Genetics, development and evolution of adaptive pigmentation in vertebrates

The study of pigmentation has played an important role in the intersection of evolution, genetics, and developmental biology. Pigmentation's utility as a visible phenotypic marker has resulted in over 100 years of intense study of coat color mutations in laboratory mice, thereby creating an impressive list of candidate genes and an understanding of the developmental mechanisms responsible for the phenotypic effects. Variation in color and pigment patterning has also served as the focus of many classic studies of naturally occurring phenotypic variation in a wide variety of vertebrates, providing some of the most compelling cases for parallel and convergent evolution. Thus, the pigmentation model system holds much promise for understanding the nature of adaptation by linking genetic changes to variation in fitness-related traits. Here, I first discuss the historical role of pigmentation in genetics, development and evolutionary biology. I then discuss recent empirically based studies in vertebrates, which rely on these historical foundations to make connections between genotype and phenotype for ecologically important pigmentation traits. These studies provide insight into the evolutionary process by uncovering the genetic basis of adaptive traits and addressing such long-standing questions in evolutionary biology as (1) are adaptive changes predominantly caused by mutations in regulatory regions or coding regions? (2) is adaptation driven by the fixation of dominant mutations? and (3) to what extent are parallel phenotypic changes caused by similar genetic changes? It is clear that coloration has much to teach us about the molecular basis of organismal diversity, adaptation and the evolutionary process.     

Phylogeny,fossils, and model systems in the study of evolutionary developmental biology

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of "model organisms" selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the "model organism" paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on "model groups." These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a "model group" for the evo-devo study of vertebrate skeletal elements.     

HISTORICAL VERSUS SELECTIONIST EXPLANATIONS IN EVOLUTIONARY BIOLOGY

Abstract— Evolutionary changes require historical explanations, yet these are limited by the evolutionary processes we entertain and investigate. Using phylogenetic analysis, adaptation and natural selection can be tested as historical claims, but this is appropriate only in those special cases where change follows the scheme of one character-one function, singled out in new environmental circumstances. Systematic treatment of the evolutionary origin of characters (in particular, origin through ecological and developmental flexibility) lies outside the scope of selectionist explanations. Structural hypotheses about regularities in the directions of change, also analyzed phylogenetically, expand the scope of historical explanation to include the origin of characters, yet retain the view of organisms as passive and constrained objects of evolutionary change. Historical biology needs to encompass both the active responses of organisms and the construction by organisms of their own environments. For this to be realized will require changes in the concepts and practices of evolutionary biology, including a re-examination of the Lamarckian theme that the active responses of organisms have evolutionary significance—the rarity of individual-to-individual transmission of "acquired" characters does not disprove the possibility of their frequency increasing in a population.     

Proximate and ultimate causes: how come? and what for?

Proximate and ultimate causes in evolutionary biology have come to conflate two distinctions. The first is a distinction between immediate and historical causes. The second is between explanations of mechanism and adaptive function. Mayr emphasized the first distinction but many evolutionary biologists use proximate and ultimate causes to refer to the second. I recommend that ‘ultimate cause’ be abandoned as ambiguous.     

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

Dual Causality and the Autonomy of Biology

Ernst Mayr’s concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical sciences.     

An untold story in biology: the historical continuity of evolutionary ideas of Muslim scholars from the 8th century to Darwin’s time

Textbooks on the history of biology and evolutionary thought do not mention the evolutionary ideas of Muslim scholars before Darwin’s time. This is part of a trend in the West to minimise the contributions of non-Western scientists to biology, human anatomy and evolutionary biology. Therefore, this paper focuses on the contributions of pre-Darwinian Muslim scholars to the history of evolutionary thought. Our review of texts from a wide range of historical times, and written in various languages, reveals that there were in fact several Muslim scholars who postulated evolutionary ideas, some with remarkable similarities to Darwin’s theory. These ideas included the adaptation and survival of the fittest, a specific origin of humans from apes/monkeys, the notion of evolutionary constraints, the occurrence of extinctions within taxa and hereditary variability. Moreover, while both the scientific community and the broader public generally base their knowledge on Western textbooks, several parts of the Muslim world have indicated an overall rejection of biological–including human–evolution. Therefore, to improve historical accuracy and create a better understanding of scientific history, the world’s diverse civilisations and their philosophies, this untold story should be widely disseminated to the scientific community and the general public.     

Function without purpose

Philosophers of evolutionary biology favor the so-called etiological concept of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cummins's account has received attention but little support from philosophers of biology. This paper will show that a similar non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cummins's concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions.     

Chance as an explanatory factor in evolutionary biology.

Darwinian evolutionary biology has often been criticized for appealing to the notion of 'chance' in its explanations. According to some critics, such appeals exhibit the explanatory poverty of evolutionary theory. In response, defenders of Darwinism sometimes downplay the importance of 'chance' in evolution. I believe that both of these approaches are mistaken. The main thesis of this paper is that the term 'chance' encompasses a number of distinct concepts, and that at least some of these concepts serve essential explanatory functions in evolutionary biology. This claim is defended by way of an historical survey of the major concepts of 'chance' in the history of evolutionary biology, especially the concepts used by Jean Baptiste Lamarck, Charles Darwin, and Sewall Wright. An examination of their biologies shows how the concepts of 'chance' used cohere with their major scientific objectives and methods. These concepts survive and continue to function as important explanatory factors in contemporary evolutionary biology. Examples of such usage are given, and the explanatory status of 'chance' assessed.     

