Patterns Of Evolutionary Change Research Articles

Patterns of Evolutionary Change in Baikalian Gammarids Inferred from DNA Sequences (Crustacea, Amphipoda)

The Baikalian gammarids (Crustacea, Amphipoda) are the most widely known and most spectacular example of an adaptive radiation among contemporary freshwater invertebrates. To study the phylogeny of the Baikalian gammarids we sequenced a 622-bp-long fragment of the nuclear gene coding for 18S rRNA from species of 18 endemic Baikalian genera andGammarus pulex—a non-Baikalian taxon. Some important morphological characters appear independently in both lineages and suggest parallelism in the development of gigantism and body armament. The first lineage comprises benthic, mostly unarmed taxa. The second lineage contains predominantly armed taxa, most of which are detrivorous or carnivorous.

Microhabitat use, trophic patterns, and the evolution of brain structure in African cichlids.

The species assemblages of cichlids in the three largest African Great Lakes are among the richest concentrations of vertebrate species on earth. The faunas are broadly similar in terms of trophic diversity, species richness, rates of endemism, and taxonomic composition, yet they are historically independent of each other. Hence, they offer a true and unique evolutionary experiment to test hypotheses concerning the mutual dependencies of ecology and brain morphology. We examined the brains of 189 species of cichlids from the three large lakes: Victoria, Tanganyika, and Malawi. A first paper demonstrated that patterns of evolutionary change in cichlid brain morphology are similar across taxonomic boundaries as well as across the three lakes [van Staaden et al., 1995 ZACS 98: 165-178]. Here we report a close relationship between the relative sizes of various brain structures and variables related to the utilization of habitat and prey. Causality is difficult to assign in this context, nonetheless, prey size and agility, turbidity levels, depth, and substrate complexity are all highly predictive of variation in brain structure. Areas associated with primary sensory functions such as vision and taste relate significantly to differences in feeding habits. Turbidity and depth are closely associated with differences in eye size, and large eyes are associated with species that pick plankton from the water column. Piscivorous taxa and others that utilize motile prey are characterized by a well developed optic tectum and a large cerebellum compared to species that prey on molluscs or plants. Structures relating to taste are well developed in species feeding on benthos over muddy or sandy substrates. The data militated against the existence of compensatory changes in brain structure. Thus enhanced development of a particular function is generally not accompanied by a parallel reduction of structures related to other modalities. Although genetic and environmental influences during ontogeny of the brain cannot be isolated, this study provides a rich source of hypotheses concerning the way the nervous system functions under various environmental conditions and how it has responded to natural selection.

Phylogenies and Physiological Processes—The Evolution of Sexual Dimorphism in Southeast Asian Frogs

There are a number of species of Southeast Asian Rana that are characterized by an unusual suite of sexually dimorphic features and derived reproductive modes. These frogs lack the usual secondary sexual characteristics of ranid frogs: nuptial pads, vocal sacs, and enlarged flexor muscles. Secondary sexual characteristics in frogs are under androgenic control. Phyloge- netic analyses using morphological and molecular data indicate that a drop in androgen level and/or a shift in androgen sensitivity may have been involved in the evolution of male parental care and the loss of the common suite of secondary sexual characteristics in these Asian frogs. Phylogenetic analyses also provide important information on experimental design by indicating the most appropriate taxa to use in the exploration of physiological processes controlling the expression of sexual dimorphism. This work is an example of how emergent properties from phylogenetic analyses can be used to formulate and test hypotheses of process and pattern of evolutionary change. (Frog; Rana; hormone; sexual dimorphism; parental care.)

