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PubMed1979

Dynamics of density- and frequency-dependent selection.

The evolution of a multiallelic locus in a diploid monoecious population is investigated for weak selection in both discrete and continuous time. It is assumed that in the absence of selection the rate of change of population size N is a function only of N, and N converges exponentially to a unique, globally stable equilibrium, ;N. With arbitrary density- and frequency-dependent selection, after several generations have elapsed, N differs from ;N by terms of O(s) (i.e., bounded by a constant times s), where s is the selection intensity. The mean absolute fitness deviates from its equilibrium value (1 in discrete, 0 in continuous time) by only O(s(2)); its rate of change is O(s(3)). The evolution of the gene frequencies may be approximated with an error of O(s) by assuming that N = ;N and Hardy-Weinberg proportions obtain. When the frequency dependence is weaker than the selection intensity, the mean absolute fitness generally exceeds its equilibrium value by a quantity approximately proportional to the genic variance, the constant of proportionality being simply related to the rate of convergence of N to ;N in the absence of selection. Thus, after a short time, the population generally increases, and the rate of growth is proportional to the genic variance.

Journal Article↗
PubMed1994

Evolutionary factors influencing the nature of parasite specificity.

This article considers how specificity patterns are shaped during the course of parasite evolution. Parasites are first and foremost specific to site, or microhabitat; host ranges are far more subject to change than is microhabitat. Specificity results from a number of convergent phenomena starting with habits (microhabitat and feeding styles) of free-living progenitors and the way in which the parasitic association arises (e.g., passive oral contamination as opposed to intrusive entry). These bias the types of interaction parasites have with the host, and, through this, the way specificity develops. Host ecology acts as an external factor affecting specificity and predominates in parasites that interact minimally with the hosts physiological and immune systems. Coevolutionary factors are more important in parasites that feed on host tissues or occur in extraintestinal sites. Here, parasites must present the right cues, and respond appropriately to the host defense system. The ability to generalize these cues and responses across host boundaries may act as a constraint on host range. The functional role of the host in the parasite life history also affects the degree of specificity; thus, parasites may act as host generalists in hosts that act as trophic channels to the final host. The role of competition in determining specificity is difficult to assess. However, competition has been reported to influence microhabitat and host distribution through interactive site selection and/or competitive seclusion.

Animals↗
PubMed2005

Symmetry breaking and convergent extension in early chordate development.

The initiation of axis, polarity, cell differentiation, and gastrulation in the very early chordate development is due to the breaking of radial symmetry. It is believed that this occurs by an external signal. We suggest instead spontaneous symmetry breaking through the agency of the Turing-Child field. Increased size or decreased diffusivity, both brought about by mitotic activity, cause the spontaneous loss of stability of the homogeneous state and the evolution of the metabolic pattern during development. The polar metabolic pattern is the cause of polar gene expression, polar morphogenesis (gastrulation), and polar mitotic activity. The Turing-Child theory explains not only the spontaneous formation of the invagination in gastrulation but also the coherent cell movement observed in convergence and extension during gastrulation and neurulation. The theory is demonstrated with respect to experimental observations on the early development of fish, amphibian, and the chick. The theory can explain a multitude of experimental details. For example, it explains the splayed polar progression of reduction in the fish blastoderm. Reduction starts on that side of the blastoderm margin, which will initiate invagination several hours later. It progresses toward the blastoderm center and somewhat laterally from this future "dorsal lip". This is precisely as predicted by a Turing-Child system in a circle. And for a fish like zebrafish with a blastoderm that is slightly oval, reduction is observed to progress along the long axis of the ellipse, which is what Turing-Child theory predicts. In general the shape and the chemical nature of the experimental patterns are the same as predicted by the Turing couple (cAMP, ATP). Embryological polarity and convergent extension are based on polar eigenfunction and saddle-shaped eigenfunction, respectively.

Animals↗
PubMed1994

Evolution of concepts in DNA repair.

A short personalized history of the development of the field of DNA excision repair is presented, beginning with the early insights of radiation biologists and extending to the present-day convergence of the fields of DNA repair and transcription. It is becoming increasingly clear that excision repair is not merely an extraordinary scheme to help UV-exposed cells survive but rather one that operates upon a wide range of structural defects in DNA, some of which are due to environmental chemicals and others are a consequence of normal metabolic activities. It is an important challenge to researchers and risk assessors to determine the relative contributions to biological endpoints from endogenous events and the intrinsic instability of DNA as compared to exogenous environmental exposures. This should be one of the goals of the Environmental Mutagen Society as it embarks upon its second quarter-century.

Animals↗
PubMed2002

Evolution of fast development of planktonic embryos to early swimming.

