The main postulate of the vertical evolution theory

In the series of previous publications by the author (2000, 2002, 2005), a genetic model explaining the phenomenon of evolutionary progress was presented. In the present paper, this model is described in general terms. The model is based on views on regular changes of ecological potential of organisms on a macroevolutionary time scale. According to these views, macroevolution has its own pattern, which cannot be seen in the microevolutionary process. Hence, the statement of the synthetic theory of evolution that "macroevolution proceeds via microevolution" is incorrect.     

Unifying macroecology and macroevolution to answer fundamental questions about biodiversity

The study of biodiversity started as a single unified field that spanned both ecology and evolution and both macro and micro phenomena. But over the 20th century, major trends drove ecology and evolution apart and pushed an emphasis towards the micro perspective in both disciplines. Macroecology and macroevolution re‐emerged as self‐consciously distinct fields in the 1970s and 1980s, but they remain largely separated from each other. Here, we argue that despite the challenges, it is worth working to combine macroecology and macroevolution. We present 25 fundamental questions about biodiversity that are answerable only with a mixture of the views and tools of both macroecology and macroevolution.     

R. Goldschmidt and J. Huxley: creative parallelisms

The comparative analysis of scientific heritage of Richard Goldschmidt and Julian Huxley shows convincingly the resemblance of these two scientists' views over the core problems of evolutionary theory, genetics and development biology. They both contributed to developing a triad "genetics--development--evolution". The problem of a relative growth of animals was the central point in both Goldschmidt's and Huxley's works. Huxley developed a formula of the allometric growth (law of constant differential growth) while Goldschmidt was the first to draw up the broad interpretation of the consequences of that phenomenon. Both scientists belonged to initiators of development genetics and used the "non-morganian" genetics in their efforts of solving problems of macroevolution. Goldschmidt tended toward an idea of an important role of macromutation in the process of macroevolution, though Huxley adhered to more moderate views. But at the same time the concept of preadaptive mutations proposed by Huxley was close to Goldschmidt's idea of macromutants. It is shown that both scientists analyzed profoundly the changes in early stages of embryogenesis in respect to macroevolution. It is not likely to be reasonable to oppose firmly Goldschmidt's saltationism to the evolutionary synthesis of Huxley. They developed the larger biological problems in a similar way, and undoubtedly their works in the field helped to enrich the development of the views over genetics and evolution. The open-minded analysis of Goldschmidt's and Huxley's concepts leads to creating modern and up-to-date views over the theory of evolution where seemingly incompatible things go together rather well and supplement each other. Evo-Devo rediscovered Goldshmidt's Biology and Huxley's Synthesis.     

The concept of macroevolution in view of modern data

Macroevolution, or evolution of superspecies taxa is the process of transformation of “organismal” life flows on the Earth during its geological history. In the present study, this process is analyzed with using the system and evolutionarily?ecological approaches. Based on modern paleontological, evolutionary biological, molecular, and genetic data, mostly on vertebrates and hominins, the major factors and patterns of macroevolution and also the role of macroevolution in the biosphere evolution are discussed. The fundamental bases of the concept of macroevolution, the problems of methodology and methods of the study of organismal evolution are considered. It is shown that the processes at the macroevolutionary level agree with the epigenetic theory of evolution.     

Integrating selection,niche, and diversification into a hierarchical conceptual framework

Recently, new phylogenetic comparative methods have been proposed to test for the association of biological traits with diversification patterns, with species ecological “niche” being one of the most studied traits. In general, these methods implicitly assume natural selection acting at the species level, thus implying the mechanism of species selection. However, natural selection acting at the organismal level could also influence diversification patterns (i.e., effect macroevolution). Owing to our scarce knowledge on multi-level selection regarding niche as a trait, we propose a conceptual model to discuss and guide the test between species selection and effect macroevolution within a hierarchical framework. We first assume niche as an organismal as well as a species’ trait that interacts with the environment and results in species-level differential fitness. Then, we argue that niche heritability, a requirement for natural selection, can be assessed by its phylogenetic signal. Finally, we propose several predictions that can be tested in the future by disentangling both types of evolutionary processes (species selection or effect macroevolution). Our framework can have important implications for guiding analyses that aim to understand the hierarchical perspective of evolution.     

Examining the Interaction of Acceptance and Understanding: How Does the Relationship Change with a Focus on Macroevolution?

