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Tempo and mode in evolution
... Common to all these approaches is the use of mathematical models that aim at approximating the tempo and mode of evolutionary change (Simpson 1944;Fitch and Ayala 1994). These models are rooted in similar methods first developed in paleontology to explore how phenotypes evolve. ...
... These models are rooted in similar methods first developed in paleontology to explore how phenotypes evolve. Researchers in this field have long been concerned with evolutionary tempo and mode, which they study by using data from the fossil record to infer these evolutionary parameters (Gingerich 1976;Gould and Eldredge 1977;Gould 1980;Fitch and Ayala 1994). Paleontological studies were profoundly influenced by the hallmark contribution of George Gaylord Simpson (1944) in which he used the word "tempo" to define the pace at which phenotypic evolution proceeds. ...
The comparison of mathematical models that represent alternative hypotheses about the tempo and mode of evolutionary change is a common approach for assessing the evolutionary processes underlying phenotypic diversification. However, because model parameters are estimated simultaneously, they are inextricably linked, such that changes in tempo, the pace of evolution, and mode, the manner in which evolution occurs, may be difficult to assess separately. This may potentially complicate biological interpretation, but the extent to which this occurs has not yet been determined. In this study, we examined 160 phylogeny × trait empirical datasets, and conducted extensive numerical phylogenetic simulations, to investigate the efficacy of phylogenetic comparative methods to distinguish between models that represent different evolutionary processes in a phylogenetic context. We observed that, in some circumstances, a high uncertainty exists when attempting to distinguish between alternative evolutionary scenarios underlying phenotypic variation. When examining datasets simulated under known conditions, we found that evolutionary inference is straightforward when phenotypic patterns are generated by simple evolutionary processes that are represented by modifying a single model parameter at a time. However, inferring the exact nature of the evolutionary process that has yielded phenotypic variation when facing complex, potentially more realistic, mechanisms is more problematic. A detailed investigation of the influence of different model parameters showed that changes in evolutionary rates, marked changes in phylogenetic means, or the existence of a strong selective pull on the data, are all readily recovered by phenotypic model comparison. However, under evolutionary processes with a milder restraining pull acting on trait values, alternative models representing very different evolutionary processes may exhibit similar goodness-of-fit to the data, potentially leading to the conflation of interpretations that emphasize tempo and mode during empirical evolutionary inference. This is a mathematical and conceptual property of the considered models that, while not prohibitive for studying phenotypic evolution, should be taken into account and addressed when appropriate.
... Francisco Ayala's voluminous publications included only one from the APS Press, a biological memoir of Walter Monroe Fitch, who was Ayala's colleague, co-author, and friend at the University of California-Irvine. Together Fitch and Ayala led some four colloquia at the National Academy of Sciences between 1994 and 2005 (Ayala & Fitch, 1997;Ayala, Fitch, & Clegg, 2000;Ayala, Fitch, & Hey, 2005;Fitch & Ayala, 1994), each of which was based on a major work "in the formulation of the modern theory of evolution," and led to the publication of an edited volume. Also, many more of Francisco José Ayala's edited works have been published by the National Academy of Sciences and are readily available on its website. ...
... The fact that the ancestors of Palaeomutela began to colonize new uninhabited environments (new ecological niches), which suddenly (catastrophically fast) replaced the marine ecological niches, suggests the absence of competition from the indigenous fauna, which simply did not exist. The lack of competition enhances the ability for freshwater adaptation and allows further habitat expansion (Fitch & Ayala 1994;Lee & Bell 1999). ...
Non-marine bivalves are key fossils in Permian continental stratigraphy and palaeogeography. Although known since the end of 19 th century, the occurrences from the continental basins of the Southern Alps have never been extensively studied. The non-marine bivalves from the Lower Permian Collio Formation (Brescian pre-Alps) are herein revised, and those from the Guncina Formation (Athesian District) are described for the first time. These two units yielded non-marine bivalves belonging to the genus Palaeomutela sensu lato, which is widespread in the Permian continental successions of eastern Euramerica. Three Palaeomutela morphotypes have been herein described: oval-subtriangular, subtrapezoidal and elongated. The latter includes several specimens herein assigned to Palaeomutela (Palaeanodonta) berrutii sp. nov. and dominates the Collio Formation association. The Guncina Formation yielded also the genus Redikorella, for the first time co-occurring on the same stratigraphic horizon of Palaeomutela, herein assigned to Palaeomutela (Palaeanodonta) guncinaensis sp. nov. To-date, it was generally accepted that the first members of the genera Palaeomutela and Redikorella occurred during the Ufimian (late Kungurian of the global scale) in the non-marine basins of the Cis-Ural Foredeep and of Angara, respectively. Such new finds in the early-middle Kungurian of southwestern Europe, well constrained by radioisotopic dating, suggest new global first appearance (First Appearance Datum) and a possible new center of origin of these genera. This fact raises new questions on biostratigraphy, palaeobiogeography and palaeoecology, which will require further research. If we assume that the genera Palaeomutela and Redikorella had only one center of origin, we need to hypothesise possible migration routes from SW Europe to the continental basins of Eastern Europe and Angara. Apparently, such migration could be better supported by a Pangaea B palaeogeographic configuration.
