Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous.

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene-Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth's biota.

Cladogenesis and replacement in the fossil record of Microsyopidae (?Primates) from the southern Bighorn Basin, Wyoming.

The early Eocene of the southern Bighorn Basin, Wyoming, is notable for its nearly continuous record of mammalian fossils. Microsyopinae (?Primates) is one of several lineages that shows evidence of evolutionary change associated with an interval referred to as Biohorizon A. Arctodontomys wilsoni is replaced by a larger species, Arctodontomys nuptus, during the biohorizon interval in what is likely an immigration/emigration or immigration/local extinction event. The latter is then superseded by Microsyops angustidens after the end of the Biohorizon A interval. Although this pattern has been understood for some time, denser sampling has led to the identification of a specimen intermediate in morphology between A. nuptus and M. angustidens, located stratigraphically as the latter is appearing. Because specimens of A. nuptus have been recovered approximately 60 m above the appearance of M. angustidens, it is clear that A. nuptus did not suffer pseudoextinction. Instead, evidence suggests that M. angustidens branched off from a population of A. nuptus, but the latter species persisted. This represents possible evidence of cladogenesis, which has rarely been directly documented in the fossil record. The improved understanding of both evolutionary transitions with better sampling highlights the problem of interpreting gaps in the fossil record as punctuations.

A dense sample of fossil primates (Adapiformes, Notharctidae, Notharctinae) from the Early Eocene Willwood Formation, Wyoming: Documentation of gradual change in tooth area and shape through time.

OBJECTIVES: The Willwood Formation of the southern Bighorn Basin, Wyoming is a fluvial rock sequence that spans approximately 3 million years of early Eocene time. It has yielded one the largest collections of fossil mammals in the world including thousands of dentitions of extinct lemur-like primates known as notharctines. In the southern Bighorn Basin, specimens of these primates have been collected on numerous paleontological expeditions and the stratigraphic levels yielding the dentitions have been carefully recorded. Notharctine dentitions represent a rare opportunity to study morphological variation in a single anatomical system through time among closely related individuals. MATERIALS AND METHODS: Prior studies of Bighorn Basin notharctines through time produced measurements of hundreds of specimens but I report here results from measurement and comparison of the dentitions and dentaries of more than 3,000 specimens, all stratigraphically mapped. RESULTS: Variation in premolar and molar area and variation in dentary depth are apparent throughout the section. Specimens with relatively small teeth and dentaries are known from the older part of the section. In younger rocks, variation in tooth area among specimens increases. Variation in tooth area is continuous and overlaps extensively both within and between stratigraphic levels. Other dental variables examined by inspection change in a mosaic and continuous fashion through the section. These features include variation in the presence and number of paraconids on the lower fourth premolar (p4), the size and shape of the entoconid notch on the lower first and second molars, and the relative development of the pseudohypocone, mesostyle, and cingula on the upper molars. DISCUSSION: These broad patterns can be identified despite notharctine alpha taxonomy being in need of extensive revision and, importantly, simplification. Such revision is beyond the scope of this article but is essential if we are to develop a taxonomy that is both free of stratigraphic influence and useful for rapid, repeatable species assignment. Boundaries among the patterns of tokogenesis, anagenesis, and cladogenesis are blurred in this dense sample of extinct primates. While pattern of evolution, a population-level phenomenon, may be difficult to falsify in the fossil record, this notharctine sample suggests that in the rare instance such as this, when the fossil record is densely sampled, change through time is continuous and more consistent with gradual evolution.

The origin of Darwin's "abominable mystery".

The phrase "Darwin's abominable mystery" is frequently used with reference to a range of outstanding questions about the evolution of the plant group today known as the angiosperms. Here, I seek to more fully understand what prompted Darwin to coin the phrase in 1879, and the meaning he attached to it, by surveying the systematics, paleobotanical records, and phylogenetic hypotheses of his time. In the light of this historical research, I argue that Darwin was referring to the origin only of a subset of what are today called angiosperms: a (now obsolete) group equivalent to the "dicotyledons" of the Hooker and Bentham system. To Darwin and his contemporaries, the dicotyledons' fossil record began abruptly and with great diversity in the Cretaceous, whereas the gymnosperms and monocotyledons were thought to have fossil records dating back to the Carboniferous or beyond. Based on their morphology, the dicotyledons were widely seen by botanists in Darwin's time (unlike today) as more similar to the gymnosperms than to the monocotyledons. Thus, morphology seemed to point to gymnosperm progenitors of dicotyledons, but this hypothesis made the monocotyledons, given their (at the time) apparently longer fossil record, difficult to place. Darwin had friendly disagreements about the mystery of the dicotyledons' abrupt appearance in the fossil record with others who thought that their evolution must have been more rapid than his own gradualism would allow. But the mystery may have been made "abominable" to him because it was seen by some contemporary paleobotanists, most notably William Carruthers, the Keeper of Botany at the British Museum, as evidence for divine intervention in the history of life. Subsequent developments in plant systematics and paleobotany after 1879 meant that Darwin's letter was widely understood to be referring to the abrupt appearance of all angiosperms when it was published in 1903, a meaning that has been attached to it ever since.

