Otoliths speak out: why the Pacific halibut in Puget sound are different

Pacific halibut, Hippoglossus stenolepis, is one of the most important commercial groundfish and is managed as a single coast-wide population from Alaska to northern California. Nevertheless, genetic investigations did not show success in detecting the population structure of the species. Here I report stable oxygen and carbon isotope analyses (δ¹⁸O and δ¹³C) in otoliths to discriminate the stock differences from two sample locations between the Washington coast (WC) and the northern Puget Sound (PS), and two sample years in 2007 and 2008. In general the δ¹⁸O values of halibut otoliths from WC ranged from ?0.2 to 1.8‰, higher than the PS samples from ?0.5 to 1.4‰. In contrast, the δ¹³C values from WC ranged from ?3.6 to ?1.0‰, lower than the PS samples from ?3.2 to ?1.2‰. Results from the otolith nuclei (age-0 halibut) and the 8^th (the earliest maturity age for male halibut) and edge otolith rings (the latest location where the fish lived) showed significant differences between halibut samples from PS and WC. In particular, the sample location difference (between PS and WC) in both δ¹³C and δ¹⁸O data was significant and markedly larger than the sample year difference (between 2007 and 2008). These isotopic signatures provide evidence that the PS halibut may belong to a distinct stock that is significantly different from WC halibut.     

How far details are important in ecosystem modelling: the case of multi-limiting nutrients in phytoplankton-zooplankton interactions

We try to answer the question of to what extent details in nutrient uptake and phytoplankton physiology matter for population and community dynamics. To this end, we study how two nutrients interact in limiting phytoplankton growth. A popular formulation uses a product-rule for nutrient uptake, which we compare with that on the basis of synthesizing units. We first fit different nutrient uptake models to a dataset and conclude that the quantitative differences between the models are small. Then we study the sensitivity of phytoplankton growth and zooplankton-phytoplankton interactions (ZPi) models to uptake formulations. Two population models are compared; they are based on different assumptions on the relation between nutrient uptake and phytoplankton growth. We find that the population and community models are sensitive to uptake formulations. According to the uptake formulation used in the ZPi models, qualitative differences can be observed. Indeed, although two models based on functions with similar shapes have close equilibria, these can differ in stability properties. Since stability involves the derivatives of formulas, even if two formulas provide close values, large numerical differences in the stability criterion may occur after derivation. We conclude that mechanistic details can be of importance for community modelling.     

Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution

A major macroevolutionary question concerns how long-term patterns of body-size evolution are underpinned by smaller scale processes along lineages. One outstanding long-term transition is the replacement of basal therapsids (stem-group mammals) by archosauromorphs, including dinosaurs, as the dominant large-bodied terrestrial fauna during the Triassic (approx. 252-201 million years ago). This landmark event preceded more than 150 million years of archosauromorph dominance. We analyse a new body-size dataset of more than 400 therapsid and archosauromorph species spanning the Late Permian-Middle Jurassic. Maximum-likelihood analyses indicate that Cope's rule (an active within-lineage trend of body-size increase) is extremely rare, despite conspicuous patterns of body-size turnover, and contrary to proposals that Cope's rule is central to vertebrate evolution. Instead, passive processes predominate in taxonomically and ecomorphologically more inclusive clades, with stasis common in less inclusive clades. Body-size limits are clade-dependent, suggesting intrinsic, biological factors are more important than the external environment. This clade-dependence is exemplified by maximum size of Middle-early Late Triassic archosauromorph predators exceeding that of contemporary herbivores, breaking a widely-accepted 'rule' that herbivore maximum size greatly exceeds carnivore maximum size. Archosauromorph and dinosaur dominance occurred via opportunistic replacement of therapsids following extinction, but were facilitated by higher archosauromorph growth rates.     

Dynamics of filaments: modelling the dynamics of driven microfilaments

We describe a method for simulating the inertialess dynamics of a flexible filament immersed in a fluid. Typically, this regime is appropriate for filaments a few micrometres or less in size (flagella that propel micro-organisms for example). We apply the model to two systems; a filament that is wiggled at one end and planar swimming motion characteristic of simple spermatozoa. For the former we find qualitative agreement with theory. The shape is determined by a balance between bending and viscous forces and there is an optimal balance that maximizes the propulsion generated by this mechanism. Quantitatively we find less satisfactory agreement. For the spermatozoa, assuming a relatively naive bending mechanism in the form of a travelling force quadrupole wave, the model generates waveforms in very good agreement with experiment. This is only true, however, if the bending forces acting on the filament are large compared with the viscous forces. Experimental measurements of the tail stiffness imply this should not be the case. We discuss the implications of this observation in the context of the sperm's swimming mechanism.     

