Evolutionary stasis, constraint and other terminology describing evolutionary patterns

Current use of terms to describe evolutionary patterns is vague and inconsistent. In this paper, logical definitions of terms that describe specific evolutionary patterns are proposed. Evolutionary inertia is defined in a manner analogous to inertia in physics. A character in a static state of evolutionary inertia represents evolutionary stasis while a character showing consistent directional evolutionary change represents evolutionary thrust. I argue that evolutionary stasis should serve as the null hypothesis in all character evolution studies. Deviations from this null model consistent with alternative hypotheses (e.g. random drift, adaptation) can then give us insight into evolutionary processes. Failure to reject a null hypothesis of evolutionary stasis should not be used as a serious explanation of data. The term evolutionary constraint is appropriate only when a selective advantage for a character state transition is established but this transition is prevented by specific, identified factors. One type of evolutionary constraint discussed is evolutionary momentum. A final pattern of evolutionary change discussed is closely related to evolutionary thrust and is referred to as evolutionary acceleration. I provide examples of how this set of definitions can improve our ability to communicate interpretations of evolutionary patterns.     

CHARACTER DEFINITIONS AND CHARACTER STATE DELINEATION: THE BETE NOIRE OF PHYLOGENETIC INFERENCE

Abstract— Currently characters are static concepts whose definition and state delineations seldom undergo any scrutiny. Common systematic practice tends to synthesize character slates by combining or dividing observed conditions, a situation most likely due to current theoretical limitations in phylogenetic inference, which tends to ignore problems of multistate characters. This process we refer to as the “synthetic” method for character definition. Character definitions derived for the genera of North American Cochylini (Lepidoptera: Tortricidae) using “synthetic” character states postulated that the cochylines were not monophyletic. The use of cladogram characters and nearest neighbor matrices in uncovering potential flaws in character state delineation is demonstrated. The “synthetic” set of character definitions proved deficient upon such analysis, principally due to its attempt to force highly variable features into a few states. The set of character definitions produced from this analysis is referred to as “reflective” because it does not ignore observed variation. It produces characters with many states and presents problems of setting up transformation series. Three means lor deriving transformations are applied to produce transformation series for the reflective set of character definitions: the unordered outgroup method, morphocline analysis and Transformation Series Analysis (TSA). All three data sets postulated the Cochylini as monophyletic. The three sets of phylogenies were compared. Consensus trees are ambiguous when analysing changes in hierarchy. In order to summarize these results in a manner which does not destroy the phylogenetic structure, positional subtrees, a new means for summarizing multiple solution cladograms, are introduced. It was found that all three sets of transformations produced very different cladograms which in turn were very different from the tree produced by the original, synthetic definitions. The results of each of these methods were assessed for their internal consistency. TSA gave the least contradictory results.     

Clustering HLA Class I Superfamilies Using Structural Interaction Patterns

Human leukocyte antigen (HLA) class I molecules are critical components of the cell-mediated immune system that bind and present intracellular antigenic peptides to CD8⁺ T cell receptors. To understand the interaction mechanism underlying human leukocyte antigen (HLA) class I specificity in detail, we studied the structural interaction characteristics of 16,393 nonameric peptides binding to 58 HLA-A and -B molecules. Our analysis showed for the first time that HLA-peptide intermolecular bonding patterns vary among different alleles and may be grouped in a superfamily dependent manner. Through the use of these HLA class I ‘fingerprints’, a high resolution HLA class I superfamily classification schema was developed. This classification is capable of separating HLA alleles into well resolved, non-overlapping clusters, which is consistent with known HLA superfamily definitions. Such structural interaction approach serves as an excellent alternative to the traditional methods of HLA superfamily definitions that use peptide binding motifs or receptor information, and will help identify appropriate antigens suitable for broad-based subunit vaccine design.     

On the relationship between evolutionary and psychological definitions of altruism and selfishness

I examine the relationship between evolutionary definitions of altruism that are based on fitness effects and psychological definitions that are based on the motives of the actor. I show that evolutionary altruism can be motivated by proximate mechanisms that are psychologically either altruistic or selfish. I also show that evolutionary definitions do rely upon motives as a metaphor in which the outcome of natural selection is compared to the decisions of a psychologically selfish (or altruistic) individual. Ignoring the precise nature of both psychological and evolutionary definitions has obscured many important issues, including the biological roots of psychological altruism.     