The good fairy godmother of evolutionary genetics

Most evolutionary geneticists would agree that the major problems of the field have been solved. We understand both the nature of the mutational processes that generate novel genetic variants and the populational processes which cause them to change in frequency over time — most importantly, natural selection and random genetic drift, respectively. While there is plenty of debate about the relative importance of different processes in patterns of evolutionary change, no serious evolutionist will now defend onceprevalent views such as orthogenesis (predetermined evolution) or the inheritance of acquired characteristics. Indeed, jaded researchers might claim that all the soluble and interesting problems have been disposed of, leaving us with the insoluble and the trivial, as Wolpert suggests for developmental biology [1]. My own feeling is that there are still many intellectually exciting and potentially soluble problems, although we will never again come up with concepts as fundamental as those formulated by the ‘founding fathers’ of population genetics (Fisher, Wright and Haldane), or do experiments as path-breaking as Dobzhansky’s demonstration of natural selection acting on polymorphic chromosome inversions. The two most pressing questions I would put to a good fairy godmother of evolutionary genetics are these. First, what is the frequency distribution of selective effects among new mutations — how often do they have positive, negative or neutral selective effects, and how large are these effects? And second, what is the total rate per genome at which mutations that have a sizeable impact on fitness appear? I would like my questions answered for my favourite organism, Drosophila melanogaster, as much of the empirical work relevant to these questions has already been done using this delightful creature. Answering the first question would bring us close to understanding the role of selection in controlling the frequency within a population of variants at particular nucleotide sites. This issue was first raised thirty years ago, with the discovery of large amounts of within-population variation at the amino-acid sequence level [2], but has never been conclusively answered. The discovery of large amounts of silent and noncoding site variation has simply modified the question: are most nucleotide changes so slightly advantageous or disadvantageous that their fate is controlled mainly by genetic drift? Or is a significant fraction of variants subject to selection that is so weak as to be undetectable by direct measurement but strong enough to exert an influence on their evolutionary fate? We simply do not know, despite increasing statistical evidence from case studies of sequence variation and evolution of both DNA and protein which suggest a role for selection [3]. The other reason for asking this question is that many features of genetic systems are likely to have been shaped by the input of deleterious mutations at loci scattered across the genome [4]. From several Drosophila experiments, along with indirect evidence from other sources, it seems likely that a newly formed zygote in a higher eukaryote has a probability close to one of carrying a new deleterious mutation with an effect on its fitness of the order of one or two per cent relative to the fitness of nonmutant individuals [5]. If true, this has major implications for the evolution of sexual reproduction and genetic recombination, diploidy versus haploidy, outbreeding versus inbreeding, sex chromosome evolution and the evolution of ageing [4]. In addition, rates of evolution and variation for less strongly selected mutations may be influenced by strongly deleterious alleles at neighbouring sites on the chromosome; we may have to modify current theories that treat loci as essentially independent units before we can properly test hypotheses about the causes of nucleotide site evolution and variation [6]. In the absence of good fairy godmothers, I am much more sanguine about answering the second question than the first; it essentially requires brute-force application of mutation-accumulation methods, on a sufficiently large scale that one can have confidence in the resulting estimates. The first is more elusive, but will no doubt provide population geneticists with harmless employment for years to come.

Feeding, Function, and Phylogeny: Analysis of Historical Biomechanics in Labrid Fishes Using Comparative Methods

Recently developed methods in phylogenetic systematics enable the discovery of as? sociations among diverse characters of organisms such as morphology, biomechanics, and ecology among clades. In this study, the results of multiple character correlation techniques were compared using a data set on the functional morphology and ecology of feeding in the Cheilinini and outgroups (Perciformes: Labridae). The following two questions were addressed: What are the patterns of evolutionary change in structure and function of the feeding mechanisms of labrid fishes? Are evolutionary changes in trophic structure, feeding biomechanics, and feeding ecology congruent at different levels of labrid phylogeny? This study integrated previous work on the phylogenetic relationships of labrid fishes, quantitative modeling of jaw protrusion and hyoid depression mechanisms, analysis of morphometric variation in the trophic apparatus, and descrip? tion of the natural diet of labrids. Analysis of phylogenetic association between dietary and bio- mechanical characters within the phylogeny was performed using character optimization to map characters onto the phylogeny. Statistical tests of association between pairs of discrete characters involved contingent states tests and concentrated changes tests. Phylogenetic correlations between continuous quantitative characters were determined using the methods of squared-change parsi? mony, independent contrasts, and phylogenetic autocorrelation. A diversity of techniques yielded similar answers in this case study, suggesting that evolution of dietary habits and feeding behavior is tightly linked to the biomechanics of the feeding apparatus. (Functional morphology; system? atics; ecology; character correlation; comparative methods; phylogeny; Labridae.)

Evolution in vitro: analysis of a lineage of ribozymes

Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population.Results: Beginning with a pool of 1013 variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Cat2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca2+-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics — logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme.Conclusions:In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonably short time scale.