Random variations, gradualism and the role of natural selection.

While the modern synthesis has at its core the claim that evolution can be entirely explained by the natural selection of random variations, neither "random" nor "variation" is adequately defined. Neo-Darwinists explicitly deny that they use random with the meaning of haphazard, but it is what they assume in their work; if they did not, they could not justify their total concentration on selection and neglect of variations. They conflate variations in the genotype with those in the phenotype. This might be justifiable if the connection between the two were simple and straightforward, but it is not. Like Darwin, neo-Darwinists are committed to the belief that evolution is always gradual. Also like Darwin, they justify this on theoretical rather than empirical grounds and despite acknowledging that the evidence does not support them. The paradox could be resolved by relaxing the commitment to gradualism, but only at the cost of significant consequences for the paradigm.

Early male aging or poor clinical consideration for males in IVF centers? An original study.

The Italian law 40/2004 allows the use of assisted reproduction techniques only if there are no other effective therapeutic approaches to overcome infertility. According to article 4 paragraph 1, the impossibility of removing the otherwise impeding causes to achieve a pregnancy must be ascertained before the couple undergoes assisted reproduction techniques. On this premises, we sought to evaluate the percentage of couples who underwent or were addressed to assisted reproduction techniques despite a known and potentially treatable male infertility factor in fertility centers in the city of Catania, Italy. To accomplish this, andrologists, urologists and endocrinologists were asked to report the number of couples already addressed to assisted reproduction techniques which they counseled in the trimester April-June 2018 having a under 35-year-old female partner and at least one among the following untreated conditions: (A) oligoasthenoteratozoospermia and FSH <8 mIU/ml, (B) third-degree varicocele (mono or bilateral form), and (C) leukocytospermia or urogenital infections. Of the 320 enrolled couples, 75 (23%) met the criterion A, 45 (14%) the criterion B, and 62 (19%) the criterion C. More than a half couples were addressed to assisted reproduction techniques despite a potentially treatable male infertility factor.

Measuring cancer evolution from the genome.

The temporal dynamics of cancer evolution remain elusive, because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences made from a single point in time - the endpoint in the cancer's evolution, when it is removed from the body and studied in the laboratory. Fortuitously however, the cancer genome, by virtue of ongoing mutations that uniquely mark clonal lineages within the tumour, provides a rich, yet surreptitious, record of cancer development. In this review, we describe how a cancer's genome can be analysed to reveal the temporal history of mutation and selection, and discuss why both selective and neutral evolution feature prominently in carcinogenesis. We argue that selection in cancer can only be properly studied once we have some understanding of what the absence of selection looks like. We review the data describing punctuated evolution in cancer, and reason that punctuated phenotype evolution is consistent with both gradual and punctuated genome evolution. We conclude that, to map and predict evolutionary trajectories during carcinogenesis, it is critical to better understand the relationship between genotype change and phenotype change. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

New Evidence from Linguistic Phylogenetics Identifies Limits to Punctuational Change.

Since the early 1970s, biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium. We replicate this result for branch lengths, but find no support for punctuated equilibrium using a different, automated measure of linguistic divergence and a much larger data set. With the automated measure, segments of trees containing more nodes show no greater divergence from an outgroup than segments containing fewer nodes.

New paradigms in clonal evolution: punctuated equilibrium in cancer.