The goal of this research was to illuminate the relationship between students’ acceptance and understanding of macroevolution. Our research questions were: (1) Is there a relationship between knowledge of macroevolution and acceptance of the theory of evolution?; (2) Is there a relationship between the amount of college level biology course work and acceptance of evolutionary theory and knowledge of macroevolution?; and (3) Can college student acceptance of the theory of evolution and knowledge of macroevolution change over the course of a semester? The research participants included 667 students from a first-semester biology course and 74 students from the evolutionary biology course. Data were collected using both the MATE (a measure of the acceptance of evolutionary theory) and the MUM (a measure of understanding of macroevolution). Pre-instruction data were obtained for the introductory biology course, and pre- and post-data were obtained for the evolutionary biology course. Analysis revealed acceptance of evolution (as measured by the MATE) was correlated to understanding of macroevolution, and the number of biology courses was significantly correlated to acceptance and knowledge of macroevolution. Finally, there was a statistically significant change in students’ understanding of macroevolution and acceptance of evolution after the one-semester evolutionary biology course. Significance of these findings is discussed.     

Chromosome Rearrangements Recovered following Transformation of Neurospora Crassa

Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within and between populations, the predictions of the changes of the variation are qualitatively different in the long term. In this paper a more general mutation model, called the regression mutation model, is proposed to bridge the gap of the two models. The model regards the regression coefficient, γ, of the effect of an allele after mutation on the effect of the allele before mutation as a parameter. When γ = 1 or 0, the model becomes the random walk model or the house-of-cards model, respectively. The additive genetic variances within and between populations are formulated for this mutation model, and some insights are gained by looking at the changes of the genetic variances as γ changes. The effects of γ on the statistical test of selection for quantitative characters during macroevolution are also discussed. The results suggest that the random walk mutation model should not be interpreted as a null hypothesis of neutrality for testing against alternative hypotheses of selection during macroevolution because it can potentially allocate too much variation for the change of population means under neutrality.     

Detecting the macroevolutionary signal of species interactions

Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad‐scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, although the evidence for species interactions shaping macroevolution is strong, further work using integrative and model‐based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space.     

Macroevolution is more than repeated rounds of microevolution

SUMMARY Arguments over macroevolution versus microevolution have waxed and waned through most of the twentieth century. Initially, paleontologists and other evolutionary biologists advanced a variety of non-Darwinian evolutionary processes as explanations for patterns found in the fossil record, emphasizing macroevolution as a source of morphologic novelty. Later, paleontologists, from Simpson to Gould, Stanley, and others, accepted the primacy of natural selection but argued that rapid speciation produced a discontinuity between micro- and macroevolution. This second phase emphasizes the sorting of innovations between species. Other discontinuities appear in the persistence of trends (differential success of species within clades), including species sorting, in the differential success between clades and in the origination and establishment of evolutionary novelties. These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns. Recent developments in comparative developmental biology suggest a need to reconsider the possibility that some macroevolutionary discontinuites may be associated with the origination of evolutionary innovation. The attractiveness of macroevolution reflects the exhaustive documentation of large-scale patterns which reveal a richness to evolution unexplained by microevolution. If the goal of evolutionary biology is to understand the history of life, rather than simply document experimental analysis of evolution, studies from paleontology, phylogenetics, developmental biology, and other fields demand the deeper view provided by macroevolution.     

Macroevolution of plasmids: a model for plasmid speciation.

A new evolutionary model for diversification in plasmid incompatibility groups (plasmid speciation) is suggested. The model is based on the formation of plasmid cointegrates from two compatible plasmids. The existence of plasmid cointegrates is well known, however, their potential key role in plasmid macroevolution has not yet been recognized. In a hypothesis presented here, one of the rep genes is supposed to be relaxed from selection in plasmid cointegrates and thus becomes free to accumulate mutations. These mutations can lead to a change in incompatibility specificity. Evidence supporting this hypothesis comes from the common occurrence of multi-replicon plasmids in nature as well as from experimental studies on plasmid cointegrate formation. A more speculative extension of this model hypothesizes an evolutionary scenario for origin of the eubacterial single-replicon genome and the eukaryotic multi-replicon genome, as well as the place of plasmids and viruses in this picture.     

Catfishes as a case study for discussions on general evolution: the importance of functional uncouplings in morphological macroevolution

Many evolutionary biologists have stressed that functional uncouplings play an important role in morphological macroevolution, as they facilitate diversification and speciation by increasing the number of degrees of freedom and allowing more mechanical solutions for functional problems. In the present paper, the importance of functional uncouplings in the evolution of six major catfish structural complexes is briefly discussed, namely those constituted by the mandibular barbels and associated structures, the pectoral girdle complex, the elastic spring apparatus, the suspensorium, the palatine-maxillary system, and the adductor mandibulae complex. The overview of these major structural complexes indicates that functional uncouplings did effectively play an essential role on catfish evolutionary history. The study of this cosmopolitan and particularly diverse group representing about one-third of all freshwater fishes thus supports the importance of functional uncouplings in morphological macroevolution.     

The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?