Biogeographic and evolutionary patterns of change in the terrestrial biota across the Cretaceous\Tertiary boundary

The currently available fossil record suggests, 1) biogeographic differentiation of the Late Cretaceous terrestrial biota and, 2) distinctly different patterns of evolution of terrestrial faunas and floras across the Cretaceous\Tertiary boundary.Discovery in Alaska of dinosaurs and mammals that lived at Late Cretaceous northern high latitudes provides evidence that many groups of terrestrial vertebrates had extensive geographic ranges and faunas were biogeographically differentiated. The Alaskan dinosaurs, represented by individuals that range in size from hatchlings to adults, might have been migratory forms living at high latitudes only during the summer months. In contrast, the small mammals probably were not migratory.Although recent discoveries are expanding our knowledge of the evolution of the terrestrial biota, the fossil record of terrestrial vertebrates during the Cretaceous\Tertiary transition is still heavily biased in favor of the northern Western Interior of North America. Here evolutionary change of the terrestrial fauna did not just involve extinction of lineages, some already decreasing in taxonomic diversity, and survival of many others. Shifts in biogeographic range and immigration of new groups played a significant role in remodeling the terrestrial fauna. The paleobotanical record is more extensive but also is biased with the most detailed record coming from the Western Interior where floral change is characterized as “massive” or “catastrophic” in scope.These conflicting evolutionary patterns are well founded being based on analysis of substantial fossil records. A new program of research directed toward resolution of the apparent paradox tests the hypothesis that at the end of the Cretaceous the terrestrial biota was biogeographically heterogeneous and evolutionary patterns of faunal and floral change in the Western Interior cannot be taken as globally representative.

Evolutionary trends in the articulate brachiopod hinge mechanism

Evolutionary patterns in the articulate brachiopod hinge are investigated and this empirical example is used as a model to examine evolutionary trends and evolutionary constraints. Several features of the hinge-system geometry exhibit persistent directional change from the Cambrian to the Recent and result in increased mechanical advantage in opening the valves. These geometric changes are reflected also in general features of shell morphology and growth and in patterns of familial diversity through time. Specific, identifiable constraints on brachiopod morphology and function related to the position of the pedicle and muscles and nature of the hinge line and hinge structures may be said to direct the observed trends. The pattern of evolutionary change among all articulate brachiopods is most satisfactorily accommodated by a diffusion model of morphological change. Examined independently, the deltidiodonts (with noninterlocking hinge structures) appear to reflect a process of directional selection through time, whereas change in the cyrtomatodont hinge mechanism (with interlocking teeth and sockets) may reflect the incidental effects of selection for increasing mantle-cavity volume rather than increasing diductor (opening) muscle moment. The “transition” from deltidiodont to cyrtomatodont hinge structures over the course of brachiopod evolutionary history may be interpreted from at least two distinctly different perspectives. Paleoecologically, this transition appears to reflect a habitat shift from soft sediment to hard, rocky substrates. Phylogenetically, the transition reflects the process of evolution: deltidiodonts persist as their modified descendants, the cyrtomatodonts. Investigating the acquisition of evolutionary novelties over time, or the transition from primitive to derived morphological features, may be the most informative approach to follow in studying evolutionary trends.

Homologs of eleven loci on human chromosome 11 assigned to two owl monkey chromosomes

We localized 11 loci mapped to human chromosome 11 to two chromosomes, 4 and 19 of owl monkey karyotype VI (2n = 49/50), by the use of somatic cell hybrids. Furthermore, using in situ hybridization to chromosomes of two owl monkey karyotypes, the HSTF1 oncogene locus was precisely localized on homologs 19q (K-VI) and 2q (K-II). Comparative analysis of available gene-mapping data among human, mouse, and owl monkey chromosomes revealed a pattern of evolutionary change in a syntenic group on human chromosome 11. These structural changes could be explained as having derived from a pericentric inversion of human chromosome region 11cen----q13 and a translocation involving human region 11q22----qter during primate evolution.

Contrasting modes and tempos of genome evolution in land plant organelles

Despite inhabiting the same cell lineage for roughly a billion years and being dependent on the same nucleus for most of their gene products and genetic control, the two organelle genomes of land plants exhibit remarkably different tempos and patterns of evolutionary change. With a few notable exceptions, chloroplast genomes are highly conserved in size and gene arrangement, whereas mitochondrial gesomes vary emormously in size and organization. Conversely, nucleotide substitution rates are on average several times higher in chloroplast DNA than in mitochondrial DNA. Mechanistic and selective forces underlying these differences are only poorly understood.

Darwinian gradualism and its limits: The development of Darwin's views on the rate and pattern of evolutionary change

The major tenets of the recent hypothesis of punctuated equilibrium are explicit in Darwin's writing. His notes from 1837–1838 contain references to stasis and rapid change. In the first edition of the Origin (1859), Darwin described the importance of isolation of local varieties in the process of speciation. His views on the tempo of speciation were influenced by Hugh Falconer and also, perhaps, by Edward Suess (1831–1914). It is paradoxical that, although both topics were recorded in his unpublished notes of 1837–1838, the second was not explicitly and fully discussed until the fourth edition of the Origin (1866). While no wholly satisfactory explanation of this paradox suggests itself, it seems probable that Falconer's work on the persistence of fossil species of elephant helped Darwin to see the wider significance of the tempo of evolution for his general theory.

