Detection of punctuated equilibrium from molecular phylogenies

Abstract The theory of ‘punctuated equilibrium’ hypothesises that most morphological change in species takes place in rapid bursts triggered by speciation. Eldregde and Gould postulated the theory in 1972, as an alternative to the idea that morphological change slowly accumulates in the course of time, a then common belief they dubbed ‘phyletic gradualism’. Ever since its introduction the theory of punctuated equilibrium has been the subject of speculation rather than empirical validation. Here I present a method to detect punctuated evolution without reference to fossil data, based on the phenotypes of extant species and on their relatedness as revealed by molecular phylogeny. The method involves a general mathematical model describing morphological differentiation of two species over time. The two parameters in the model, the rates of punctual (cladogenetic) and gradual (anagenetic) change, are estimated from plots of morphological diversification against time since divergence of extant species.     

Positive correlation between diversification rates and phenotypic evolvability can mimic punctuated equilibrium on molecular phylogenies

The hypothesis of punctuated equilibrium proposes that most phenotypic evolution occurs in rapid bursts associated with speciation events. Several methods have been developed that can infer punctuated equilibrium from molecular phylogenies in the absence of paleontological data. These methods essentially test whether the variance in phenotypes among extant species is better explained by evolutionary time since common ancestry or by the number of estimated speciation events separating taxa. However, apparent "punctuational" trait change can be recovered on molecular phylogenies if the rate of phenotypic evolution is correlated with the rate of speciation. Strong support for punctuational models can arise even if the underlying mode of trait evolution is strictly gradual, so long as rates of speciation and trait evolution covary across the branches of phylogenetic trees, and provided that lineages vary in their rate of speciation. Species selection for accelerated rates of ecological or phenotypic divergence can potentially lead to the perception that most trait divergence occurs in association with speciation events.     

Speciation and Bursts of Evolution

A longstanding debate in evolutionary biology concerns whether species diverge gradually through time or by rapid punctuational bursts at the time of speciation. The theory of punctuated equilibrium states that evolutionary change is characterised by short periods of rapid evolution followed by longer periods of stasis in which no change occurs. Despite years of work seeking evidence for punctuational change in the fossil record, the theory remains contentious. Further there is little consensus as to the size of the contribution of punctuational changes to overall evolutionary divergence. Here we review recent developments which show that punctuational evolution is common and widespread in gene sequence data.     

Species,speciation and human evolution

Human evolution is considered from the perspective of the recognition concept of species, which views species as an epiphenomenon of shared fertilisation systems in sexually reproducing organisms. It is argued that this concept predicts the controversial pattern of punctuated equilibrium, and offers an understanding of the hominid fossil evidence in line with that pattern. Changes in the nature of the fertilization system in the human lineage over time are discussed in relation to the pattern of morphological continuity between proposed species.     

A game-theoretic model for punctuated equilibrium: species invasion and stasis through coevolution

A general theory of coevolution is developed that combines the ecological effects of species' densities with the evolutionary effects of changing phenotypes. Our approach also treats the evolutionary changes between coevolving species with discreet traits after the appearance of a new species. We apply this approach to habitat selection models where new species first emerge through competitive selection in an isolated habitat. This successful invasion is quickly followed by evolutionary changes in behavior when this species discovers the other habitat, leading to punctuated equilibrium as the final outcome.     

Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium

The olive shells of the genus Amalda comprises readily recognized species of marine neogastropod mollusks found around the world. The New Zealand Amalda fauna has particular notoriety as providing one of the best demonstrations of evolutionary morphological stasis, a prerequisite for punctuated equilibrium theory. An excellent fossil record includes representation of three extant endemic Amalda species used to explore patterns of form change. However, the phylogenetic relationship of the New Zealand Amalda species and the timing of their lineage splitting have not been studied, even though these would provide valuable evidence to test predictions of punctuated equilibrium. Here, we use entire mitogenome and long nuclear rRNA gene cassette data from 11 Amalda species, selected from New Zealand and around the world in light of high rates of endemicity among extant and fossil Amalda. Our inferred phylogenies do not refute the hypothesis that New Zealand Amalda are a natural monophyletic group and therefore an appropriate example of morphological stasis. Furthermore, estimates of the timing of cladogenesis from the molecular data for the New Zealand group are compatible with the fossil record for extant species and consistent with expectations of punctuated equilibrium.     