Status of Divisions of the International Geologic Time Scale

Each chronostratigraphic unit of the International Geologic Time Scale will be defined at its base by a Global Stratotype Section and Point (GSSP) or Global Standard Stratigraphic Age (GSSA). Nearly 50 GSSPs and 10 GSSAs have now been ratified. Ideally, the GSSP coincides with events having a global correlation potential. The international stage divisions of some systems, such as the Jurassic or Neogene, are similar to traditional usage in European geology. However, in order to utilize global correlation horizons, the international stage divisions of other systems, such as the Ordovician or Permian, have required assembling new stage nomenclatures or hybrids of different regional stages. A reference table by the International Commission on Stratigraphy itemizes the current or potential GSSP and GSSA definitions of all international geologic time units.     

ORPHANS BY DESIGN: THE FUTURE OF GENETIC PARENTHOOD

Establishing the nature of genetic parenthood is an important task. This is, firstly, because many people desire that relationship and it is in their interest to know what that is, and secondly, because there is a view that it may incur certain moral obligations between the genetic parent and their child. Many theorists have made attempts to define exactly what genetic parenthood is. I show that these definitions are deficient if they wish to fully capture all reproductive scenarios in ways that are intuitive and/or meaningful. Through a series of cases involving technologies such as cloning and genome editing, we see that in lieu of the traditional two parents, there are possible beings who have no genetic parents, one genetic parent, or many genetic parents. Establishing these cases complicates our understanding of genetic parenthood. From this, we must reconsider current definitions, as well as the usefulness of defining genetic parenthood in these complex cases. Here I do not aim to establish a new definition, but rather to suggest that this complexity makes it necessary to re‐assess the importance of the connection between genetic parenthood and parental obligations and authorities.     

Lekking in Gryllotalpa major, the Prairie Mole Cricket (Insecta: Gryllotalpidae)

Gryllotalpa major is a rare, burrowing insect native to the tallgrass prairie of the south-central United States and is known to exhibit 'lek-like' behavior during mating. Here I report on a study carried out in the field that demonstrates that the prairie mole cricket meets all criteria defining a classical lekking species. Males construct specialized acoustic burrows from which they call to attract females for mating. I show that these burrows, which seem to serve no purpose other than for sexual advertisement and mating, are aggregated spatially on at least three scalar levels. Females fly through the aggregation of burrows and drop to the ground in the vicinity of calling males, and are, thus, not constrained in choosing a mate. Females enter the males' acoustic burrows, but I argue that the burrows are not used as oviposition sites, and that the males do not otherwise sequester resources important to females. Although the term 'lek' is useful for the discussion of mating systems, its definition remains ambiguous. I discuss the current usage of the term and suggest extensions.     

Reliability of medial-longitudinal-arch measures for skin-markers based kinematic analysis

The medial-longitudinal arch (MLA) is perhaps the most important feature characterizing foot morphology. While current skin-markers based models of the MLA angle used in stereophotogrammetry allow to estimate foot arch shape and deformation, these do not always appear consistent with foot anatomy and with standard clinical definitions. The aim of this study was to propose novel skin-markers based measures of MLA angle and investigate their reliability during common motor tasks.Markers on the calcaneus, navicular tuberosity, first metatarsal head and base, and on the two malleoli were exploited to test eight definitions of MLA angle consistent with foot anatomy, both as angles between two 3-dimensional vectors and as corresponding projections on the sagittal plane of the foot. The inter-trial, inter-session and inter-examiner reliability of each definition was assessed in multiple walking and running trials of two volunteers, tested by four examiners in three sessions.Inter-trial variability in walking was in the range 0.7–1.2 deg, the inter-session 2.8–7.5 deg, and the inter-examiner in the range 3.7–9.3 deg across all MLA definitions. The Rizzoli Foot Model definition showed the lowest inter-session and inter-examiner variability. MLA measures presented similar variability in walking and running.This study provides preliminary information on the reliability of MLA measurements based on skin-markers. According to the present study, angles between 3-dimensional vectors and minimal marker sets should be preferred over sagittal-plane projections. Further studies should be sought to investigate which definition is more accurate with respect to the real MLA deformation in different loading conditions.     

