The world is not inhabited by schematic patterns: Reply to the article by Z.S. Kaufman

In this reply to Z.S. Kaufman’s article Some Problems of Regressive Evolution, sedentary and parasitic modes of life are regarded as evolutionary strategies requiring morphological and functional rearrangements of organs, systems of organs, and the structure of the body as a whole that are not regressive. First of all, this applies to adaptations to sedentary life. Regress and degradation of parasitic forms take place only at the last stages of evolution, in parasites living in body cavities and tissues.     

Neutrale Mutationen und evolutionäre Fortentwicklung

Neutral mutation and evolutionary progress The process and causes of regressive evolution are still under debate. Contrary to DARWIN'S original assumption, Neo-Darwinian proponents make selection responsible for reduction. Biologically functionless structures like eye and pigmentation in cave animals deliver excellent material to study this problem. Comparison of regressive (eye, pigmentation, aggression, dorsal light reaction) and constructive traits (gustatory equipment, egg yolk content, feeding behavior) in epigean and cave fish (Astyanax fasciatus, Characidae) reveal a high variability of the regressive features in the cave forms. Contrary to this, the constructive traits are characterized by a low variability in epigean and cave fish. This difference is attributed to the lack of selection on regressive structures. The existence of an intermediate cave population between epigean and true cave fish of A. fasciatus makes possible the study of evolutionary rates. It is shown that the regressive traits do not evolve more quickly than the constructive ones do. On the contrary, constructive traits like egg yolk content are even more rapid because they are of great biological value in the cave biotope. Especially energy economy is claimed by Neo-Darwinists to play a decisive role as a selective force. Comparison of the development of epi- and hypogean larvae of A. fasciatus shows that the formation of a smaller and less differentiated eye in the cave specimens has no effect on body growth. Furthermore, even behavioral traits like aggressiveness, schooling, dorsal light reaction, or negative phototaxis, which all are not performed in darkness by the epigean ancestor, become genetically reduced in the cave fish. The principles of regressive evolution, loss of selection and increase in variability, play a central role in evolution in general. When biota with empty niches are colonized, stabilizing selection relaxes from the special adaptations to the niche inhabited before by the invading species. Variability may arise in these and is permitted as long as fitness is guaranteed. Such processes characterize adaptive radiation. Examples are given by the species flocks on isolated islands or in chemically abnormal lakes like those of the East African Rift Valley. Only secondarily, on the basis of the arisen variability, does directional selection promote the newly developing species into different niches. The loss of stabilizing selection is an important factor for the evolutionary process to be open for evolutionary progress.     

The evolution of plant-insect mutualisms

Mutualisms (cooperative interactions between species) have had a central role in the generation and maintenance of life on earth. Insects and plants are involved in diverse forms of mutualism. Here we review evolutionary features of three prominent insect-plant mutualisms: pollination, protection and seed dispersal. We focus on addressing five central phenomena: evolutionary origins and maintenance of mutualism; the evolution of mutualistic traits; the evolution of specialization and generalization; coevolutionary processes; and the existence of cheating. Several features uniting very diverse insect-plant mutualisms are identified and their evolutionary implications are discussed: the involvement of one mobile and one sedentary partner; natural selection on plant rewards; the existence of a continuum from specialization to generalization; and the ubiquity of cheating, particularly on the part of insects. Plant-insect mutualisms have apparently both arisen and been lost repeatedly. Many adaptive hypotheses have been proposed to explain these transitions, and it is unlikely that any one of them dominates across interactions differing so widely in natural history. Evolutionary theory has a potentially important, but as yet largely unfilled, role to play in explaining the origins, maintenance, breakdown and evolution of insect-plant mutualisms.     

Regressive evolution of an eye pigment gene in independently evolved eyeless subterranean diving beetles

Regressive evolution, the reduction or total loss of non-functional characters, is a fairly common evolutionary phenomenon in subterranean taxa. However, the genetic basis of regressive evolution is not well understood. Here we investigate the molecular evolution of the eye pigment gene cinnabar in several independently evolved lineages of subterranean water beetles using maximum likelihood analyses. We found that in eyeless lineages cinnabar has an increased rate of sequence evolution, as well as mutations leading to frame shifts and stop codons, indicative of pseudogenes. These results are consistent with the hypothesis that regressive evolution of eyes proceeds by random mutations, in the absence of selection, that ultimately lead to the loss of gene function in protein-coding genes specific to the eye pathway.     

