Generic physical mechanisms of morphogenesis and pattern formation as determinants in the evolution of multicellular organization

Early embryos of metazoan species are subject to the same set of physical forces and interactions as any small parcels of semi-solid material, living or nonliving. It is proposed that such “generic” properties of embryonic tissues have played a major role in the evolution of biological form and pattern by providing an array of morphological templates, during the early stages of metazoan phylogeny, upon which natural selection could act. The generic physical mechanisms considered include sedimentation, diffusion, and reaction-diffusion coupling, all of which can give rise to chemical nonuniformities (including periodic patterns) in eggs and small multicellular aggregates, and differential adhesion, which can lead to the formation of boundaries of non-mixing between adjacent cell populations. Generic mechanisms that produce chemical patterns, acting in concern with the capacity of cells to modulate their adhesivity (presumed to be a primitive, defining property of metazoa), could lead to multilayered gastrulae of various types, segmental organization, and many of the other distinguishing characteristics of extant and extinct metazoan body plans. Similar generic mechanisms, acting on small tissue primordia during and subsequent to the establishment of the major body plans, could have given rise to the forms of organs, such as the vertebrate limbs. Generic physical processes acting on a single system of cells and cell products can often produce a widely divergent set of morphological phenotypes, and these are proposed to be the raw material of the evolution of form. The establishment of any ecologically successful form by these mechanisms will be followed, under this hypothesis, by a period of genetic evolution, in which the recruitment of gene products to produce the “generically templated” morphologies by redundant pathways would be favoured by intense selection, leading to extensive genetic change with little impact on the fossil record. In this view, the stabilizing and reinforcing functions of natural selection are more important than its ability to effect incremental change in morphology. Aspects of evolution which are problematic from the standard neo-Darwinian viewpoint, or not considered within that framework, but which follow in a straightforward fashion from the view presented here, include the beginnings of an understanding of why organisms have the structure and appearance they’ do, why homoplasy (the recurrent evolution of certain forms) is so prevalent, why evolution has the tempo and mode it does (“punctuated equilibrium”), and why a “rapid” burst of morphological evolution occurred so soon after the origin of the metazoa.     

The phylogeny of polar fishes and the structure,function and molecular evolution of hemoglobin

Fishes thriving in polar habitats offer many opportunities for comparative approaches to understanding protein thermal adaptations. Investigations on the remarkable evolutionary adaptations to these environments of basic proteins such as hemoglobin, the oxygen carrier, can provide new insights into the mechanisms studied in temperate organisms and can shed light on convergent processes evolved in response to thermal adaptations. At the molecular level, hemoglobins are one of the most intriguing systems for studying the relationships between environmental conditions and adaptations. This review summarizes the current knowledge on molecular structure, biological function and phylogeny of hemoglobins of fish species living in both polar habitats but having different evolutionary histories. In benthic, non-migratory, cold-adapted fishes, the stability of thermal conditions may have generated no or few variations in selective pressures on globin sequences through evolutionary time, so that sequences retain the species phylogenetic “signal”. In pelagic, migratory, cold-adapted or temperate fishes, variations in selective pressures on globin sequences caused by variations in temperature accompanying the dynamic life style may have disrupted the phylogenetic “signal” in phenetic trees.     

Can inverse density dependence at small spatial scales produce dynamic instability in animal populations?