Planktonic embryos of marine animals swim at an early stage and age. Although natural selection has apparently favored rapid development of structures for swimming, taxa have not converged on the same, minimal time from first cell division to first swimming. Comparisons of 34 species with planktonic embryos in 10 phyla revealed factors that account for variation in time to swimming. Time to first swimming correlated significantly with time from first to second cleavage (first cell cycle) in analyses of all embryos sampled and separately within the Spiralia and Echinodermata. Time to first swimming also correlated significantly with egg diameter in some clades, but not in all. Correlations between egg diameter and cell cycle duration were low except for the three species of Urochordata. Development to a feeding or nonfeeding larva did not affect time to first swimming beyond effects attributable to egg size. Time to first swimming did not correlate with type of locomotion developed (uniciliated cells, multiciliated cells, or muscle). Nonetheless, differences in locomotion are associated with changes in cell cycle durations prior to swimming. The ratios of time to first swimming and time for first cell cycle suggests that allocation of time to multiplication of cells versus differentiation of cells is resolved differently in species with different types of locomotion.

Animals↗
PubMed2005

Fine structure of distributions and central limit theorem in diffusive billiards.

We investigate deterministic diffusion in periodic billiard models, in terms of the convergence of rescaled distributions to the limiting normal distribution required by the central limit theorem; this is stronger than the usual requirement that the mean-square displacement grow asymptotically linearly in time. The main model studied is a chaotic Lorentz gas where the central limit theorem has been rigorously proved. We study one-dimensional position and displacement densities describing the time evolution of statistical ensembles in a channel geometry, using a more refined method than histograms. We find a pronounced oscillatory fine structure, and show that this has its origin in the geometry of the billiard domain. This fine structure prevents the rescaled densities from converging pointwise to Gaussian densities; however, demodulating them by the fine structure gives new densities which seem to converge uniformly. We give an analytical estimate of the rate of convergence of the original distributions to the limiting normal distribution, based on the analysis of the fine structure, which agrees well with simulation results. We show that using a Maxwellian (Gaussian) distribution of velocities in place of unit speed velocities does not affect the growth of the mean-square displacement, but changes the limiting shape of the distributions to a non-Gaussian one. Using the same methods, we give numerical evidence that a nonchaotic polygonal channel model also obeys the central limit theorem, but with a slower convergence rate.

Journal Article↗
PubMed1997

The evolutionary origin of the language areas in the human brain. A neuroanatomical perspective.

The capacity to learn syntactic rules is a hallmark of the human species, but whether this has been acquired by the process of natural selection has been the subject of controversy. Furthermore, the cortical localization of linguistic capacities has prompted some authors to suggest a modular representation of language in the brain. In this paper, we rather propose that the neural device involved in language is embedded into a large-scale neurocognitive network comprising widespread connections between the temporal, parietal and frontal (especially prefrontal) cortices. This network is involved in the temporal organization of behavior and motor sequences, and in working (active) memory, a sort of short-term memory that participates in immediate cognitive processing. In human evolution, a precondition for language was the establishment of strong cortico-cortical interactions in the postrolandic cortex that enabled the development of multimodal associations. Wernicke's area originated as a converging place in which such associations (concepts) acquired a phonological correlate. We postulate that these phonological representations projected into inferoparietal areas, which were connected to the incipient Broca's area, thus forming a working memory circuit for processing and learning complex vocalizations. As a result of selective pressure for learning capacity and memory storage, this device yielded a sophisticated system able to generate complicated utterances (precursors of syntax) as it became increasingly connected with other brain regions, especially in the prefrontal cortex. This view argues for a gradual origin of the neural substrate for language as required by natural selection.

Animals↗
PubMed1993

Telomeric repeat [TTAGGG]n sequences of human chromosomes are conserved in chimpanzee (Pan troglodytes).

Using a series of genetic parameters, attempts have been made for more than two decades to establish the close kinship of human (Homo sapiens) with chimpanzee (Pan troglodytes). Molecular and cytogenetic data presently suggest that the two species are closely related. The recent isolation of a human telomeric probe (P5097-B.5) has prompted us to cross hybridize it to chimpanzee chromosomes in order to explore convergence and/or divergence of the telomeric repeat sequences (TTAGGG)n. On hybridization, the human probe bound to both ends (telomeres) of chimpanzee chromosomes, suggesting a concerted evolution of tandemly repeated short simple sequences (TTAGGG)n. Even the terminal heterochromatin of chimpanzee chromosomes was found to be endowed with telomeric repeats, suggesting that evolution of heterochromatin and capping with tandemly repeated short sequences are highly complex phenomena.