The influence of species diversity on ecosystem productivity: how,where, and why?

The effect of species diversity on ecosystem productivity is controversial, in large part because field experiments investigating this relationship have been fraught with difficulties. Unfortunately, there are few guidelines to aid researchers who must overcome these difficulties and determine whether global species losses seriously threaten the ecological and economic bases of terrestrial ecosystems. In response, I offer a set of hypotheses that describe how diversity might influence productivity in plant communities based on three well-known mechanisms: complementarity, facilitation, and the sampling effect. Emphasis on these mechanisms reveals the sensitivity of any diversity-productivity relationship to ecological context (i.e., where this relationship should be found); ecological context includes characteristics of the surrounding environment, temporal and spatial scales of observation, and the intensity of human management. In particular, the legitimacy of the sampling effect as a mechanism of productivity enhancement is dependent upon the degree to which stochastic events influence immigration and extinction processes in a given ecosystem. A mechanistic approach also requires that the three mechanisms be separated and quantified in diversity experiments, and I examine the most appropriate analyses for doing so, focusing on the overyielding technique. Finally, I question why productivity per se is a relevant management concern in non-agricultural systems once relationships among diversity, productivity, and the qualities of the surrounding environment are considered.     

The scientific status of metazoan cladistics: why current research practice must change

Jenner, R. A. (2004). The scientific status of metazoan cladistics: why current research practice must change. —Zoologica Scripta, 33, 293–310. Metazoan phylogenetics is bustling with activity. The use of comprehensive morphological data sets in recent phylogenetic analyses of the Metazoa indicates that morphological evidence continues to play a key role in the reconstruction of metazoan deep history. In this paper I review the scientific status of morphological metazoan cladistics from the perspective of cladistic research cycles. Each research cycle consists of three main steps: (1) the compilation of a data matrix (2) the simultaneous evaluation of all possible cladograms in a character congruence test, and (3) the assessment of the relationship between evidence and hypothesis after finding the optimal tree. I identify a striking discrepancy between the sophistication of the analysis of given data sets (Step 2), and their compilation and the interpretation of the results (Steps 1 and 3). The latter two steps deserve far greater attention than is current practice. Uncritical and nonexplicit character selection, character coding, and character scoring seriously compromise Step 1. Careful comparative morphological study prior to data matrix construction is necessary to remedy this problem in future cladistic analyses. Step 2 is the locus of most recent advances in metazoan cladistics through the increasing availability of computing power, and the development of increasingly efficient phylogenetic software that allows analysis of large data sets. Failure to identify problems and errors generated in Step 1 of the research cycle is testament to the general failure of Step 3. Consequently, recent progress in metazoan cladistics is primarily analytical, while the only empirical anchor of the discipline receives surprisingly little attention. Not surprisingly, the first generation of modern metazoan phylogeneticists used computers principally as a relatively quick and easy means to generate abundant phylogenies from morphological data. The next phase should build on this foundation by critically testing these alternative hypotheses by a thorough qualitative reassessment and elaboration of morphological data matrices, and a more critical approach to data selection. A rigorous research program for metazoan cladistics can only be established when the cladistic research cycle is properly completed, and when subsequent research cycles are effectively linked to previous efforts.     

The notion of minimum distance or why rare species are clumped

Summary The prevalence of statistical clumping in natural populations can sometimes obscure mutual avoidance behavior and the adaptive role of spacing out among population members. The problem is particularly severe in rare species where the inverse square relationship between expected nearest neighbor distance and population density demands mean distances between individuals be excessively large to maintain randomness or overdispersion. Realistically, individuals dispersing from a central nucleus might be expected to establish a minimum distance from neighbors to obtain a substantial gain in fitness but further dispersal would be undesirable due to increasing costs and decreasing gains. The result would be higher clumping at low densities. Data on clumping of rare species in an oak-cynipid gall wasp complex are interpreted in the context of the minimum distance notion, and the influence of parasitism on cynipid host population dispersion is discussed.     

The role of molecular modelling in biomedical research

The synergy between experimental and computational biology has greatly benefited both fields, providing invaluable information in many different areas of the life sciences. This minireview will focus on one specific aspect of computational biology, molecular modelling, and describe a few examples highlighting the effectiveness of protein structural analysis and modelling in providing relevant information about systems of biomedical interest.     

The peck orders of chickens: How do they develop and why are they linear?

