Processes generating macroevolutionary patterns of morphological variation in birds: a simulation study

Multivariate patterns of morphological variation in birds are analysed. In general, there are strong allometric patterns among characters such that most of the variation is confined to a major “size” axis. To analyse the possible evolutionary processes behind this pattern I employed a computer simulation of cladogenesis and anagenesis based on a genetic and a random walk model (drift). All runs started with one species and speciation occurred to generate 100 species. Three levels of correlations were allowed. The results from the simulations were compared with the pattern of variation in finches (Fringillidae). The simulations showed two things. First, the univariate drift model was inappropriate in terms of the level of variation; the observed level was lower than expected by drift. Univariate drift was also unable to create tight correlations among characters as observed in several taxa. Second, to create the pattern observed, either relatively strong genetic correlations (r_g ≈ 0.5), or alternatively strong correlated selection, was needed. This suggests that morphological change in birds in general consists of changes in growth such that species become larger or smaller than their ancestors but retain their ancestral shape. The results stress the importance of stabilising selection in shaping the macroevolutionary patterns of morphological variation in birds.     

On statistical inference for the random set generated Cox process with set-marking

Cox point process is a process class for hierarchical modelling of systems of non-interacting points in Rd under environmental heterogeneity which is modelled through a random intensity function. In this work a class of Cox processes is suggested where the random intensity is generated by a random closed set. Such heterogeneity appears for example in forestry where silvicultural treatments like harvesting and site-preparation create geometrical patterns for tree density variation in two different phases. In this paper the second order property, important both in data analysis and in the context of spatial sampling, is derived. The usefulness of the random set generated Cox process is highly increased, if for each point it is observed whether it is included in the random set or not. This additional information is easy and economical to obtain in many cases and is hence of practical value; it leads to marks for the points. The resulting random set marked Cox process is a marked point process where the marks are intensity-dependent. The problem with set-marking is that the marks are not a representative sample from the random set. This paper derives the second order property of the random set marked Cox process and suggests a practical estimation method for area fraction and covariance of the random set and for the point densities within and outside the random set. A simulated example and a forestry example are given.     

Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters

Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. “Selection” was more important than “dispersal limitation” in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of “selection”. While “homogenizing dispersal” also considerably governed their biogeography. MGI‐Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI‐phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII‐bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.     

Relationship between neurophysiological indices of cognitive processes and MRI characteristics of some brain structures in healthy subjects and patients with schizophrenia

The relationships between the parameters of waves of auditory event-related potentials (ERPs) in the oddball paradigm and the volumes of the hippocampus, amygdala, and caudate nuclei were analyzed in healthy subjects and patients with schizophrenia. The data obtained suggest that faster mental processes and stronger activation and/or synchronization of the activity of ERP wave generators in healthy subjects correspond to smaller volumes of the structures studied. The structure of the relationships in patients with schizophrenia differed from the normal one; significant correlations were observed with the volume of the caudate nuclei, and more pronounced “normalization” of neurophysiological characteristics was associated with large volumes of these structures.     

Hydraulic aspects of pool-weir fishways as ecologically friendly water structure

Today, natural rivers are increasingly fragmented by human-made obstacles such as dams. Due to these structures fish populations in natural rivers rapidly diminish. In this context, fishways are a useful hydraulic structure in the creation of ecosystem for fish migration. Three dimensional mean flow and turbulence structure of pool-weir fishways were experimentally explored. During the experiments, three different notch sizes were applied while the size of the orifice was kept constant. Two acoustic Doppler velocimeters were employed throughout the velocity measurements. Three-dimensional mean velocity and normalized turbulent kinetic energy patterns in the pool were experimentally analyzed considering the swimming ability of different fish species to check whether the given design conditions provide suitable flow patterns. Based on the data, a linear relationship between the parameters “the discharge” and “the average depth in a pool” was generated. An equation was derived which gives the “energy dissipation rate per unit pool volume” in terms of the parameters “geometrical characteristics of the fishway”, “head difference between pools”, “slope”, and “acceleration due to gravity”. The discharge ratios between “flow through orifice” and “flow over notch” were expressed based on the data.     

Multiple hysteretic patterns from elementary population models

Critical transitions whereby small changes in conditions can cause large and irreversible changes in ecosystem states are a cause of increasing concern in ecology. Here, we focus on the irreversibility of these transitions, formally known as hysteresis. We explore how simple correlations between parameters in Lotka-Volterra predator-prey equations result in a variety of complicated hysteretic patterns. These patterns include “unattainable” stable states that once lost may never be recovered. We suspect these patterns to be common in natural systems, where interactions between diverse assemblages are unavoidable. Thus, understanding underlying hysteretic structures may be necessary for rescuing lost ecosystem states and avoiding future losses.     