Evolutionary theories are themselves subject to evolution. Clonal evolution - the model that describes the initiation and progression of cancer - is entering a period of profound change, brought about largely by technological developments in genome analysis. A flurry of recent publications, using modern mathematical and bioinformatics techniques, have revealed both punctuated and neutral evolution phenomena that are poorly explained by the conventional graduated perspectives. In this review, we propose that a hybrid model, inspired by the evolutionary model of punctuated equilibrium, could better explain these recent observations. We also discuss the conceptual changes and clinical implications of variable evolutionary tempos. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Simple versus complex models of trait evolution and stasis as a response to environmental change.

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Quantifying the effects of anagenetic and cladogenetic evolution.

An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

El estatus del embrión humano desde el gradualismo / The status of the human embryo from a gradualistic perspective

La bioética cubre temas clásicos del inicio al final de la vida humana. Al inicio de la vida humana, los problemas parten del mismo punto: el estatus del embrión humano.Existen numerosos e interesantes trabajos que abordan problemas alrededor de este tema, tales como la reproducción asistida, la recolección y manejo de gametos y embriones en el laboratorio, la investigación en células embrionarias, fuentes de células troncales (o células madre), la anticoncepción de emergencia, la interrupción voluntaria del embarazo, etc. Todos ellos se apoyan en conceptos filosóficos que pueden estar implícitos o explícitos. Las posturas filosóficas en torno al estatus del embrión humano se pueden dividir en dos: el personalismo y el gradualismo. El personalismo considera que el embrión es persona desde la fecundación. El gradualismo considera que es persona en un momento posterior a la fecundación. En este trabajo se aborda la definición de las palabras “estatus” y “embrión”, se resumen criterios para considerar a partir de que momento un ser humano es una persona, se presenta el gradualismo como una alternativa actual frente al personalismo y se enfatiza en la postura gradualista propuesta por Alonso Bedate sobre el estatus del embrión humano, sugiriendo que el gradualismo tiene sus fundamentos metafísicos en la biología moderna.

Bioethics debates topics regarding the beginning and ending of human life. The beginning of human life includes when a human embryo reaches full human status. There are multiple and interesting issues surrounding human embryo status. These include assisted reproduction, seeking and management of human gametes and embryos at specialized laboratories, embryonic and stem cell research, emergency contraception, voluntary interruption of pregnancy, etc. They are based on implicit or explicit philosophical concepts. Philosophical positions about human embryo status could be summarized in two postures: personalism and gradualism. Personalism considers that human embryos reach the status of persons from the moment of fertilization. On the other hand, gradualism considers human embryos become persons at a later time after fertilization. The present work discusses the definitions of [quot ]status[quot ] and [quot ]embryo[quot ], summarizes criteria to consider a human being as a person, presents gradualism as an alternate posture to personalism, and finally emphasizes Alonso Bedate's gradualist position about human embryo status, suggesting that gradualism has its metaphysical foundation in modern biology.

PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY.

We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and define alternative evolutionary correlations that may be of interest. We focus on Felsenstein's (1985) method and some variations of it and on several "minimum evolution" methods (of which the procedure of Huey and Bennett [1987] is a special case), as compared with a nonphylogenetic correlation. The last, a simple correlation of trait values across the tips of a phylogeny, virtually always yields inflated Type I error rates, relatively low power, and relatively poor estimates of evolutionary correlations. We therefore cannot recommend its use. In contrast, Felsenstein's (1985) method yields acceptable significance tests, high power, and good estimates of what we term the input correlation and the standardized realized evolutionary correlation, given complete phylogenetic information and knowledge of the rate and mode of character change (e.g., gradual and proportional to time ["Brownian motion"] or punctuational, with change only at speciation events). Inaccurate branch length information may affect any method adversely, but only rarely does it cause Felsenstein's (1985) method to perform worse than do the others tested. Other proposed methods generally yield inflated Type I error rates and have lower power. However, certain minimum evolution methods (although not the specific procedure used by Huey and Bennett [1987]) often provide more accurate estimates of what we term the unstandardized realized evolutionary correlation, and their use is recommended when estimation of this correlation is desired. We also demonstrate how correct Type I error rates can be obtained for any method by reference to an empirical null distribution derived from computer simulations, and provide practical suggestions on choosing an analytical method, based both on the evolutionary correlation of interest and on the availability of branch lengths and knowledge of the model of evolutionary change appropriate for the characters being analyzed. Computer programs that implement the various methods and that will simulate (correlated) character evolution along a known phylogeny are available from the authors on request. These programs can be used to test the effectiveness of any new methods that might be proposed, and to check the generality of our conclusions with regard to other phylogenies.