The development of peck orders in mixed sex groups of domestic chickens was observed to determine how linearity occurred. Based on threats, head-pecks and submission, dominance relationships emerged in a virtual peck right form. Leaping by males, however, did not closely conform to dominance relationships. There were no rank reversals in 50% of male-male and 80% of female-female relationships, and only single changes occurred in most of the others. These resulted from the movements of individuals up the hierarchy rather than from any general reorganization of relationships. Reversals did not necessarily occur between rank neighbours, and stable triangles were sometimes introduced. The initial status of males and females depended upon the age at which they first showed aggression, while the final, stable status of males depended upon the age at which they were first submitted to. Sexual maturity of the males produced a number of changes, with earlier-maturing birds tending to rise in status above their later-maturing companions. Linear hierarchies therefore appear to result from birds developing at different rates.     

Beyond apical ballooning: computational modelling reveals morphological features of Takotsubo cardiomyopathy

Abstract

Takotsubo cardiomyopathy (TCM) is characterized by transient myocardial dysfunction, typically at the left ventricular (LV) apex. Its pathophysiology and recovery mechanisms remain unknown. We investigated LV morphology and deformation in n?=?28 TCM patients. Patients with MRI within 5?days from admission (“early TCM”) showed reduced LVEF and higher ventricular volumes, but no differences in ECG, global strains or myocardial oedema. Statistical shape modelling described LV size (Mode 1), apical sphericity (Mode 2) and height (Mode 3). Significant differences in Mode 1 suggest that “early TCM” LV remodeling is mainly influenced by a change in ventricular size rather than apical sphericity.     

Dispersal through stream networks: modelling climate‐driven range expansions of fishes

Aim To incorporate dispersal through stream networks into models predicting the future distribution of a native, freshwater fish given climate change scenarios. Location Sweden. Methods We used logistic regression to fit climate and habitat data to observed pike (Esox lucius Linnaeus) distributions in 13,476 lakes. We used GIS to map dispersal pathways through streams. Lakes either (1) contained pike or were downstream from pike lakes, (2) were upstream from pike lakes, but downstream from natural dispersal barriers, or (3) were isolated from streams or were upstream from natural dispersal barriers. We then used climate projections to model future distributions of pike and compared our results with and without including dispersal. Results Given climate and habitat, pike were predicted present in all of 99,249 Swedish lakes by 2100. After accounting for dispersal barriers, we only predicted pike presence in 31,538 lakes. Dispersal barriers most strongly limited pike invasion in mountainous regions, but low connectivity also characterized some relatively flat regions. Main conclusions The dendritic network structure of streams and interconnected lakes makes a two‐dimensional representation of the landscape unsuitable for predicting range shifts of many freshwater organisms. If dispersal through stream networks is not accounted for, predictions of future fish distributions in a warmer climate might grossly overestimate range expansions of warm and cool‐water fishes and underestimate range contractions of cold‐water fishes. Dispersal through stream networks can be modelled in any region for which a digital elevation model and species occurrence data are available.     

The prominence of and biases in biodiversity and ecosystem functioning research

The sub-discipline of biodiversity and ecosystem functioning (BEF) has emerged as a central topic in contemporary ecological research. However, to date no study has evaluated the prominence and publication biases in BEF research. Herein we report the results of a careful quantitative assessment of BEF research published in five core general ecology journals from 1990 to 2007 to determine the position of BEF research within ecology, identify patterns of research effort within BEF research, and discuss their probable proximal and historical causes. The relative importance of BEF publications increased exponentially during the period analyzed and was significantly greater than the average growth of ecological literature, affirming the prominence of BEF as a current paradigm in ecology. However, BEF research exhibited a strong bias toward experimental studies on terrestrial plant communities, with significantly lower effort devoted to the functional aspects of biodiversity in aquatic systems, multiple trophic level systems, and animal or microbial communities. Such trends may be explained by a combination of methodological adequacy and historic epistemological differences in ecological thinking. We suggest that BEF researchers should direct more effort toward the study of aquatic systems and animal communities, emphasize long-term and trophically complex experiments, such as those with multi-trophic microbial communities, employ larger-scale field observational studies and increase the use of integrative and theoretical studies. Many technical and analytical methodologies that are already employed in ecological research, such as stable isotopes, paleobiology, remote sensing, and model selection criteria, can facilitate these aims. Overcoming the above-mentioned shortcomings of current BEF research will greatly improve our ability to predict how biodiversity loss will affect ecosystem processes and services in natural ecosystems.