It is a basis of darwinian evolution that the microevolutionary mechanisms that can be studied in the present are sufficient to account for macroevolution. However, this idea needs to be tested explicitly, as highlighted here by the example of the superceding of dinosaurs and pterosaurs by birds and placental mammals that occurred near the Cretaceous/Tertiary boundary approximately 65 million years ago. A major problem for testing the sufficiency of microevolutionary processes is that independent ideas (such as the existence of an extraterrestrial impact, and the extinction of dinosaurs) were linked without the evidence for each idea being evaluated separately. Here, we suggest and discuss five testable models for the times and divergences of modern mammals and birds. Determination of the model that best represents these events will enable the role of microevolutionary mechanisms to be evaluated. The question of the sufficiency of microevolutionary processes for macroevolution is solvable, and available evidence supports an important role for biological processes in the initial decline of dinosaurs and pterosaurs.     

Modeling the age distribution of gene duplications in vertebrate genome using mixture density

Gene duplication is a fundamental source of genetic novelty in vertebrate evolution. In this study, we hypothesized that both continuous small-scale and discrete large-scale duplication play crucial roles in vertebrate genome. On the basis of the hypothesis, we developed mixture density to model the age distribution of gene duplications. The results of formal statistical inference suggest that the contribution of both duplication modes can be confirmed by the model, and one or two successive rounds of large-scale duplication are placed at the early origin of vertebrates. The half life of a duplicate becomes much longer in the long run than in the short run, which implies its functional evolution from redundancy to conservation. In addition, the model reveals disparate impact of the duplication modes, which appears to be correlated with macroevolution.     

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges,Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.     

What is macroevolution?

Definitions of macroevolution fall into three categories: (1) evolution of taxa of supraspecific rank; (2) evolution on the grand time-scale; and (3) evolution that is guided by sorting of interspecific variation (as opposed to sorting of intraspecific variation in microevolution). Here, it is argued that only definition 3 allows for a consistent separation of macroevolution and microevolution. Using this definition, speciation has both microevolutionary and macroevolutionary aspects: the process of morphological transformation is microevolutionary, but the variation among species that it produces is macroevolutionary, as is the rate at which speciation occurs. Selective agents may have differential effects on intraspecific and interspecific variation, with three possible situations: effect at one level only, effect at both levels with the same polarity but potentially different intensity, and effects that oppose between levels. Whereas the impact of all selective agents is direct in macroevolution, microevolution requires intraspecific competition as a mediator between selective agents and evolutionary responses. This mediating role of intraspecific competition occurs in the presence of sexual reproduction and has therefore no analogue at the macroevolutionary level where species are the evolutionary units. Competition between species manifests both on the microevolutionary and macroevolutionary level, but with different effects. In microevolution, interspecific competition spurs evolutionary divergence, whereas it is a potential driver of extinction at the macroevolutionary level. Recasting the Red Queen hypothesis in a macroevolutionary framework suggests that the effects of interspecific competition result in a positive correlation between origination and extinction rates, confirming empirical observations herein referred to as Stanley's rule.     

再谈“有希望的怪物”

1933年,遗传学家Goldschmidt提出＂有希望的怪物＂假说,以解释宏演化（macroevolution）中有别于＂达尔文式＂的演化机制。近年来,有关内共生和基因倍增等进展表明,＂有希望的怪物＂在自然界中其实非常普遍。这虽然与＂现代综合进化论＂的观点不甚一致,但却能在经典达尔文主义找到契合点：作为自然选择的补充,＂有希望的怪物＂可以为宏演化提供一种潜在的候选机制。这种建立在多元论基础上的进化观是达尔文留给后人最宝贵的遗产。     

The rate and pattern of cladogenesis in microbes

Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.     

Taxic evolutionary paleoecology and the ecological context of macroevolutionary change

Summary A traditional focus of evolutionary paleoecology has been the reconstruction of the selective forces that have affected evolving lineages through time. If the history of those lineages is dominated by stasis and punctuation, however, this is at best an inadequate and at worst a misdirected research strategy for macroevolution, because long-term stasis implies that environmental factors may have less influence on evolving lineages than previously believed. Such reasoning has led some proponents of punctuated views to reject ecological interactions as predominant or even significant forces in evolution. This is not a necessary conclusion. It is possible to accept the empirical predominance of stasis in evolution and at the same time the importance of ecology in affecting the course of evolutionary trends within lineages. If stasis prevails, ecology matters in the evolution of lineages if either (1) stabilizing selection is an important cause of stasis or (2) ecological interactions play an important role in controlling the speciation process. Viewing allopatric speciation explicitly as a three-stage process (consisting of formation, persistence and differentiation of isolated populations) clarifies testing of the role of ecology in speciation and may redirect clade-specific evolutionary paleoecology towards more enlightening interaction with other areas of macroevolutionary study.