times to selective sweeps, lower standing genetic variation, and larger fitness effects of adaptive mutations. This may cause epistatic networks to either adapt more slowly or more quickly relative to a nonepistatic system. Interestingly, epistatic networks may adapt faster even when epistatic effects of mutations are on average deleterious. Further, we study the evolution of epistatic properties of adaptive mutations in gene networks. Our results show that adaptive mutations with small fitness effects typically evolve positive synergistic interactions, whereas adaptive mutations with large fitness effects evolve positive synergistic and negative antagonistic interactions at approximately equal frequencies. These results provide testable predictions for adaptation of traits governed by epistatic networks and the evolution of epistasis within networks.

Author: Yukilevich R, True J.R. 2008
Title: Incipient sexual isolation among cosmopolitan Drosophila melanogaster populations.
Journal: Evolution 62:2112-21.
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Understanding the biological conditions and the genetic basis of early stages of sexual isolation and speciation is an outstanding question in evolutionary biology. It is unclear how much genetic and phenotypic variation for mating preferences and their phenotypic cues is segregating within widespread and human-commensal species in nature. A recent case of incipient sexual isolation between Zimbabwe and cosmopolitan populations of the human-commensal fruit fly Drosophila melanogaster indicates that such species may initiate the process of sexual isolation. However, it is still unknown whether other geographical populations have undergone evolution of mating preferences. In this study we present new data on multiple-choice mating tests revealing partial sexual isolation between the United States and Caribbean populations. We relate our findings to African populations, showing that Caribbean flies are partially sexually isolated from Zimbabwe flies, but mate randomly with West African flies, which also show partial sexual isolation from the United States and Zimbabwe flies. Thus, Caribbean and West African populations seem to exhibit distinct mating preferences relative to populations in the United States and in Zimbabwe. These results suggest that widespread and human-commensal species may harbor different types of mating preferences across their geographical ranges.