All else being equal, inversely density-dependent (IDD) mortality destabilizes population dynamics. However, stability has not been investigated for cases in which multiple types of density dependence act simultaneously. To determine whether IDD mortality can destabilize populations that are otherwise regulated by directly density-dependent (DDD) mortality, I used scale transition approximations to model populations with IDD mortality at smaller “aggregation” scales and DDD mortality at larger “landscape” scales, a pattern observed in some reef fish and insect populations. I evaluated dynamic stability for a range of demographic parameter values, including the degree of compensation in DDD mortality and the degree of spatial aggregation, which together determine the relative importance of DDD and IDD processes. When aggregation-scale survival was a monotonically increasing function of density (a “dilution” effect), dynamics were stable except for extremely high levels of aggregation combined with either undercompensatory landscape-scale density dependence or certain values of adult fecundity. When aggregation-scale survival was a unimodal function of density (representing both “dilution” and predator “detection” effects), instability occurred with lower levels of aggregation and also depended on the values of fecundity, survivorship, detection effect, and DDD compensation parameters. These results suggest that only in extreme circumstances will IDD mortality destabilize dynamics when DDD mortality is also present, so IDD processes may not affect the stability of many populations in which they are observed. Model results were evaluated in the context of reef fish, but a similar framework may be appropriate for a diverse range of species that experience opposing patterns of density dependence across spatial scales.     

Typostrophism in Palaeozoic Ammonoids?

The anti-Darwinian “Typostrophe Theory” of O.H.Schindewolf can be put to the test by revisiting the ammonoid examples on which this macroevolutionary model was founded. It is shown that none of the three theoretical elements saltationism, internalism, and cyclism can be supported by empirical data obtained from ammonoid research. Putative saltations (“Typogenesis”) were feigned because of the lack of knowledge of intermediate forms. Internalistic and orthogenetic development (“Typostasis”) can only be favoured by neglecting possible functions of morphological characters. Preprogrammed extinction of “degenerated” clades (“Typolysis”) is unlikely when ruling out anthropocentric views regarding ammonoid morphology. In terms of evolution of Palaeozoic ammonoids, there is no basis for the preference of the “Typostrophe Theory” or some of its composing elements, including the “Type Concept” and “Proterogenesis”, over the Darwinian evolutionary model and the Modern Synthesis.      

Hidden treatments in ecological experiments: re-evaluating the ecosystem function of biodiversity

Interactions between biotic and abiotic processes complicate the design and interpretation of ecological experiments. Separating causality from simple correlation requires distinguishing among experimental treatments, experimental responses, and the many processes and properties that are correlated with either the treatments or the responses, or both. When an experimental manipulation has multiple components, but only one of them is identified as the experimental treatment, erroneous conclusions about cause and effect relationships are likely because the actual cause of any observed response may be ignored in the interpretation of the experimental results. This unrecognized cause of an observed response can be considered a “hidden treatment.” Three types of hidden treatments are potential problems in biodiversity experiments: (1) abiotic conditions, such as resource levels, or biotic conditions, such as predation, which are intentionally or unintentionally altered in order to create differences in species numbers for “diversity” treatments; (2) non-random selection of species with particular attributes that produce treatment differences that exceed those due to “diversity” alone; and (3) the increased statistical probability of including a species with a dominant negative or positive effect (e.g., dense shade, or nitrogen fixation) in randomly selected groups of species of increasing number or “diversity.” In each of these cases, treatment responses that are actually the result of the “hidden treatment” may be inadvertently attributed to variation in species diversity. Case studies re-evaluating three different types of biodiversity experiments demonstrate that the increases found in such ecosystem properties as productivity, nutrient use efficiency, and stability (all of which were attributed to higher levels of species diversity) were actually caused by “hidden treatments” that altered plant biomass and productivity. Received: 16 December 1996 / Accepted: 2 March 1997     

Multisequence comparisons in protein coding genes

A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments,c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered “constrained” or “hypervariable”. The constrained regions are of two types: α and β. The α regions result from constraints at the amino acid level, whereas the β regions are those probably involved in “control” processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.     