What's History Got to Do with It? A Response to Seddon's Definition of Reintroduction

A recent article in Restoration Ecology by Philip Seddon aims at unraveling the definitions of various types of species translocations—from reintroductions to assisted colonization—and points out the slippery slope of misused words. I argue here that defining reintroduction is not as straightforward as Seddon presents it. Commonly used definitions of what constitutes a reintroduction all include some reference to “historical” conditions, but what exactly that encompasses is left open. I examine two parts of the reintroduction confusion: first, how the guidance documents and laws define reintroduction and second, how these definitions might be interpreted when reintroductions are presented in public forums. Rather than moving away from reintroductions toward interventions of other names, I encourage scientists to use a broad definition of reintroduction presented by the IUCN to open up reintroduction as a viable label for bringing a species back to an area regardless of when it was previously there or why it became extinct.     

Measuring Gender

Over the past several years, various operational definitions of gender have been used in studies of gender conformity in homosexual males. The goal of these studies is to demonstrate that childhood gender nonconformity (CGN) is either the proximate cause of adult homosexuality or an intermediate step in a biologically mediated process. The hypothesis of a causal connection between the development of gender and sexual orientation is embedded within the context of a biological (evolutionary) understanding of human behavior. Thus, testing the hypothesis of a causal connection between CGN and sexuality requires a concept of gender that is compatible with the basic principles of biological causation and our current understanding of evolutionary processes. I will argue that the concepts of gender used in the attempt to demonstrate a causal connection between CGN and sexual orientation are inappropriate because they provide no uniform, consistent method for identifying and measuring the biologically significant components of gender. I will also argue that the concept of gender that does emerge from these studies suggests an hypothesis about the connection between sexuality and gender that is not consistent with the cross-gendered theory of the etiology of homosexuality.     

Problematic Internet Usage and Immune Function

Problematic internet use has been associated with a variety of psychological comorbidities, but it relationship with physical illness has not received the same degree of investigation. The current study surveyed 505 participants online, and asked about their levels of problematic internet usage (Internet Addiction Test), depression and anxiety (Hospital Anxiety and Depression Scales), social isolation (UCLA Loneliness Questionnaire), sleep problems (Pittsburgh Sleep Quality Index), and their current health – General Health Questionnaire (GHQ-28), and the Immune Function Questionnaire. The results demonstrated that around 30% of the sample displayed mild or worse levels of internet addiction, as measured by the IAT. Although there were differences in the purposes for which males and females used the internet, there were no differences in terms of levels of problematic usage between genders. The internet problems were strongly related to all of the other psychological variables such as depression, anxiety, social-isolation, and sleep problems. Internet addiction was also associated with reduced self-reported immune function, but not with the measure of general health (GHQ-28). This relationship between problematic internet use and reduced immune function was found to be independent of the impact of the co-morbidities. It is suggested that the negative relationship between level of problematic internet use and immune function may be mediated by levels of stress produced by such internet use, and subsequent sympathetic nervous activity, which related to immune-supressants, such as cortisol.     

Definitions of pathogenicity and virulence in invertebrate pathology

Accurate definition and usage of terminology are critical to effective communication in science. In a recently published article, the clarity and consistency of the terms pathogenicity and virulence as used in invertebrate pathology were called into question, and a revision of these terms was proposed. Our objective was to examine definitions of pathogenicity and virulence and their use in invertebrate pathology, and respond to this article. Although usage of the terms pathogenicity and virulence varies, we found considerable consistency in the published definitions of these terms in the invertebrate pathology literature throughout the history of the discipline, as well as among related disciplines such as medicine and microbiology. We did not find the established definitions to be lacking in clarity or utility. Therefore, we recommend that the definition and use of these terms adhere to precedence. Specifically, pathogenicity is the quality or state of being pathogenic, the potential ability to produce disease, whereas virulence is the disease producing power of an organism, the degree of pathogenicity within a group or species. Pathogenicity is a qualitative term, an “all-or-none” concept, whereas virulence is a term that quantifies pathogenicity.     

