Symposium Summary: Evolutionary Patterns in Actinopterygian Fishes

SYNOPSIS. The actinopterygian fishes are an exemplary cladefor the study of structural and functional evolutionary patterns.With over half of all vertebrate species, ray-finned fisheshave diversified into a wide variety of habitats, and considerableprogress has been made over the last fifteen years in understandingthe genealogical relationships of actinopterygians. This symposiumhas contributed to our understanding of phylogenetic patternsin actinopterygians and to knowledge of the major structuraland functional patterns in locomotor, auditory, trophic, andneural systems. A number of key areas for future research havebeen identified. (1) The relationships of "palaeonisciform"fishes, (2) the study of trends in feeding and locomotor systemswithin a phylogenetic context, (3) the identification of primitivepatterns of pharyngeal jaw movement and steady and unsteadylocomotor patterns in actinopterygians, (4) the homologies,identification, and functional significance of neural pathwaysin the telencephalon, and (5) the comparative study of form-functionrelations in the auditory system. The study of teleost fishbiology has proceeded at the expense of data on primitive actinopterygians(e.g., Polypterus, Polyodon, Aapenser, Lepisosteus, Amia) whichare especially important in the analysis of structural and functionalpatterns in ray-finned fishes.     

Biosemantics: An Evolutionary Theory of Thought

Evolutionary theory has an unexpected application in philosophy of mind, where it is used by the so-called biosemantic program—also called the teleosemantic program—to account for the representational capacities of neural states and processes in a way that conforms to an overarching scientific naturalism. Biosemantic theories account for the representational capacities of neural states and processes by appealing in particular to their evolutionary function, as that function is determined by a process of natural selection. As a result, biosemantic theories have distinct advantages over other theories of mental representation—e.g., Fodor’s causal theory. Foremost among the advantages of biosemantic theories is their ability to account for the possibility of mental misrepresentation.     

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.     

Evolutionary Medicine: A Key to Introducing Evolution

Science teachers can use examples and concepts from evolutionary medicine to teach the three concepts central to evolution: common descent, the processes or mechanisms of evolution, and the patterns produced by descent with modification. To integrate medicine into common ancestry, consider how the evolutionary past of our (or any) species affects disease susceptibility. That humans are bipedal has produced substantial changes in our musculoskeletal system, as well as causing problems for childbirth. Mechanisms such as natural selection are well exemplified in evolutionary medicine, as both disease-causing organism and their targets adapt to one another. Teachers often use examples such as antibiotic resistance to teach natural selection: it takes little alteration of the lesson plan to make explicit that evolution is key to understanding the principles involved. Finally, the pattern of evolution can be illustrated through evolutionary medicine because organisms sharing closer ancestry also share greater susceptibility to the same disease-causing organisms. Teaching evolution using examples from evolutionary medicine can make evolution more interesting and relevant to students, and quite probably, more acceptable as a valid science.     

Improving How Evolution Is Taught: Facilitating a Shift from Memorization to Evolutionary Thinking

In North America, public understanding and acceptance of evolution is alarmingly low. Moreover, acceptance rates are declining, and studies suggest that even students who have taken courses in evolution have the same misunderstandings as the general public. These data signal deficiencies in our educational system and provide a “call to arms” to improve how evolution is taught. Many studies show that student education can be improved by replacing lecture-based pedagogy with active learning approaches—where the role of students changes from passive note taking to active problem solving. Here, we describe changes made to a second-year undergraduate evolution course to facilitate a shift to active learning and improve student understanding of evolution. First, lectures were used only sparingly and were largely replaced by problem-solving activities. Second, standard textbooks were replaced by “popular” books applying evolutionary thinking to topics students encounter on a daily basis. Lastly, predefined laboratory exercises were replaced by student-designed and implemented research projects. These changes led to increased student engagement and enjoyment, improved understanding of evolution and ability to apply evolutionary thinking to biological problems, and increased student recognition that evolutionary thinking is important not only in the classroom but also in their daily lives.     

Evolutionary Implications of Changing Nutritional Patterns in Human Populations

Malnutrition is a widespread problem in the tropical regions of the world, the same areas which are believed to be man's ancestral home. Much of the adaptive complex characterizing contemporary Homo sapiens was assembled during the period of at least partial reliance on dietary intake of animal protein. Adjustments to low protein intake are most difficult during the period of growth and development. Selection against individuals unable to make suitable adjustments exerts pressure on the human population to retain adaptability while maintaining appropriate body proportions and sexual dimorphisms for body size .     

Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences

We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts.     