Ecological explanations for successful invasion of exotic plants

The intentional introduction of exotic species can increase the level of local biodiversity, enrich people’s material lives, and bring significant social and economic benefits that are also the symbols of human progress. However, along with the frequent intercourse among countries and regions, the frequency of uncontrolled crossregional migration of species is increased and there is a lack of scientific management strategy for the intentional introduction of exotic species. Exotic species invasion, which is behind habitat fragmentation, has become the second largest threatening factor to the maintenance of the global-scale level of biological diversity. Exotic species invasion can destroy the structure of an ecosystem, disturb the economic life of a society, and do harm to human health. In this paper, the authors review some of the ecological explanations for issues such as “what causes or mechanisms have led to the successful invasion of exotic species”, including the “ideal weeds characteristics”, “biodiversity resistance hypothesis”, “enemies release hypothesis”, “evolution of increased competitive ability hypothesis”, “niche opportunity hypothesis”, and “novel weapon hypothesis”. The authors also analyze and evaluate the background and theoretical basis of the hypotheses, providing explanations for some phenomena, as well as the deficiencies of these explanations.     

The invasiveness of an introduced species does not predict its impact

Inconsistent use of terminology plagues the study and management of biological invasions. The term “invasive” has been used to describe inter alia (1) any introduced non-indigenous species; (2) introduced species that spread rapidly in a new region; and (3) introduced species that have harmful environmental impacts, particularly on native species. The second definition in various forms is more commonly used by ecologists, while the third definition is pervasive in policy papers and legislation. We tested the relationship between the invasiveness of an introduced species and its impact on native biodiversity. We quantified a species’ invasiveness by both its rate of establishment and its rate of spread, while its impact was assigned a categorical ranking based on the documented effects of the invader on native species populations. We found no correlations between these variables for introduced plants, mammals, fishes, invertebrates, amphibians and reptiles, suggesting that the mechanisms of invasion and impact are not strongly linked. Our results support the view that the term “invasive” should not be used to connote negative environmental impact.     

Monitoring and manipulation of a sublittoral hard bottom biocoenosis in Balsfjord,northern Norway

Sublittoral hard bottom biocoenoses in Balsfjord, Norway (69°31′ N, 19°1′ E), were monitored using underwater stereophotogrammetry. The study includes manipulation of natural densities of organisms and testing the importance of biological interactions and “key species ” for the structure of biocoenoses. Underwater photography has the advantages of being a non-destructive method, but it is selective because small or hidden organisms cannot always be observed. Field experiments with exclusion of organisms from cages seem suitable for testing hypotheses concerning which animals are “key species ” in certain biocoenoses. Sea-urchins(Strongylocentrotus droebachiensis, S. pallidus) were suspected to be “key species ” in the present study, and their removal from cages caused an increase in abundance of barnacles(Balanus balanoides), the limpetAcmaea testudinalis and algal cover.     

The Evolution of Language: A Comparative Review

For many years the evolution of language has been seen as a disreputable topic, mired in fanciful “just so stories” about language origins. However, in the last decade a new synthesis of modern linguistics, cognitive neuroscience and neo-Darwinian evolutionary theory has begun to make important contributions to our understanding of the biology and evolution of language. I review some of this recent progress, focusing on the value of the comparative method, which uses data from animal species to draw inferences about language evolution. Discussing speech first, I show how data concerning a wide variety of species, from monkeys to birds, can increase our understanding of the anatomical and neural mechanisms underlying human spoken language, and how bird and whale song provide insights into the ultimate evolutionary function of language. I discuss the “descended larynx” of humans, a peculiar adaptation for speech that has received much attention in the past, which despite earlier claims is not uniquely human. Then I will turn to the neural mechanisms underlying spoken language, pointing out the difficulties animals apparently experience in perceiving hierarchical structure in sounds, and stressing the importance of vocal imitation in the evolution of a spoken language. Turning to ultimate function, I suggest that communication among kin (especially between parents and offspring) played a crucial but neglected role in driving language evolution. Finally, I briefly discuss phylogeny, discussing hypotheses that offer plausible routes to human language from a non-linguistic chimp-like ancestor. I conclude that comparative data from living animals will be key to developing a richer, more interdisciplinary understanding of our most distinctively human trait: language.     