Inbreeding shapes the evolution of marine invertebrates

Inbreeding is a potent evolutionary force shaping the distribution of genetic variation within and among populations of plants and animals. Yet, our understanding of the forces shaping the expression and evolution of nonrandom mating in general, and inbreeding in particular, remains remarkably incomplete. Most research on plant mating systems focuses on self-fertilization and its consequences for automatic selection, inbreeding depression, purging, and reproductive assurance, whereas studies of animal mating systems have often assumed that inbreeding is rare, and that natural selection favors traits that promote outbreeding. Given that many sessile and sedentary marine invertebrates and marine macroalgae share key life history features with seed plants (e.g., low mobility, modular construction, and the release of gametes into the environment), their mating systems may be similar. Here, we show that published estimates of inbreeding coefficients (F_IS) for sessile and sedentary marine organisms are similar and at least as high as noted in terrestrial seed plants. We also found that variation in F_IS within invertebrates is related to the potential to self-fertilize, disperse, and choose mates. The similarity of F_IS for these organismal groups suggests that inbreeding could play a larger role in the evolution of sessile and sedentary marine organisms than is currently recognized. Specifically, associations between traits of marine invertebrates and F_IS suggest that inbreeding could drive evolutionary transitions between hermaphroditism and separate sexes, direct development and multiphasic life cycles, and external and internal fertilization.     

轮藻和陆地植物系统发育及其进化

Charophytic algae and land plants together make up a monophyletic group, streptophytes, which represents one of the main lineages of multicellular eukaryotes and has contributed greatly to the change of the environment on earth in the Phanerozoic Eon. Significant progress has been made to understand phylogenetic relationships among members of this group by phylogenetic studies of morphological and molecular data over the last twenty-five years. Mesostigma viride is now regarded as among the earliest diverging unicellular organisms in streptophytes. Characeae are the sister group to land plants. Liverworts represent the first diverging lineage of land plants. Hornworts and lycophytes are extant representatives of bryophytes and vascular plants, respectively, when early land plants changed from gametophyte to sporophyte as the dominant generation in the life cycle. Equisetum, Psilotaceae, and ferns constitute the monophyletic group of monilophytes, which are sister to seed plants. Gnetales are related to conifers, not to angiosperms as previously thought. Amborella, Nymphaeales, Hydatellaceae, Illiciales, Trimeniaceae, and Austrobaileya represent the earliest diverging lineages of extant angiosperms. These phylogenetic results, together with recent progress on elucidating genetic and developmental aspects of the plant life cycle, multicellularity, and gravitropism, will facilitate evolutionary developmental studies of these key traits, which will help us to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

Evolution of Primate Social Systems

We review evolutionary processes and mechanisms that gave rise to the diversity of primate social systems. We define social organization, social structure and mating system as distinct components of a social system. For each component, we summarize levels and patterns of variation among primates and discuss evolutionary determinants of this variation. We conclude that conclusive explanations for a solitary life and pair-living are still lacking. We then focus on interactions among the 3 components in order to identify main targets of selection and potential constraints for social evolution. Social organization and mating system are more closely linked to each other than either one is to social structure. Further, we conclude that it is important to seek a priori measures for the effects of presumed selective factors and that the genetic contribution to social systems is still poorly examined. Finally, we examine the role of primate socio-ecology in current evolutionary biology and conclude that primates are not prominently represented because the main questions asked in behavioral ecology are often irrelevant for primate behavior. For the future, we see a rapprochement of these areas as the role of disease and life-history theory are integrated more fully into primate socio-ecology.     

Methodological and contextual factors in the Dawkins/Gould dispute over evolutionary progress

Biologists Richard Dawkins and Stephen Jay Gould have recently extended their decades-old disagreements about evolution to the issue of the nature and reality of evolutionary progress. According to Gould, ‘progress’ is a noxious notion that deserves to be expunged from evolutionary biology. In Dawkins' view, on the other hand, progress is one of the most important, pervasive and inevitable aspects of evolution. Simple appeals to ‘the evidence’ are clearly insufficient to resolve this disagreement, since it is precisely the interpretation of the evidence that is in dispute. Scientific controversies in general, and the Dawkins/Gould dispute over evolutionary progress in particular, are worth examining in some detail because doing so sheds light on the interconnected roles of methodological and contextual factors in the formation, articulation and defense of scientific claims. My aim in this paper is to clarify the structure of the Dawkins/Gould dispute by analyzing it in terms of a tri-level model of scientific controversies, involving ‘top-level’ substantive disagreements, ‘middle-level’ methodological differences, and ‘bottom-level’ differences in historical and social factors. This simple three-tiered model is sufficiently abstract to have more general applicability to other scientific controversies.     