Distribution Patterns of Tropical Plant Foods as an Evolutionary Stimulus to Primate Mental Development

Primates are noted for their mental abilities but the selective basis for such traits has remained obscure. It is hypothesized that the element of predictability associated with the spatial and temporal distribution patterns of plant foods in tropical forests has served to stimulate mental development in primates taking much of their food from the first trophic level. Primates able to remember the locations and phenological patterns of a wide variety of plant foods could move directly to such foods when and where available without wasting time and energy in random search. This would enhance overall foraging success by lowering procurement costs associated with a varied and patchily distributed plant diet. Membership in a cohesive social unit, that utilized the same supplying area over many consecutive generations, would also enhance foraging success by serving to transmit important information about diet to close kin. Data on the foraging behavior of howler and spider monkeys are presented to test certain implications of this hypothesis. Similar selective pressures, but applied to foods from the second trophic level, may have been of critical importance in the mental development of hominids . [primates, evolution, intelligence, plant foods, Aleles, Alouatta ]     

Patterns and Mechanisms of Evolutionary Transitions between Genetic Sex-Determining Systems

The diversity and patchy phylogenetic distribution of genetic sex-determining mechanisms observed in some taxa is thought to have arisen by the addition, modification, or replacement of regulators at the upstream end of the sex-determining pathway. Here, I review the various evolutionary forces acting on upstream regulators of sexual development that can cause transitions between sex-determining systems. These include sex-ratio selection and pleiotropic benefits, as well as indirect selection mechanisms involving sex-linked sexually antagonistic loci or recessive deleterious mutations. Most of the current theory concentrates on the population–genetic aspects of sex-determination transitions, using models that do not reflect the developmental mechanisms involved in sex determination. However, the increasing availability of molecular data creates opportunities for the development of mechanistic models that can clarify how selection and developmental architecture interact to direct the evolution of sex-determination genes.Biparental sexual reproduction is a common mode of reproduction in higher organisms. It is found in gonochorous animals (Bull 1983; Barnes et al. 2001), heterothallic fungi (Heitman et al. 2013), and dioecious flowering plants and algae (Ainsworth 2000; Umen 2011). Species belonging to this diverse group of organisms have distinct sexes, and their development typically passes through a critical stage at which the zygote commits irreversibly to either the male or the female sexual fate (Valenzuela 2008) (except in sequential hermaphrodites, which change sex during their life). This ontogenetic process, known as sex determination, triggers the differentiation of specialized male or female reproductive organs and organizes many sex-specific differences in gene expression, physiology, morphology, and behavior (sex differentiation) (Badyaev 2002; Ellegren and Parsch 2007).Despite the universal and simple dichotomous outcome of sex determination, sex-determining mechanisms are highly diverse across taxa. Some species use a specific environmental cue (e.g., temperature, photoperiod, or population density) as the primary sex-determining signal (environmental sex determination; ESD), whereas others rely on various types of genetic sex determination (GSD), including male or female heterogamety, haplodiploidy or multilocus sex-determining mechanisms (Bull 1983; Marshall Graves 2008; Janousek and Mrackova 2010). In addition, sex determination can depend on epigenetic factors such as imprinting or maternal gene products deposited in the egg (Verhulst et al. 2010a). The apparent variability of sex determination is even more puzzling given that other processes acting in mid-development are evolutionarily conserved, presumably as a result of strong ontogenetic constraints (Marín and Baker 1998; Kalinka and Tomancak 2012). Considerable effort has therefore been directed at explaining the function and evolutionary origin of diversity in the mechanisms determining sex.Here I review this literature, concentrating on transitions between genetic sex determination systems (for other recent reviews, see Beukeboom and Perrin 2014; van Doorn 2014). An important ultimate cause of such transitions is sexually antagonistic selection, which interacts with various other evolutionary forces shaping the sex-determining system. To disentangle these factors, I will first discuss the current paradigm for how sex-determination pathways have been modified, before reviewing the various mechanisms thought to be responsible for transitions in sex determination. The final part of this review will straddle the proximate/ultimate divide by exploring how adaptive mechanisms interact with the developmental architecture of sex determination.     

A Homage to Homology: Patterns of Copepod Evolution

Lack of attention to determining the homology of character states is recognized as being responsible for the ever increasing numbers of phylogenetic schemes for the Crustacea that appear and disappear so rapidly. Detailed study of musculature, segmentation and setation of the limbs of all 10 orders of copepods revealed numerous phylogenetically informative characters, based on segmental fusion patterns and the presence of individually identified setation elements. Simple counts of limb segments (or of setae) were found to be virtually useless for constructing phylogenies in the copepods. This conclusion can probably be extended to other crustacean groups.