Evidence for Evolution Versus Evidence for Intelligent Design: Parallel Confusions

The popular defense of intelligent design/creationism (ID) theories, as well as theories in evolutionary biology, especially from the perspective that both are worthy of scientific consideration, is that empirical evidence has been presented that supports both. Both schools of thought have had a tendency to rely on the same class of evidence, namely, the observations of organisms that are in need of being explained by those theories. The result is conflation of the evidence that prompts one to infer hypotheses applying ID or evolutionary theories with the evidence that would be required to critically test those theories. Evidence is discussed in the contexts of inferring theories/hypotheses, suggesting what would be possible tests, and actual testing. These three classes of inference being abduction, deduction, and induction, respectively. Identifying these different inferential processes in evolutionary biology and ID allow for showing that the evidence to which theories and hypotheses provide understanding cannot be the same evidence supporting those theories and hypotheses. This clarification provides a strong criterion for showing the inability of an ID theory to be of utility in the ongoing process of acquiring causal understanding, that is the hallmark of science.     

Historical laws in modern biology

Several important analyses of the structure of evolutionary explanation have explicitly or implicitly required that historical laws be among the explanans statements. The required historical laws take the form of a generalization which relates some property or event to a developmental sequence of properties or events. The thesis of this paper is that historical laws of this kind are precluded by modern biological theory and, hence, analysis of evolutionary explanation within modern biology that require such laws are defective.     

Erich Wasmann, Ernst Haeckel, and the limits of science

Summary In the late nineteenth century, two German evolutionary biologists, Ernst Haeckel and Erich Wasmann, argued publicly about how to apply evolutionary biology and where its explanatory limits, if any, lay. The German Jesuit evolutionist entomologist Wasmann’s (1859–1931) faith and Jesuit philosophical training intersected to reconcile evolution and Catholicism by delineating the philosophical limits of science: Wasmann demarcated a material and historical world, which science can describe, and the realm of subjective experience and the soul, which it cannot. Wasmann’s evolution contrasted (and conflicted) strongly with contemporary German atheistic and anticlerical monistic evolutionary biology. This paper discusses Wasmann’s very public debates with monism’s prophet, Ernst Haeckel.     

Ernst Mayr,the tree of life,and philosophy of biology

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes.     

The evolution of insecticide resistance: Have the insects won?

While insecticides have greatly improved human health and agricultural production worldwide, their utility has been limited by the evolution of resistance in many major pests, including some that became pests only as a result of insecticide use. Insecticide resistance is both an interesting example of the adaptability of insect pests, and, in the design of resistance management programmes, a useful application of evolutionary biology. Pest susceptibility is a valuable natural resource that has been squandered; at the same time, it is becoming increasingly expensive to develop new insecticides. Pest control tactics should therefore take account of the possibility of resistance evolution. One of the best ways to retard resistance evolution is to use insecticides only when control by natural enemies fails to limit economic damage. This review summarizes the recent literature on insecticide resistance as an example of adaptation, and demonstrates how population genetics and ecology can be used to manage the resistance problem.     

Developing a Curriculum for Evolutionary Medicine: Case Studies of Scurvy and Female Reproductive Tract Cancers

Most early evolutionary thinkers came from medicine, yet evolution has had a checkered history in medical education. It is only in the last few decades that serious efforts have begun to be made to integrate evolutionary biology into the medical curriculum. However, it is not clear when, where (independently or as part of preclinical or clinical teaching courses) and, most importantly, how should medical students learn the basic principles of evolutionary biology applied to medicine, known today as evolutionary or Darwinian medicine. Most clinicians are ill-prepared to teach evolutionary biology and most evolutionary biologists ill-equipped to formulate clinical examples. Yet, if evolutionary science is to have impact on clinical thought, then teaching material that embeds evolution within the clinical framework must be developed. In this paper, we use two clinical case studies to demonstrate how such may be used to teach evolutionary medicine to medical students in a way that is approachable as well as informative and relevant.     

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB-the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical levels of organization to address questions central to EDB. We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB.     

Atomism, transformism and the fossil record

The modern debate between exponents of classical evolutionary classification and of cladistic analysis of phylogenetic relationships mirrors to some extent the arguments that were put forward in the debate between Cuvier and Geoffroy Saint-Hilaire in 1830. Put into a historical perspective the problems of comparative biology centre around two complementary traditions, atomism and transformism.     

Parent-offspring conflict and the cultural ecology of breast-feeding

Lactation constitutes a major focus for research in international health because of its dramatic impact on child survival; evolutionary biology has investigated lactation as an important aspect of parenting strategy, with implications for understanding parent-offspring conflict. These perspectives are brought together in an attempt to develop integrated models for an issue of key international health concern: the duration of exclusive breast-feeding and the timing of weaning. This analysis highlights the relevance of evolutionary theory for practical problems in public health, and it suggests the utility of public health outcomes for addressing evolutionary questions. Thomas McDade received his Ph.D. degree in anthropology from Emory University in 1999 and is currently an assistant professor in the anthropology department at Northwestern University. His research interests include biocultural perspectives on issues related to health and human development, with current attention focused on the cultural and evolutionary ecology of human immune function.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.     

Development and Macroevolution: Introduction to the Symposium

Despite the historical relationship between embryology and evolutionarybiology, during most of the 20th century developmental biologyand evolutionary biology have existed as two separate subdisciplinesof biology. Recently a reunion of these subdisciplines beganto take place. This reunion involves the formulation of evolutionaryexplanations of developmental phenomena and the applicationof developmental processes as mechanisms of evolutionary change.The symposium speakers have considered both aspects of the reunionas well as some of the theoretical and methodological issuesthat are emerging from it.