Anatomical diversity and regressive evolution in trichomanoid filmy ferns (Hymenophyllaceae): a phylogenetic approach

To infer the anatomical evolution of the Hymenophyllaceae (filmy ferns) and to test previously suggested scenarios of regressive evolution, we performed an exhaustive investigation of stem anatomy in the most variable lineage of the family, the trichomanoids, using a representative sampling of 50 species. The evolution of qualitative and quantitative anatomical characters and possibly related growth-forms was analyzed using a maximum likelihood approach. Potential correlations between selected characters were then statistically tested using a phylogenetic comparative method. Our investigations support the anatomical homogeneity of this family at the generic and sub-generic levels. Reduced and sub-collateral/collateral steles likely derived from an ancestral massive protostele, and sub-collateral/collateral types appear to be related to stem thickness reduction and root apparatus regression. These results corroborate the hypothesis of regressive evolution in the lineage, in terms of morphology as well as anatomy. In addition, a heterogeneous cortex, which is derived in the lineage, appears to be related to a colonial strategy and likely to a climbing phenotype. The evolutionary hypotheses proposed in this study lay the ground for further evolutionary analyses that take into account trichomanoid habitats and accurate ecological preferences.     

The evolutionary expansion of the Sporozoa

The sporozoans comprise a coherent group of protozoans, with characteristic and complex life cycles, containing 4–5000 species parasitic in invertebrates, particularly annelids and arthropods, and vertebrates. The group is a very successful one but neither its origins nor evolution are well understood. Considerations of traditional life cycles combined with newer molecular methodologies have thrown some light on the evolutionary expansions of the main groups of sporozoans, the gregarines, coccidia, haemosporidians and piroplasms. The sporozoans of economic importance such as the coccidia, malaria parasites and piroplasms have received most attention but the data obtained have also thrown new light on the possible evolution of less well studied groups and it is concluded that conclusions based on simple comparisons of life cycles will have to be modified. It is also clear that humans have played a major part in affecting the distribution and present abundance of many sporozoans of economic significance and probably also those of less importance, and that the rates of evolutionary expansion are much more rapid than previously thought.     

The origin and evolution of carpels and fruits from an evo-devo perspective

The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and stamens.Therefore,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary bi...     

The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species

The incredible development of comparative genomics during the last decade has required a correct use of the concept of homology that was previously utilized only by evolutionary biologists. Unhappily, this concept has been often misunderstood and thus misused when exploited outside its evolutionary context. This review brings back to the correct definition of homology and explains how this definition has been progressively refined in order to adapt it to the various new kinds of analysis of gene properties and of their products that appear with the progress of comparative genomics. Then, we illustrate the power and the proficiency of such a concept when using the available genomics data in order to study the evolution of individual genes, of entire genomes and of species, respectively. After explaining how we detect homologues by an exhaustive comparison of a hundred of complete proteomes, we describe three main lines of research we have developed in the recent years. The first one exploits synteny and gene context data to better understand the mechanisms of genome evolution in prokaryotes. The second one is based on phylogenomics approaches to reconstruct the tree of life. The last one is devoted to reminding that protein homology is often limited to structural segments (SOH=segment of homology or module). Detecting and numbering modules allows tracing back protein history by identifying the events of gene duplication and gene fusion. We insist that one of the main present difficulties in such studies is a lack of a reliable method to identify genuine orthologues. Finally, we show how these homology studies are helpful to annotate genes and genomes and to study the complexity of the relationships between sequence and function of a gene.     

The Importance of Population Growth and Regulation in Human Life History Evolution

Explaining the evolution of human life history traits remains an important challenge for evolutionary anthropologists. Progress is hindered by a poor appreciation of how demographic factors affect the action of natural selection. I review life history theory showing that the quantity maximized by selection depends on whether and how population growth is regulated. I show that the common use of R, a strategy’s expected lifetime number of offspring, as a fitness maximand is only appropriate under a strict set of conditions, which are apparently unappreciated by anthropologists. To concretely show how demography-free life history theory can lead to errors, I reanalyze an influential model of human life history evolution, which investigated the coevolution of a long lifespan and late age of maturity. I show that the model’s conclusions do not hold under simple changes to the implicitly assumed mechanism of density dependence, even when stated assumptions remain unchanged. This analysis suggests that progress in human life history theory requires better understanding of the demography of our ancestors.     

Ecosystem evolution: main stages and potential mechanisms

Major differences between the Western and "Russian" (Zavarzin, 1995) paradigms in ecology and evolutionary biology are described. The "Russian" paradigm suggests that there exist two, rather than one, quite independent lineages--species evolution and ecosystem evolution. This is based on the idea that life may exist just as a nutrient cycle. The main terms and concepts of the "Russian" paradigm are defined more exactly. An attempt is made to develop this paradigm so that it would be possible to describe not only phenomenology, but also mechanisms of ecosystem evolution. To simplify evolutionary phenomena logically, it is suggested to use the concept of conditionally complete causal explanation (Lekevicius, 1984; 1985), i.e. deduce evolutionary mechanisms from major principles of functioning. This methodology is adapted to model the main stages of the evolution of nutrient cycles (3.8-2.0 bln. y.a.) and the appearance and evolution of biophagy (1.7-0 bln. y.a.). Based on a multitude of examples, it is shown that these are functional constraints that are the forces directing evolution; those constraints emerge during the interaction of organisms and while the latter interact with the abiotic environment. Since the structure of an ecosystem is non-rigid, each species is able to accumulate features useful to both an ecosystem and itself. Those are individuals that die and reproduce, whereas all structures, from macromolecules to ecosystems, evolve.     