Guest-Editorial Introduction: Converging Evolutionary Patterns in Life and Culture

The natural world demonstrates signs of spatial–temporal order, an order that appears to us through a series of recognizable, recurring and consecutive patterns, i.e. regularities in forms, functions, behaviors, events and processes. These patterns lend insight into the modes and tempos of evolution and thus into the units, levels, and mechanisms that underlie the evolutionary hierarchy. Contributors to this special issue analyze converging patterns in the biological and sociocultural realm across and beyond classic divisions between micro- and macro-evolution; horizontal/reticulate and vertical evolution; phylogeny, ontogeny and ecology; synchronic and diachronic sociocultural and linguistic research; and tree and network diagrams. Explanations are sought in complexity theory, major transitions of evolution, and process and mechanism approaches to change; and consequences for notions such as “life”, “species”, “biological individuality”, “units” and “levels” of evolution are given.     

The ripples of modernity: How we can extend paleoanthropology with the extended evolutionary synthesis

Contemporary understandings of paleoanthropological data illustrate that the search for a line defining, or a specific point designating, “modern human” is problematic. Here we lend support to the argument for the need to look for patterns in the paleoanthropological record that indicate how multiple evolutionary processes intersected to form the human niche, a concept critical to assessing the development and processes involved in the emergence of a contemporary human phenotype. We suggest that incorporating key elements of the Extended Evolutionary Synthesis (EES) into our endeavors offers a better and more integrative toolkit for modeling and assessing the evolution of the genus Homo. To illustrate our points, we highlight how aspects of the genetic exchanges, morphology, and material culture of the later Pleistocene complicate the concept of “modern” human behavior and suggest that multiple evolutionary patterns, processes, and pathways intersected to form the human niche.     

Defensive behaviour and its inheritance in the anabantoid fish, Macropodus opercularis and Macropodus opercularis concolor

In this preliminary study defense behaviour patterns (fear responses) are described in two closely related, behaviourally different inbred labyrinth fish subspecies and in their F₁ generation. The subspecies M. opercularis (characterized briefly by “active escape”) and M. opercularis concolor (characterized by “passive escape”) showed specific differences in the manifestation of certain defense behaviour patterns. In the F₁ hybrid generation dominance and overdominance of M. opercularis was found in most defense behaviour patterns. Analysing the frequencies and sequences of movement patterns it could be shown that defensive behaviour is not a random or entirely “plastic” process but that there is sequential linkage between the patterns and they form characteristic clusters. Our results suggest that manifestations of different patterns are under genetic control and presumably, genetic determination of certain patterns is not very complex. Attempts were made to determine whole brain noradrenaline, serotonine and dopamine levels of the two subspecies and a significant difference was found in the noradrenaline content.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

Patterns,structures, and amino acid frequencies in structural building blocks,a protein secondary structure classification scheme

To study local structures in proteins, we previously developed an autoassociative artificial neural network (autoANN) and clustering tool to discover intrinsic features of macromolecular structures. The hidden unit activations computed by the trained autoANN are a convenient low-dimensional encoding of the local protein backbone structure. Clustering these activation vectors results in a unique classification of protein local structural features called Structural Building Blocks (SBBs). Here we describe application of this method to a larger database of proteins, verification of the applicability of this method to structure classification, and subsequent analysis of amino acid frequencies and several commonly occurring patterns of SBBs. The SBB classification method has several interesting properties: 1) it identifies the regular secondary structures, α helix and β strand; 2) it consistently identifies other local structure features (e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the “random coil” regions of proteins. Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as “building blocks” in the analysis of protein structure. This type of pattern analysis should increase our understanding of the relationship between protein sequence and local structure, especially in the prediction of protein structures. © 1997 Wiley-Liss, Inc.     

Differential sensitivity to rotation measured on potentials evoked by electrical stimulation of the guinea-pig ear

Responses to electrical stimulation of the ear applied between round-window and vertex electrodes were recorded in awake guinea-pigs from the same electrodes or from separate vertex/mastoid subdermal needle electrodes. They were averaged during opposite phases of sinusoidal rotation or before and after constant velocity rotation. In both cases the responses were subtracted from each other and yielded differential per- or post-rotatory “electrovestibular” responses. For comparison, responses were also recorded in the same animals and conditions of electrical stimulation during silence and during presentation of a broad-band noise. The difference yielded “electroacoustic” responses. In round-window records, electrovestibular and electroacoustic responses presented typical compound nerve action potential patterns. Electrovestibular responses could be recorded for head angular velocities as low as 3° sec⁻¹ at 0.1 Hz. Response amplitude showed a logarithmic relation to head velocity. Changes in amplitude, as a function of time after rotation, were comparable to those reported for vestibular nerve fibre responses. In vertex/mastoid records, electroacoustic responses presented a sequence of peaks similar to the click-evoked auditory brain-stem responses, and electrovestibular responses presented two peaks, presumably representing contributions of central vestibular structures. Such “electrovestibulography” permits the study of an individual ear and makes available to the investigator a large range of vestibular stimulation conditions.     