Evolutionary ecology and the use of natural selection in ecological theory.

Studies in ecology focus on two basic problems: the first is determining what controls the distribution and abundance of organisms, the second is describing the interrelationships of living organisms with their biotic and abiotic environment. These problems are complementary, because the size of a population depends on interactions between the individuals in that population and its biotic and abiotic environment. Similarly, describing the interrelationships of organisms helps to reveal why the relative abundance of a species varies from one area to another. Fundamentally, ecologists seek to explain where organisms occur by understanding the interactions affecting the relative abundance of plants and animals. Studies in evolutionary biology, like those in ecology, focus on two basic problems: first, describing the historical record of life, the pattern of evolutionary change; second, discovering the mechanisms affecting the evolution of species. Ecologists study processes such as competition, predation, energy flow, and nutrient availability to understand why species vary in abundance. In addition, some ecologists have argued for considering the mechanisms of organic evolution as factors that help explain ecological patterns. In an evaluation of six introductory textbooks in ecology, for example, one of the criteria Gordon Orians used was the degree of pervasiveness of the concept of natural selection.' In this review he wrote, "Perhaps the greatest challenge for contemporary ecology is the development of theories about the properties of communities on the basis of selection for their component individuals." This emphasis on uniting concepts from ecology and evolu-

Introduction to the Symposium on Tempo and Mode of Evolution from Micropaleontological Data

The concept of punctuated equilibria was introduced by Eldredge and Gould (1972) as an interpretation of the sequential occurrence of species as actually observed in the fossil record. The pattern of sudden appearance of a new species followed by little or no morphological change during the remainder of the species' existence contrasts with phyletic gradualism, the pattern of slower, more evenly distributed change which was long considered to be the principal mode of species formation (Simpson 1944). The question of which is the dominant pattern of evolutionary change has continued as an actively debated theme in much of the paleontological literature of the past decade.

Oral traditions: Whose history?

Historians rarely pause to reflect on the history and theory of our own discipline, but it is a salutary exercise, particularly when the discipline is as young as African history. Twenty years ago a majority of African peoples emerged from colonial domination and acquired their independence. In that same year their history was also symbolically liberated from domination by the activities of Europeans in Africa through the inauguration of the Journal of African History. And one year later the new African history was given what was to become one of its dominant methodologies with the publication of Jan Vansina's De la tradition Orale.' African history was to be the history of Africans, a history that had begun well before the European 'discovery' of Africa. The problem was sources. Western historiography was firmly based on written sources which could be arranged in sequence and analyzed to trace incremental changes and establish cause and effect relationships in evolutionary patterns of change. Unlike written documents which were recorded in the past and passed down unchanged into the present, oral traditions had to be remembered and retold through successive generations to reach the present. Their accuracy was thus subject to lapses in memory and falsification in the long chains of transmission from the initial report of the event in the past to the tradition told in the present. To overcome these problems Vansina established an elaborate and meticulous methodology by which traditions should be collected and transcribed, their chains of transmission traced and variants compared, and obvious biases and falsifications stripped off to produce primary documents suitable for writing history within the western genre.2 The emphasis was on method, as scores of graduate students took to the field clutching Vansina's book and attempted to observe his demanding tenets that they learn the language fluently, master the social structure, collect as many variants as possible of any given oral tradition and traditions at all levels of society, and observe subtle nuances in values and expressions, in addition to dabbling in linguistics, anthropology, and archeology. As the data came in, however, it became apparent

Oral Traditions: Whose History

Historians rarely pause to reflect on the history and theory of our own discipline, but it is a salutary exercise, particularly when the discipline is as young as African history. Twenty years ago a majority of African peoples emerged from colonial domination and acquired their independence. In that same year their history was also symbolically liberated from domination by the activities of Europeans in Africa through the inauguration of the Journal of African History. And one year later the new African history was given what was to become one of its dominant methodologies with the publication of Jan Vansina's De la tradition Orale.African history was to be the history of Africans, a history that had begun well before the European ‘discovery’ of Africa. The problem was sources. Western historiography was firmly based on written sources which could be arranged in sequence and analyzed to trace incremental changes and establish cause and effect relationships in evolutionary patterns of change. Unlike written documents which were recorded in the past and passed down unchanged into the present, oral traditions had to be remembered and retold through successive generations to reach the present. Their accuracy was thus subject to lapses in memory and falsification in the long chains of transmission from the initial report of the event in the past to the tradition told in the present. To overcome these problems Vansina established an elaborate and meticulous methodology by which traditions should be collected and transcribed, their chains of transmission traced and variants compared, and obvious biases and falsifications stripped off to produce primary documents suitable for writing history within the western genre.