Punctuated equilibrium and species selection: what does it mean for one theory to suggest another?

McMullin (In: Cohen et al. (eds.) Essays in memory of Imre Lakatos, 1976, In: Leplin (ed.) Scientific realism, 1984) argues that fertility is a theoretical virtue. He thinks of a fertile theory as one whose central metaphors suggest new directions for theoretical development, where those new developments help solve previous problems and anomalies. Nolan (Br J Philos Sci 50:265–282, 1999) argues that fertility in this sense is not a distinctive theoretical virtue in its own right. Rather, Nolan thinks that fertility is reducible to predictive novelty. This article explores the relationship between punctuated equilibrium (PE) and species selection in the light of this philosophical debate about the nature of theoretical fertility, or suggestiveness. I argue that (1) PE suggests, but does not imply, that species selection is a mechanism of evolution; (2) the suggestiveness in this case is not reducible to predictive novelty; (3) species selection is not a metaphorical extension of PE; and (4) getting clear about the way in which PE suggests species selection can help solve a puzzle about punctuated equilibrium. The puzzle is that Eldredge and Gould’s initial presentation of PE seems to presuppose a minimalist or extrapolationist view of macroevolution, even though many scientists take PE to challenge that minimalist view.     

Punctuated genome size evolution in Liliaceae

Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. > or = 35 pg) are phylogenetically restricted to a few families and include Liliaceae - with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes. To gain insights into when and where genome size expansion took place during the evolution of Liliaceae and the mode and tempo of this change, data for 78 species were superimposed onto a phylogenetic tree and analysed. Results suggest that genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently rather than early in the evolution of the family. We consider that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.     

A new approach to modeling the diversity dynamics of Phanerozoic marine biota

Modeling of fossil diversity dynamics is usually done with the help of the models borrowed from the population dynamics theory. However there are principal differences between organisms and taxa, reproduction and divergence, mortality and extinction that make this approach doubtful. Another model is presented here, in which absolute origination rate does not depend on diversity, the ability of new genera to sustain unpredictable environmental changes increases three times abruptly at Cambrian/Ordovician, Permian/Triassic and Cretaceous/Tertiary boundaries. In this model the diversity increases due to accumulation of long-lived genera. The computer simulation showed that the model agrees with empirical data by 15 major criteria. The laws of community evolution apparently can explain the general pattern of punctuated equilibrium in the evolution of marine biota.     

Dimension reduction projection and our perception of evolution

The evolution of a species can be viewed as a trajectory in multidimensional space. What we perceive is only a low dimensional projection from the total dimensionality necessary to fully describe a species. Motivated by the phenomenon of punctuated equilibria, it is shown that there are projections of gradualistic evolution which will have a punctuated character. However, whether our eyes and minds would choose such a projection of the total phenotype is not resolved.     

Punctualism, non-adaptationism, neutralism and evolution

In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.     

Statistical limitations on molecular evolution

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with "RNA world" hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of "punctuated equilibrium".     

Patterns of evolution among lower Jurassic crinoids

The crinoid families Isocrinidae and Pentacrinitidae are well represented in the British Lower Jurassic, allowing a detailed investigation of their evolution at this time. The pseudopelagic pentacrinitids diverged from the benthic isocrinids during the Triassic. Seirocrinus arose from Pentacrinites through hyper‐morphosis prior to the start of the Jurassic but both genera subsequently show extreme evolutionary conservatism, perhaps attributable to constraints imposed by their unusual life‐style. From a single species in the Hettangian, the benthic isocrinids diversified in the Sinemurian and Carixian. A “central lineage”;, comprising three species of Chladocrinus, evolved along a peramorphocline by “intermittent anagenesis”;, prolonged periods of evolutionary stasis punctuated by short periods of gradualistic change. Two main offshoots, Balanocrinus and Hispidocrinus gen. nov., represent shifts into new habitats. Balanocrinus arose through progenesis, with subsequent evolution along a paedomorphocline, while Hispidocrinus may have arisen through extreme peramorphosis, although its spinose brachials are an evolutionary innovation. Both genera show an apparently punctuated mode of evolution. There is some correlation between morphology and faciès, and also between the emergence of new species and times of high sea level. Benthic isocrinids appear to have been greatly affected by the early Toarcian anoxic event but the pseudopelagic pentacrinitids were not.     