Point process models of single-neuron discharges

In most neural systems, neurons communicate via sequences of action potentials. Contemporary models assume that the action potentials' times of occurrence rather than their waveforms convey information. The mathematical tool for describing sequences of events occurring in time and/or space is the theory of point processes. Using this theory, we show that neural discharge patterns convey time-varying information intermingled with the neuron's response characteristics. We review the basic techniques for analyzing single-neuron discharge patterns and describe what they reveal about the underlying point process model. By applying information theory and estimation theory to point processes, we describe the fundamental limits on how well information can be represented by and extracted from neural discharges. We illustrate applying these results by considering recordings from the lower auditory pathway.     

Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically‐defined spectroscopic signatures derived from proteins with known three‐dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)‐type structures, whose spectral properties have not been well‐distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII‐type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid‐containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins.     

Historical foundations and future directions in macrosystems ecology

Macrosystems ecology is an effort to understand ecological processes and interactions at the broadest spatial scales and has potential to help solve globally important social and ecological challenges. It is important to understand the intellectual legacies underpinning macrosystems ecology: How the subdiscipline fits within, builds upon, differs from and extends previous theories. We trace the rise of macrosystems ecology with respect to preceding theories and present a new hypothesis that integrates the multiple components of macrosystems theory. The spatio‐temporal anthropogenic rescaling (STAR) hypothesis suggests that human activities are altering the scales of ecological processes, resulting in interactions at novel space–time scale combinations that are diverse and predictable. We articulate four predictions about how human actions are “expanding”, “shrinking”, “speeding up” and “slowing down” ecological processes and interactions, and thereby generating new scaling relationships for ecological patterns and processes. We provide examples of these rescaling processes and describe ecological consequences across terrestrial, freshwater and marine ecosystems. Rescaling depends in part on characteristics including connectivity, stability and heterogeneity. Our STAR hypothesis challenges traditional assumptions about how the spatial and temporal scales of processes and interactions operate in different types of ecosystems and provides a lens through which to understand macrosystem‐scale environmental change.     

Secondary osteon size and collagen/lamellar organization (“osteon morphotypes”) are not coupled,but potentially adapt independently for local strain mode or magnitude

In bone, matrix slippage that occurs at cement lines of secondary osteons during loading is an important toughening mechanism. Toughness can also be enhanced by modifications in osteon cross-sectional size (diameter) for specific load environments; for example, smaller osteons in more highly strained “compression” regions vs. larger osteons in less strained “tension” regions. Additional osteon characteristics that enhance toughness are distinctive variations in collagen/lamellar organization (i.e., “osteon morphotypes”). Interactions might exist between osteon diameter and morphotype that represent adaptations for resisting deleterious shear stresses that occur at the cement line. This may be why osteons often have a peripheral ring (or “hoop”) of highly oblique/transverse collagen. We hypothesized that well developed/distinct “hoops” are compensatory adaptations in cases where increased osteon diameter is mechanically advantageous (e.g., larger osteons in “tension” regions would have well developed/distinct “hoops” in order to resist deleterious consequences of co-existing localized shear stresses). We tested this hypothesis by determining if there are correlations between osteon diameters and strongly hooped morphotypes in “tension”, “compression”, and “neutral axis” regions of femora (chimpanzees, humans), radii (horse, sheep) and calcanei (horse, deer). The results reject the hypothesis—larger osteons are not associated with well developed/distinct “hoops”, even in “tension regions” where the effect was expected to be obvious. Although osteon diameter and morphotype are not coupled, osteon diameters seem to be associated with increased strain magnitudes in some cases, but this is inconsistent. By contrast, osteon morphotypes are more strongly correlated with the distribution of tension and compression.     

Reply to Rosenberg

I respond to two of the main arguments in Rosenberg’s commentary on “Mind, Matter, and Metabolism.” Rosenberg’s claim that metabolic activities are “modularized” in a way that sets them apart from cognitive processes is not true given the broad sense of the “metabolic” employed in my paper, and contemporary neuroscience, including the work on navigation cited by Rosenberg, has begun to yield an understanding of subjectivity and “point of view.”     

A Two-Stage Test for Distinguishing Random,Pseudo-Random and Nonrandom Mating Populations

There is no such an implication that a population in Hardy-Weinberg equilibrium must have undergone random mating. Therefore, it is unequivocal that the usual tests for “Hardy-Weinberg equilibrium” are indeed tests for “random union of gametes” but not for “random mating”. In this paper, utilizing population characteristics expressed in equilibrium state (equilibrium or disequilibrium) and mating behavior (random or nonrandom), a two-stage testing procedure for distinguishing random, pseudo-random and nonrandom mating populations is proposed. At the first stage, a population is tested for Hardy-Weinberg equilibrium. If insignificant result (i.e., in equilibrium) is obtained, then to a second stage the population is further tested for mating behavior. Random mating-pairs data are needed here for analysis instead of random individuals for usual Hardy-Weinberg equilibrium tests. Since distinguishing the three types of mating populations depends on the combined results of two stages, the probability of correct determination of the two-stage tests is discussed by simulation studies.