The pattern of evolutionary change in bacteria.

The pattern of evolutionary change in bacteria.

The biology of the lobe-finned fishes.

Summary1. Interpretation of structural evolution in a group such as the Sarcopterygii requires consideration of a combination of all possible functions, rather than single functions.2. The Dipnoi are probably more closely related to the Crossopterygii than to other groups of fishes. The Sarcopterygii are a ‘natural’ group. Certain characters in common between the elasmobranchs and the Dipnoi or Coelacanthini seem to be the result of convergent evolution.3. Evolution of the skull, in connexion with both respiratory and feeding mechanisms, has resulted in extreme specialization in all Sarcopterygii. The crossopterygian intracranial kinesis has evolved from an earlier mobility between the skull and neck and is adapted for increasing the power of the bite and for enclosing the prey from both above and below, in addition to other factors. Adaptive radiation is seen in the feeding mechanisms of all forms. The evolution of the Amphibia proceeded through elongation of the anterior division of the skull (which is not correlated with any changes in brain morphology) and loss of the kinetic mechanism in this sequence is at least partially associated with improved buccal pumping mechanisms for lung ventilation.4. Adaptive radiation of the respiratory system in Dipnoi shows a progressive increase in the use of aerial respiration. The aquatic condition seen in Neoceratodus is probably secondary. Comparison of the three living genera shows a striking correlation between respiratory physiology and habit. There is little indication of reduction of the branchial respiratory system in known Rhipidistia, in which respiration was probably primarily aquatic. In Dipnoi and Rhipidistia, evolution of the lung allowed a partial control of the hydrostatic properties of the body. In coelacanths, aerial respiration was abandoned, except in certain secondarily freshwater forms, and the single lung is modified as an organ of hydrostatic balance. These changes are reflected in the over‐all body proportions.5. Locomotion in Sarcopterygii (except the coelacanths Laugia and Piveteauia) is adapted for contact with the substrate in relatively shallow water in most cases. Adaptive radiation of the locomotor apparatus is seen with respect to the relative roles and functions of the paired and unpaired fins, over‐all body shape, caudal fin shape, and absolute size. An important function of the pectoral fins in advanced Rhipidistia was in supporting the body in shallow water and thus aiding lung ventilation.6. Aestivation is an early feature of dipnoan biology, but was not evolved in Rhipidistia. The common faculty of urea production via the ornithine cycle and urea retention in coelacanths and dipnoans are adaptations to conditions in which the body tissues may become dehydrated (salt water and desiccation, respectively). The common pattern of nitrogen metabolism seems to have evolved during a marine phase in sarcopterygian evolution.7. There is evidence that the earliest members of all sarcopterygian lines included marine forms. However, the subsequent major radiations of Dipnoi and Rhipidistia occurred in fresh waters. The distribution of Sarcopterygii was entirely tropical. The late Palaeozoic distribution of the freshwater forms seems to offer evidence for the occurrence of Continental Drift. Coelacanths were primarily coastal fishes.8. The evolution of a major group of organisms requires a different pattern of evolutionary change than that by which adaptive radiations are produced. It evolves the structural and temporal correlation of modification in a number of different functional systems rather than the separate modification of each system without reference to other systems.9. The first tetrapods evolved in a highly seasonal swampy environment on the shores of inland lakes or rivers, in permanently moist conditions.

DNA and the Evolution of the Vertebrates

This study attempts to correlate the amounts of DNA per nucleus in the various vertebrate classes with patterns of evolutionary change proposed by Simpson and by Rendel. It is suggested that an increase in the level of DNA/nucleus occurred in the protochordate stock ancestral to the vertebrates and that this led to a major shift from the protochordate to the vertebrate pattern (Rendel's Type 3, Simpson's quantum evolution). In the actinopterygian fishes this was followed by a loss of DNA/nucleus and by the establishment of a number of phyletic lines leading to the higher teleost orders (Rendel's Type 2, Simpson's phyletic evolution). In the Choanichthyes another major increase in the level of nuclear DNA was followed, in one line, by the quantum evolutionary shift to terrestrialism. The various tetrapod classes show varying degrees of reduction in DNA nuclear content, with the highest levels being retained by the more primitive amphibians and the lowest levels being found in the highly evolved birds. The two vertebrate groups with the lowest levels of DNA/nucleus are the higher teleosts and the birds, in which the dominant pattern of evolution today appears to be Rendel's Type 1, Simpson's speciation.