... The "mode" involves "the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo". These ideas have had a profound impact on evolutionary biology and paleontology (Fitch & Ayala, 1994;Gould & Eldredge, 1977). The main modes (or mechanisms) in evolutionary biology are natural and sexual selection, mutation, recombination, migration, and genetic drift. ...
Evolutionary scientists studying social and cultural evolution have proposed a multitude of mechanisms by which cultural change can be effected. In this article we discuss two influential ideas from the theory of biological evolution that can inform this debate: the contrast between the micro- and macro-evolution, and the distinction between the tempo and mode of evolution. We add the empirical depth to these ideas by summarizing recent results from the analyses of data on past societies in Seshat: Global History Databank. Our review of these results suggests that the tempo (rates of change, including their acceleration and deceleration) of cultural macroevolution is characterized by periods of apparent stasis interspersed by rapid change. Furthermore, when we focus on large-scale changes in cultural traits of whole groups, the most important macroevolutionary mode involves inter-polity interactions, including competition and warfare, but also cultural exchange and selective imitation; mechanisms that are key components of cultural multilevel selection (CMLS) theory.
... Phenotypic change in quantitative traits within a species or population at timescales between a few months and a few centuries (Kauffman and Levin 1987;Fitch and Ayala 1994) is of critical importance for two main reasons. First, ecological timescales are the most relevant given the accelerated environmental changes facing most ecosystems (IPCC 2014(IPCC , 2018. ...
The amount and rate of phenotypic change at ecological time scales varies widely, but there has not been a comprehensive quantitative synthesis of patterns and causes of such variation for plants. Present knowledge is based predominantly on animals, whose differences with plants in the origin of germ cells and the level of modularity (among others) could make it invalid for plants. We synthesized data on contemporary phenotypic responses of angiosperms to environmental change and show that if extinction does not occur, quantitative traits change quickly in the first few years following the environmental novelty and then remain stable. This general pattern is independent from lifespan, growth form, spatial scale or the type of trait. Our work shows that high amounts and rates of phenotypic change at contemporary timescales observed in plants are consistent with the pattern of stasis and bounded evolution previously observed over longer time frames. We also found evidence that may contradict some common ideas about phenotypic evolution: (1) the total amount of phenotypic change observed does not differ significantly according to growth form or lifespan, (2) greater and faster divergence tend to occur between populations connected at the local scale, where gene flow could be intense, than between distant populations, and that (3) traits closely related to fitness change as much and as fast as other traits.
... Slower speciations take longer to fill spaces and ecological niches made available by the universe compared to faster speciations. On Earth, speciation rates and the speed of other aspects of evolution change (see Fitch and Ayala (1994), and references therein). Also, speciation in some planets may be faster compared to other planets (Lineweaver and Chopra, 2012) so we need to adapt equation 3 to calculate speciation rates for particular planets, and for comparing among planets. ...
Extraterrestrial life is to be discovered soon so we aim to contribute to Astrobiology to go beyond by asking the same as Ecology: how many species the universe hosts and how such a number changes in space and time. Based on data from Amazonian and other tropical forests, it could be said that the universal number of species may tend to infinite because of the huge availability of space and ecological niches. However, living beings are particles of which species are groups so the just mentioned hypothesis is not viable. By falsifying that, we show how the number of species oscillates at different moments of universal history depending on the rates of speciation and extinction, each of them multiplied by a species accumulation factor to be calculated based on the age of the first planet producing life. We use the instant of the Big Bang as the time of origin for all formulations. We feature Big-Bang-time standardized formulae to estimate the number of species for each planet so the average among planets can be a proxy for the universal number of species to be updated as Astrobiology continues its progress. Effects of migration, habitat constraints, and related Natural Selection are absorbed by our equations. Our formulae are compatible with Fisher's-α biodiversity index. Once humankind will discover living and fossil life outside Earth, a major step to be made will be the discovery of the planet where life was born at first.