Rotifers: excellent subjects for the study of macro- and microevolutionary change

Rotifers, both as individuals and as a phylogenetic group, are particularly worthwhile subjects for the study of evolution. Over the past decade molecular and experimental work on rotifers has facilitated major progress in three lines of evolutionary research. First, we continue to reveal the phylogentic relationships within the taxon Rotifera and its placement within the tree of life. Second, we have gained a better understanding of how macroevolutionary transitions occur and how evolutionary strategies can be maintained over millions of years. In the case of rotifers, we are challenged to explain the evolution of obligate asexuality (in the bdelloids) as mode of reproduction and how speciation occurs in the absence of sex. Recent research with bdelloid rotifers has identified novel mechanisms such as horizontal gene transfer and resistance to radiation as factors potentially affecting macroevolutionary change. Third, we are finding that microevolutionary change can be sufficiently rapid to interact with ecological dynamics. Rotifers can be easily cultured, reproduce quickly, and occur at high levels of clonal, genetic diversity in nature. These features make them excellent eukaryotic model systems for the study of eco-evolutionary dynamics.     

Effects of Life Histories on Genome Size Variation in Squamata

Genome size changes significantly among taxonomic levels, and this variation is often related to the patterns shaped by the phylogeny, life histories and ecological factors. However, there are mixed evidences on the main factors affecting molecular evolution in animals.In this study, we used phylogenetic comparative analysis to investigate the evolutionary rate of genome size and the relationships between genome size and life histories(i.e.,hatchling mass, clutch size, clutches per year, age at sexual maturity, lifespan and body mass) among 199 squamata species. Our results showed that the evolutionary rate of genome size in Lacertilia was significantly faster than Serpentes. Moreover, we also found that larger species showed larger hatchling mass, more clutches per year and clutch size and longer lifespan. However, genome size was negatively associated with clutch size and clutches per year, but not associated with body mass we looked at.The findings suggest that larger species do not possess the evolution of large genomes in squamata.     

Evolution of the cancer genome

Human tumors result from an evolutionary process operating on somatic cells within tissues, whereby natural selection operates on the phenotypic variability generated by the accumulation of genetic, genomic and epigenetic alterations. This somatic evolution leads to adaptations such as increased proliferative, angiogenic, and invasive phenotypes. In this review we outline how cancer genomes are beginning to be investigated from an evolutionary perspective. We describe recent progress in the cataloging of somatic genetic and genomic alterations, and investigate the contributions of germline as well as epigenetic factors to cancer genome evolution. Finally, we outline the challenges facing researchers who investigate the processes driving the evolution of the cancer genome.     

Life history evolution and comparative developmental biology of echinoderms

Evolutionary biologists studying life history variation have used echinoderms in experimental, laboratory, and field studies of life history evolution. This focus on echinoderms grew originally from the tradition of comparative embryology, in which echinoderms were central. The tools for obtaining and manipulating echinoderm gametes and larvae were taken directly from comparative embryological research. In addition, the comparative embryologists employed a diverse array of echinoderms, not a few model species, and this diversity has led to a broad understanding of the development, function, and evolution of echinoderm larvae. As a result, this branch of life history evolution has deep roots in comparative developmental biology of echinoderms. Here two main aspects of this relationship are reviewed. The first is a broad range of studies of fertilization biology, dispersal, population genetics, functional morphology, and asexual reproduction in which developmental biologists might take a keen interest because of the historical origins of this research in echinoderm comparative embryology. The second is a similarly broad variety of topics in life history research in which evolutionary biologists require techniques or data from developmental biology in order to make progress on understanding patterns of life history variation among echinoderm species and higher taxa. Both sets of topics provide opportunities for interaction and collaboration.     

The Geography of Evolution and the Evolution of Geography

Insights into the geography of life have played a fundamental role in motivating major developments in evolutionary biology. The focus here is on outlining some of these major developments, specifically in the context of paleontology, by emphasizing the significance of geographic isolation and allopatric speciation, punctuated equilibria, and the Turnover Pulse Hypothesis to evolutionary theory. One of the major debates in evolution concerns the relative contributions of abiotic and biotic factors to macroevolution, and each one of these developments increasingly suggested that it was climatic and geologic factors, rather than competition, that played the primary role in motivating macroevolution. New technical developments, including in the area of Geographic Information Systems, allow continued detailed testing of the relative roles that biotic as opposed to abiotic factors play in causing evolution, and some of the work in this area will also be described.