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.     

Extant mammal body masses suggest punctuated equilibrium

Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwin''s original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the ‘punctuated equilibrium’ debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal 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.     

On atavisms and atavistic genes

The authors propose the term atavistic to designate a gene producing an ancestral phenotype (atavism). Several examples are presented, and the possible origin of atavistic genes, as well as their pathological implications discussed.     

Homeosis and atavistic regeneration: the 'biogenetic law' in Entwicklungsmechanik

Homeosis is a developmental abnormality corresponding to the transformation of a part of the body into another one. This term was introduced in 1894 by William Bateson, who aimed to make an inventory of all kinds of biological variation in order to understand how evolution proceeds. But, immediately afterwards experimental embryology, or Entwicklungsmechanik in Germany, adopted and redefined this term to refer to abnormal regenerations in which the newly developed organ was not identical to the initial one but rather resembled another part of the body. At that time, many experimental embryologists, such as Wilhelm Roux, were calling for the elimination of any phylogenetic explanation of development and were attempting to promote more mechanistic, proximate explanations. Despite these recommendations, several biologists continued to account for developmental processes by turning to phylogeny instead of mechanical forces. The case of homeosis is representative. Indeed, abnormal regenerations were often seen as examples of atavisms, or recurrence of ancestral characteristics, and many embryologists appealed to Ernst Haeckel's 'fundamental biogenetic law' to explain these strange phenomena. The break between Haeckelian tradition and Entwicklungsmechanik is thus less radical than often assumed, and the homeosis concept represents one of the factors of this continuity.     

类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins

Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to decrease the activation energy between various local energy minima smoothing the energy landscape, rescuing misfolded proteins from conformational traps and stabilizing their native structure. In kinetic terms water and chaperones may make the punctuated equilibrium of conformational changes less punctuated and help protein relaxation. Finally, water and chaperones may help the convergence of multiple energy landscapes during protein-macromolecule interactions. We also discuss the possibility of the introduction of protein games to narrow the multitude of the energy landscapes when a protein binds to another macromolecule. Both water and chaperones provide a diffuse set of rapidly fluctuating weak links (low affinity and low probability interactions), which allow the generalization of all these statements to a multitude of networks.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

Amyloplast sedimentation and organelle saltation in living corn columella cells

Amyloplast sedimentation during gravistimulation and organelle movements was studied in living central rootcap cells of Zea mays L. cv. Merit. Cells from sectioned roots were viewed with a horizontally-mounted videomicroscope. The kinetics of gravity-induced amyloplast sedimentation were comparable to those calculated from experiments using fixed material. Individual amyloplasts fell at an average velocity of 5.5 micrometers min-1; the maximal velocity of fall measured was 18.0 micrometers min-1. Amyloplasts often rotated, sometimes rose in the cytoplasm, and occasionally underwent sudden rapid movements as fast as 58 micrometers min-1. Saltations of other organelles were frequently observed. This appears to be the first report of cytoplasmic streaming in the presumptive statocytes of roots.     

Mimetic butterflies and punctuated equilibria: some old light on a new paradigm*

The horns of a dilemma are usually on the same bull–Spanish proverb. A plague o' both your houses–Veronese imprecation. Although some hypotheses explain the world better than others, making ‘pluralism’ an untenable position, it is the case that scientists frequently set up as alternative hypotheses, one of which must be rejected, models which are merely compatible aspects of some other valid hypothesis that embraces them both. For example, Miillerian mimicry was once supposed to evolve either by a single large change or by gradual convergence (the assumption of gradualism is such that the second alternative has usually been regarded as correct). Yet our genetical research with Heliconius indicates that both processes take place, one after the other, when Miillerian mimicry evolves. A reconstruction of the most plausible route, through time and space, for the evolution of mimicry in Heliconius erato and H. melpomene is used to suggest that two currently popular controversies are similarly futile: the allopatric and parapatric models of race formation are considered to be the extremes of what in nature is a continuum of populations showing varying degrees of partial isolation (ecological change rather than stoppage of gene flow being the driving force in race formation); and it is shown that jerky evolution of the type now interpreted as evidence for ‘punctuated equilibria’ and ‘hopeful monsters’ can be produced by changes in the frequencies of major but ordinary gene mutations in response to changing ecological conditions, a phenomenon well accounted for in neo-Darwinian theory.     

Sexual recombination punctuated by outbreaks and clonal expansions predicts Toxoplasma gondii population genetics

The cosmopolitan parasitic pathogen Toxoplasma gondii is capable of infecting essentially any warm-blooded vertebrate worldwide, including most birds and mammals, and establishes chronic infections in one-third of the globe’s human population. The success of this highly prevalent zoonosis is largely the result of its ability to propagate both sexually and clonally. Frequent genetic exchanges via sexual recombination among extant parasite lineages that mix in the definitive felid host produces new lines that emerge to expand the parasite’s host range and cause outbreaks. Highly successful lines spread clonally via carnivorism and in some cases sweep to pandemic levels. The extent to which sexual reproduction versus clonal expansion shapes Toxoplasma’s current, global population genetic structure is the central question this review will attempt to answer.     

Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments

A major taxon of obligate marine bacteria within the order Actinomycetales has been discovered from ocean sediments. Populations of these bacteria (designated MAR 1) are persistent and widespread, spanning at least three distinct ocean systems. In this study, 212 actinomycete isolates possessing MAR 1 morphologies were examined and all but two displayed an obligate requirement of seawater for growth. Forty-five of these isolates, representing all observed seawater-requiring morphotypes, were partially sequenced and found to share characteristic small-subunit rRNA signature nucleotides between positions 207 and 468 (Escherichia coli numbering). Phylogenetic characterization of seven representative isolates based on almost complete sequences of genes encoding 16S rRNA (16S ribosomal DNA) yielded a monophyletic clade within the family Micromonosporaceae and suggests novelty at the genus level. This is the first evidence for the existence of widespread populations of obligate marine actinomycetes. Organic extracts from cultured members of this new group exhibit remarkable biological activity, suggesting that they represent a prolific resource for biotechnological applications.     

On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.