... Darwin was an extreme gradualist, believing that only the accumulation of small successive variants could lead to adaptation, but he was criticized for this viewpoint by many contemporaries (Eldredge & Gould, 1972;Gould, 1982;Theissen, 2009), and the belief that BDarwinism = gradualism^was one reason that many early geneticists opposed Darwinism (e.g., Bateson, 1894). But by the time of the modern synthesis of evolutionary theory and genetics, it became clear that there is a continuum of both tempo (rate of change) and mode (type of change) in evolution (Gould & Eldredge, 1977;Simpson, 1944), a viewpoint that has become ever clearer as genetic mechanisms have become better understood (Fitch & Ayala 1994). At the level of DNA all evolutionary change is discrete, because there are only four discrete bases in the genetic material. ...
The study of language evolution, and human cognitive evolution more generally, has often been ridiculed as unscientific, but in fact it differs little from many other disciplines that investigate past events, such as geology or cosmology. Well-crafted models of language evolution make numerous testable hypotheses, and if the principles of strong inference (simultaneous testing of multiple plausible hypotheses) are adopted, there is an increasing amount of relevant data allowing empirical evaluation of such models. The articles in this special issue provide a concise overview of current models of language evolution, emphasizing the testable predictions that they make, along with overviews of the many sources of data available to test them (emphasizing comparative, neural, and genetic data). The key challenge facing the study of language evolution is not a lack of data, but rather a weak commitment to hypothesis-testing approaches and strong inference, exacerbated by the broad and highly interdisciplinary nature of the relevant data. This introduction offers an overview of the field, and a summary of what needed to evolve to provide our species with language-ready brains. It then briefly discusses different contemporary models of language evolution, followed by an overview of different sources of data to test these models. I conclude with my own multistage model of how different components of language could have evolved.
Substantial advances occurred in phlebological practice in the last two decades. With the use of modern diagnostic equipment, the patients' venous hemodynamics can be examined in detail in everyday practice. Application of venous segments for arterial bypasses motivated studies on the effect of hemodynamic load on the venous wall. New animal models have been developed to study hemodynamic effects on the venous system. In vivo and in vitro studies revealed cellular phase transitions of venous endothelial, smooth muscle, and fibroblastic cells and changes in connective tissue composition, under hemodynamic load and at different locations of the chronically diseased venous system. This review is an attempt to integrate our knowledge from epidemiology, paleoanthropology and anthropology, clinical and experimental hemodynamic studies, histology, cell physiology, cell pathology, and molecular biology on the complex pathomechanism of this frequent disease. Our conclusion is that the disease is initiated by limited genetic adaptation of mankind not to bipedalism but to bipedalism in the unmoving standing or sitting position. In the course of the disease several pathologic vicious circles emerge, sustained venous hypertension inducing cellular phase transitions, chronic wall inflammation, apoptosis of cells, pathologic dilation, and valvular damage which, in turn, further aggravate the venous hypertension.
Some basic aspects of human and animal biology and evolution involve the establishment of biological uniqueness of species and individuals within their huge variety. The discrimination among closely related species occurs in their offspring at the level of chromosomal DNA sequence homology, which is required for fertility as the hallmark of species. Biological identification of individuals, i.e., of their biological “self”, occurs at the level of protein sequences presented by the MHC/HLA complex as part of the immune system that discriminates non-self from self. Here, a mechanistic molecular model is presented that can explain how DNA sequence divergence and the activity of key mismatch repair proteins, MutS and MutL, lead to 1) genetic separation of closely related species (sympatric speciation) (Fitch and Ayala, Proceedings of the National Academy of Sciences, 1994, 91, 6717–6720), 2) the stability of genomes riddled by diverged repeated sequences, and 3) conservation of highly polymorphic DNA sequence blocks that constitute the immunological self. All three phenomena involve suppression of recombination between diverged homologies, resulting in prevention of gene sharing between closely related genomes (evolution of new species) as well as sequence sharing between closely related genes within a genome (e.g., evolution of immunoglobulin, MHC, and other gene families bearing conserved polymorphisms).