Ecological units: definitions and application

Concepts of ecological units, such as population, community, and ecosystem, are at the basis of ecological theory and research and have increasingly become the focus of conservation strategies. Concepts of these units still suffer from inconsistencies and confusions over terminology. The different concepts are treated here together as a common "conceptual cluster," with similar ecological functions (roles) and similar problems in their definition and use. An analysis of the multitude of existing terms and concepts that have been developed for these units reveals that they differ with respect to at least four basic criteria: (i) the questions as to whether they are defined statistically or via a network of interactions; (ii) if their boundaries are drawn by topographical or process-related criteria; (iii) how high the required internal relationships are; and (iv) if they are perceived as "real" entities or abstractions by an observer The various definitions cannot be easily sorted into just a few types, but they can be characterized by several independent criteria. I argue that serious problems arise if the different possibilities of defining ecological units are not recognized and if the concepts are perceived as self-evident. The different concepts of ecological units should be defined and used in a philosophically informed manner I propose a dual approach to the use of ecological units. Generic meanings of the main concepts (especially population, community, and ecosystem) should be retained only as heuristically useful perspectives, while specific and "operational" definitions of the concepts as units should be developed, depending on specific purposes of their use. Some thoughts on the basic requirements for such definitions and the domains of their uses are briefly explained.     

What is cyclomorphosis?

1. The history of the term cyclomorphosis and of research investigating the phenomenon it describes are reviewed briefly.
2. Several distinct definitions of this term appear in the limnological literature. Some of these definitions are consistent with earlier studies; others are not and are very restrictive and reliant upon extensive laboratory analysis.
3. We argue for the adoption of a broad definition of cyclomorphosis that is consistent with the majority of previous studies and practical to apply to the field populations it attempts to describe.
4. We also urge all researchers investigating this phenomenon to provide their working definition of this term in their reports in order to avoid terminological confusion.     

Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names

A phylogenetic definition of a taxon name associates that name with a clade through its reference to a particular ancestor and all of its descendants. Depending on one's perspective, phylogenetic definitions name either clades on the one true, but unknown, phylogeny, or components on cladograms (clades on hypotheses regarding the true phylogeny). Phylogenetic definitions do not contain enough information to identify components without a reference cladogram. As a result, (1) if clades are equated with components on cladograms, a phylogenetic definition may associate a taxon name with different clades on different cladograms, and (2) the inclusiveness, diagnostic synapomorphies, and distribution in time and space of the clade with a particular name can differ markedly depending on the phylogenetic hypothesis one chooses to adopt. This potentially unacceptable lability in the clade to which a name refers can be avoided by using a taxon name in conjunction with only phylogenetic hypotheses on which specific taxa are related in a particular fashion. This designated phylogenetic context can be described in an n-taxon statement that would be appended to the phylogenetic definition. Use of the taxon name would be considered inappropriate in conjunction with cladograms on which the relationships contradict those in the n-taxon statement. Whereas phylogenetic definitions stabilize the meaning of taxon names, designated phylogenetic contexts would stabilize the usage of those names.     

Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula

Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.     

Early usage and meaning of evolvability

Evolvability has become an enormously popular concept in evolutionary biology and in machine learning software architecture. While it is claimed that the term was coined in 1988 by Richard Dawkins, it was used as early as 1931 as a characteristic of life by John A. Thomson. We quote and review the earliest uses and definitions of evolvability in biological frameworks up until 1989, which are remarkably few. The meaning changed from simply the “ability to evolve” as a characteristic of life to various versions of including necessary variation to predict whether or not something could evolve to the rate and quality of that evolution. Or, meaning changed from the ability to evolve to the “quality” of the ability to evolve. Since then, evolvability has taken on many definitions as it has exploded in usage.     

Criteria and indicators for sustainable forest management: The road travelled and the way ahead

Criteria and indicators (C&I) have emerged as a powerful tool in implementing sustainable forest management. In a relatively short period, around 150 countries have adopted C&I. Some processes have used C&I in forest management and produced progress reports. Six of the seven thematic areas common to all processes are also being used as a basis for reporting progress towards sustainable forest management [e.g., the Food and Agriculture Organization of the United Nations (FAO) in its Global Forest Resource Assessment 2005]. However, there are significant problems in the wider application of C&I. A number of countries are not using C&I at all, and in some countries where they are being used, it is not done in an effective manner. Areas that need improvement in order to promote the use of C&I include: (1) strengthening concepts and definitions; (2) rationalising criteria and indicators; (3) further research on indicators; and (4) utilising C&I in more effective ways. The future development of C&I must be based on an active link between research effort and operational needs in order to prevent a waste of resources and effort. Some of the research undertaken to date has led to the adoption of innovative approaches to optimise resource use and simplify application. This paper identifies areas needing more research and draws from ongoing work to show where progress is being made.