The advantages and disadvantages of being introduced

Introduced species, those dispersed outside their natural ranges by humans, now cause almost all biological invasions, i.e., entry of organisms into habitats with negative effects on organisms already there. Knowing whether introduction tends to give organisms specific ecological advantages or disadvantages in their new habitats could help understand and control invasions. Even if no specific species traits are associated with introduction, introduced species might out-compete native ones just because the pool of introduced species is very large (“global competition hypothesis”). Especially in the case of intentional introduction, high initial propagule pressure might further increase the chance of establishment, and repeated introductions from different source populations might increase the fitness of introduced species through hybridization. Intentional introduction screens species for usefulness to humans and so might select for rapid growth and reproduction or carry species to suitable habitats, all which could promote invasiveness. However, trade offs between growth and tolerance might make introduced species vulnerable to extreme climatic events and cause some invasions to be transient (“reckless invader hypothesis”). Unintentional introduction may screen for species associated with human-disturbed habitats, and human disturbance of their new habitats may make these species more invasive. Introduction and natural long-distance dispersal both imply that species have neither undergone adaptation in their new habitats nor been adapted to by other species there. These two characteristics are the basis for many well-known hypotheses about invasion, including the “biotic resistance”, “enemy release”, “evolution of increased competitive ability” and “novel weapon” hypotheses, each of which has been shown to help explain some invasions. To the extent that biotic resistance depends upon local adaption by native species, altering selection pressures could reduce resistance and promote invasion (“local adaptation hypothesis”), and restoring natural regimes could reverse this effect.     

Population Waves as a Condition for Increasing Ecological Stability of Organisms in the Process of Vertical Evolution

Ecological stability of an organism, which determines the possibility of its existence under changing environmental conditions, can be estimated as the probability of the participation of each viable offspring in reproduction. In developing species, the periodic rises and falls in the population size (Chetverikov's waves of life) can lead to changes in ecological stability, which is of macroevolutionary importance. Under conditions of isolation such changes generally result in specialization of intraspecific races but they could then lead to an increase in ecological stability of hybrid forms. Ecological stability of prosperous species increases during macroevolution due to combinative recombination between specialized intraspecific races or closely related species.     

Genes versus phenotypes in the study of speciation

Despite persistent debate on the nature of species, the widespread adoption of Mayr’s biological species concept has led to a heavy emphasis on the importance of reproductive isolation to the speciation process. Equating the origin of species with the evolution of reproductive isolation has become common practice in the study of speciation, coincident with an increasing focus on elucidating the specific genetic changes (i.e.—speciation genes) underlying intrinsic reproductive barriers between species. In contrast, some have recognized that reproductive isolation is usually a signature effect rather than a primary cause of speciation. Here we describe a research paradigm that shifts emphasis from effects to causes in order to resolve this apparent contradiction and galvanize the study of speciation. We identify major elements necessary for a balanced and comprehensive investigation of the origin of species and place the study of so-called “speciation genes” into its appropriate context. We emphasize the importance of characterizing diverging phenotypes, identifying relevant evolutionary forces acting on those phenotypes and their role in the causal origins of reduced gene flow between incipient species, and the nature of the genetic and phenotypic boundaries that results from such processes. This approach has the potential to unify the field of speciation research, by allowing us to make better “historical” predictions about the fate of diverging populations regardless of taxon.     

Aluminium concentration in the biomass of native species of the Morichals (swamp palm community) at the Orinoco Llanos,Venezuela

Aluminium concentration was analyzed in roots, stems and leaves of species growing in morichals with extreme flooded acid soils, deficient in K, Ca, Mg and P. Mean aluminium saturation was 73%. Results seem to indicate that species depending on seasonal changes in the Al concentration of plant compartments, could be grouped into “perennial aluminium accumulators”, “late aluminium accumulators” and “threshold aluminium accumulators”.     

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation , to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.     