Physical maps showing the relative locations of cloned DNA fragments in the genome are important resources for research in molecular genetics, genome analysis, and evolutionary biology. In addition to affording a common frame of reference for organizing diverse types of genetic data, physical maps also provide ready access to clones containing DNA sequences from any defined region of the genome. In this paper, we present a physical map of the genome of Drosophila melanogaster based on in situ hybridization with 2461 DNA fragments, averaging approximately 80 kilobase pairs each, cloned in bacteriophage P1. The map is a framework map in the sense that most putative overlaps between clones have not yet been demonstrated at the molecular level. Nevertheless, the framework map includes approximately 85% of all genes in the euchromatic genome. A continuous physical map composed of sets of overlapping P1 clones (contigs), which together span most of the euchromatic genome, is currently being assembled by screening a library of 9216 P1 clones with single-copy genetic markers as well as with the ends of the P1 clones already assigned positions in the framework map. Because most P1 clones from D. melanogaster hybridize in situ with chromosomes from related species, the framework map also makes it possible to determine the genome maps of D. pseudoobscura and other species in the subgenus Sophophora. Likewise, a P1 framework map of D. virilis affords potential access to genome organization and evolution in the subgenus Drosophila.
A broad variety of body plans and subplans appear during a period of
perhaps 8 million years (my) within the Early Cambrian, an unequaled
explosion of morphological novelty, the ancestral lineages represented
chiefly or entirely by trace fossils. Evidence from the fossil record
can be combined with that from molecular phylogenetic trees to suggest
that the last common ancestor of (i) protostomes and deuterostomes was a
roundish worm with a blood vascular system and (ii) of arthropods and
annelids was similar, with a hydrostatic hemocoel; these forms are
probably among trace makers of the late Precambrian. Cell-phenotype
numbers in living phyla, and a model of cell-phenotype number increase,
suggest an origin of metazoans near 600 my ago, followed by a passive
rise in body-plan complexity. Living phyla appearing during the Cambrian
explosion have a Hox/HOM gene cluster, implying its presence in the
common ancestral trace makers. The explosion required a repatterning of
gene expression that mediated the development of novel body plans but
evidently did not require an important, abrupt increase in genomic or
morphologic complexity.
Although the chromosomal polymorphism for inversions in Drosophila pseudoobscura is one of the best studied systems in population genetics, the identity of the ancestral gene arrangement has remained unresolved for more than 50 years. There are more than 40 gene arrangements, and 4 of them (Standard, Hypothetical, Santa Cruz, and Tree Line) have been considered as candidates for the ancestral type. We propose a framework of competing hypotheses to distinguish among the alternatives. Two conclusions come from contrasting each hypothesis with the results from DNA sequencing and restriction mapping. First, not only Standard but also Hypothetical can be excluded as the ancestral gene arrangement. Second, although either Tree Line or Santa Cruz could be the ancestral type, the available data provide greater support for Santa Cruz.
Different regions of the Drosophila genome have very different rates of recombination. For example, near centromeres and near the tips of chromosomes, the rates of recombination are much lower than in other regions. Several surveys of polymorphisms in Drosophila have now documented that levels of DNA polymorphism are positively correlated with rates of recombination; i.e., regions with low rates of recombination tend to have low levels of DNA polymorphism within populations of Drosophila. Three hypotheses are reviewed that might account for these observations. The first hypothesis is that regions of low recombination have low neutral mutation rates. Under this hypothesis between-species divergences should also be low in regions of low recombination. In fact, regions of low recombination have diverged at the same rate as other regions of the genome. On this basis, this strictly neutral hypothesis is rejected. The second hypothesis is that the process of fixation of favorable mutations leads to the observed correlation between polymorphism and recombination. This occurs via genetic hitchhiking, in which linked regions of the genome are swept along with the selectively favored mutant as it increases in frequency and eventually fixes in the population. This hitchhiking model with fixation of favorable mutations is compatible with major features of the data. By assuming this model is correct, one can estimate the rate of fixation of favorable mutations. The third hypothesis is that selection against continually arising deleterious mutations results in reduced levels of polymorphism at linked loci. Analysis of this background selection model shows that it can produce some reduction in levels of polymorphism but cannot explain some extreme cases that have been observed. Thus, it appears that hitchhiking of favorable mutations and background selection against deleterious mutations must be considered together to correctly account for the patterns of polymorphism that are observed in Drosophila.