遗传负荷理论的一种普适框架

遗传负荷表示种群由于遗传变异能力的存在而在平均适宜度上的损失,定量讨论各种遗传负荷,对研究现实发生水平上的物种进化具有重要意义,以往的遗传负荷理论从种群平衡出发,探讨现实发生水平上的物种进化,可是,进化是种群平衡的位移;这便构成了理论与现实之间的矛盾,为拓展以往的遗传负荷理论,给出了一个描述各种遗传负荷的普适理论框架,利用这个理论框架既能探讨平衡种群的遗传负荷,又能模写非平衡种群的遗传负荷及其变化,从而克服了以往的遗传负荷理论不能描述非平衡种群和不时与生物进化现实相悖的不足之处,为研究物种的进化提供了一种可靠的模拟方法。     

Multiple-Locus Departures from Panmictic Equilibrium within and between Village Gene Pools of Amerindian Tribes at Different Stages of Agglomeration

A comparative analysis of departures from multiple-locus Hardy-Weinberg equilibrium is presented for a set of four tribal Indian groups (the Yanomama, Makiritare, Wapishana and Ticuna) from the lowlands of South America. These tribes span a range of agglomeration and acculturation from the most traditional, swidden horticulturalists to frontier townspeople. The small-group social organization typical of traditional horticulturalists leads to substantial departures from tribal panmixia, as manifested by the distribution of multiple-locus genotypes both within and between villages. Within villages, the departures from single-locus Hardy-Weinberg equilibrium are small and nonsignificant, but the departures from gametic equilibrium (independence of loci) are substantial, even for the unlinked loci we have used to characterize these populations. The departures from single-locus homogeneity across villages are also substantial. One of the normal concomitants of increasing acculturation in this setting is an increase in agglomeration. As agglomeration increases, the departures from multiple-locus panmixia decrease, a process that can be very rapid. We discuss both the shifting balance theory of evolution and punctuated evolutionary rates in light of the small group social organization that must have obtained throughout most of human evolution.     

Statistical Limitations on Molecular Evolution

Abstract

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with “RNA world” hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of “punctuated equilibrium”.     

生物进化研究的回顾与展望

生物进化是自然科学的永恒之迷。随着历史的发展和科学的进步,生物进化思想从早期的萌芽,到自然选择学说、新达尔文主义,从现代综合理论,到分子进化的中性学说。再到新灾变论和点断平衡论等。当前,由于生物学各分支学科的飞速发展．它们就各自的研究对象在宏观和微观上不断地拓展和深入,并在不同的层次上形成了广泛的交叉、渗透和融合,现代的进化生物学研究从宏观的表型到微观的分子,从群体遗传改变的微进化到成种事件以及地史上生物类群谱系演化的宏进化,从直接的化石证据到基于形态性状、分子证据和环境变迁的综合推理,从基于遗传基础的比较基因组学到演化机理的进化发育生物学等。可以预见,在新的世纪里,在哲学和具体方法论(如系统论、控制论和信息论)的指导下,在生命科学、其他自然科学乃至社会科学工作者的通力合作下,综合遗传、发育和进化等研究领域的各种理论成果,生物进化理论即将出现也一定会出现的一个新的大综合和新的大统一。     

Punctuated equilibrium, morphological stasis and the palaeontological documentation of speciation: a reply to Fryer, Greenwood and Peake's critique of the Turkana Basin mollusc sequence

Fryer, Greenwood & Peake (1983) have recently criticized my analysis of morphological variation in a sequence of Plio-Pleistocene freshwater molluse faunas from the Turkana Basin in E Africa, and question my conclusions that these faunas document speciation and the punctuated equilibrium model of evolutionary change. Unfortunately, these authors misinterpret the nature of the phenotypic variation in African freshwater molluscs and its relevance to my study, and apparently misunderstand punctuated equilibrium theory. Although the majority of their criticisms are therefore erroneous, certain of the points they raise are important: they are addressed here.     

Characterization of a branch of the phylogenetic tree

We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a "tortoise and hare effect": those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree corresponding to a genus and accurate mathematical representations of the various stages are obtained. We apply our results to address certain controversial issues that have arisen in paleontology such as the importance of punctuated equilibrium and whether unique Cambrian phyla have survived to the present.