A reconsideration of “Races” and their impact on the origins of the Chalcolithic in the Levant using available anthropological and archaeological data

Populations of the Chalcolithic Levant as defined by archaeological excavations has in many cases reinforced the traditional scheme that a number of “races” are present. This scheme is usually based not only on differential cultural traditions as identified by archeologists, but also on the available skeletal evidence as discussed by physical anthropologists. Recently this view has been challenged and it has been suggested that the metrical and anatomical range of variability as identified within Chalcolithic populations can be subsumed into a single population or “racial” range. This paper examines both the available biological and archaeological evidence from the Chalcolithic Levant and concludes that there is no strong archaeological or biological evidence to support a multiple “racial” origin for the Chalcolithic of the Levant.     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

The PhyloCode is fatally flawed, and the “Linnaean” System can easily be fixed

Promoters of the PhyloCode have mounted an intensive and deceptive publicity campaign. At the centerpiece of this campaign have been slogans such as that the Linnaean System will “goof you up,” that the PhyloCode is the “greatest thing since sliced bread,” and that systematists are “afraid” to propose new names because of “downstream consequences.” Aside from such subscientific spin and sloganeering, proponents of the PhyloCode have offered nothing real to back up claims of greater stability for their new system. They have also misled many into believing that the PhyloCode is the only truly phylogenetic system. The confusion that has been fostered involves several discrete arguments, concerning: a new “method” of “designating” names, rank-free taxonomy, uninomial nomenclature, and issues of priority. Claims that the PhyloCode produces a more stable nomenclature are false, as shown with the example of “paleoherbs.” A rank-free system of naming requires an annotated reference tree for even the simplest exchanges of information. This would be confusing at best and would cripple our ability to teach, learn, and use taxonomic names in the field or in publications. We would be confronted by a mass of polynomial names, tied together only by a tree graphic, with no agreed name (except a uninomial, conveying no hierarchy) to use for any particular species. The separate issue of stability in reference to rules of priority and rank can be easily addressed within the current codes, by implementation of some simple changes, as we will propose in this article. Thus there is no need to “scrap” the current Linnaean codes for a poorly reasoned, logically inconsistent, and fatally flawed new code that will only bring chaos.     

New species of Pogonophryne (Pisces, Artedidraconidae) from the Bellingshausen Sea, Antarctica

A new species of notothenioid fish, Pogonophryne bellingshausenensis n. sp., is described from the Bellingshausen Sea, Antarctica. The new species belongs to the dorsally-spotted “mentella” group of the genus and is characterized by having a short (about 13% SL) mental barbel with a short (about 16% of barbel length), narrow (barely wider than the stalk), and relatively inconspicuous terminal expansion composed of short, irregular, fingerlike processes. Compared to most other dorsally-spotted species of Pogonophryne (“barsukovi”, “marmorata”, and “mentella” groups), P. bellingshausenensis has a relatively wide (about 7% SL) interorbital region. An unspotted patch on the median dorsal surface of the head, posterior to the posttemporal ridges and anterior to the first dorsal fin, has not been observed previously in any dorsally-spotted species. The holotype was collected at 1,947 m, one of the deepest records for any species of Pogonophryne. A revised key to the ten species of the “mentella” group of Pogonophryne is also provided.     

Interactions among biological systems: An analysis of asymptotic stability

An analysis of the interactions among asymptotically stable dynamical systems is formulated by making use of the dynamical system theory. Some results coming from previous mathematical analyses have been slightly modified to take into account some typical biological constraints as the boundedness properties of the solutions. In particular it has been shown that when the “coupling” among the subsystems is “loose” enough (in a sense that has to be made mathematically precise) the asymptotic behaviour of a complex system is the same of that of its individual components. The mathematical theory has been used to analyze two systems of biological significance: the coupling among chemical reactions and the stability properties of a 4-dimensional system describing the kinetics of a chemical transmitter.