Animals↗
PubMed2001

M and P retinal ganglion cells of the owl monkey: morphology, size and photoreceptor convergence.

We have estimated photoreceptor convergence to M and P retinal ganglion cells of two closely related nocturnal (owl monkey, Aotus) and diurnal (capuchin monkey, Cebus) anthropoids. Rod convergence is higher in the owl monkey retina while cone convergence to both M and P cells are very similar in the retinas of the owl monkey and the capuchin monkey. These results indicate that during evolution, the owl monkey retina has undergone changes compatible with a more nocturnal lifestyle, but kept a cone to ganglion cell relation similar to that found in diurnal primates.

Animals↗
PubMed2006

Ion regulation in invertebrates: molecular and integrative aspects.

The subject of ion regulation in invertebrates is discussed, using a variety of invertebrate model species and approaches that range from the whole-organism level to tissue, subcellular, and molecular levels to illustrate the future direction of the field. These organisms inhabit a variety of aquatic, freshwater, and terrestrial environments, showing specific adaptations to each environment. This overview discusses mechanisms of metal detoxification and the presence of Cl-ATPase in marine organisms to avoid excess intracellular Cl(-); Ca(2+) regulation and endocrine aspects of adaptations to transitional (semiterrestrial) environments; adaptations to Ca(2+)-poor freshwater, particularly the reabsorption of Ca(2+) through specific transporters found in the urine; and finally, ionoregulatory mechanisms for life on land, such as Ca(2+) conservation during molting in isopods and the presence of K(+) channels in insect Malpighian tubules. Convergent mechanisms for dealing with similar problems in dissimilar habitats are discussed, taking into consideration that invertebrates will continue to serve as model systems for the evolution of ionoregulation in different habitats.

Adaptation, Physiological↗
PubMed1997

[3-D echocardiography: technical toy in search of a clinical application or logical evolution of diagnostic equipment?].

In recent years, 3D echocardiographic reconstruction and real time 3D echocardiography have been developed. Reconstruction techniques are based on one of two principles: acoustic or electromagnetic location devices that identify the spatial position of the transducer during imaging, or transducers that image from a fixed position varying the sector orientation in a predefined way. Animated, dynamic reconstructions of cardiac structures are possible, and the 3D data set can be sliced and viewed in any desired way after acquisition. The mitral annulus and congenital malformations of the heart have been imaged and studied successfully by 3D echo. Mass and volume calculations based on 3D data sets have been shown to be extraordinarily accurate by several investigators working with different techniques. Since the 3D data set is more comprehensive than any set of 2D images, such calculations are fundamentally superior to 2D or M-mode derived parameters. Color Doppler data can also be reconstructed into 3D data sets, with possible applications to proximal convergence zone calculations. However, broad implementation of 3D echo in clinical practice is hampered to date by cumbersome manual tracing to derive quantitative parameters and sometimes by insufficient image quality. Nevertheless, the rapid technical evolution, now including real-time 3D echo, ensures an important role for 3D echo in future echocardiography.

Cardiac Volume↗
PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗
PubMed1995

Calibration of a bubble evolution model to observed bubble incidence in divers.

The method of maximum likelihood was used to calibrate a probabilistic bubble evolution model against data of bubbles detected in divers. These data were obtained from a diverse set of 2,064 chamber man-dives involving air and heliox with and without oxygen decompression. Bubbles were measured with Doppler ultrasound and graded according to the Kisman-Masurel code from which a single maximum bubble grade (BG) per diver was compared to the maximum bubble radius (Rmax) predicted by the model. This comparison was accomplished using multinomial statistics by relating BG to Rmax through a series of probability functions. The model predicted the formation of the bubble according to the critical radius concept and its evolution was predicted by assuming a linear rate of inert gas exchange across the bubble boundary. Gas exchange between the model compartment and blood was assumed to be perfusion-limited. The most successful calibration of the model was found using a trinomial grouping of BG according to no bubbles, low, and high bubble activity, and by assuming a single tissue compartment. Parameter estimations converge to a tissue volume of 0.00036 cm3, a surface tension of 5.0 dyne.cm-1, respective time constants of 27.9 and 9.3 min for nitrogen and helium, and respective Ostwald tissue solubilities of 0.0438 and 0.0096. Although not part of the calibration algorithm, the predicted evolution of bubble size compares reasonably well with the temporal recordings of BGs.

Diffusion↗
PubMed2001

Phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus based on mitochondrial DNA sequences and morphology.

The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been especially difficult. The phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus were inferred from mitochondrial cytochrome oxidase gene sequences (mtDNA) and morphology. Separate and combined analyses indicated that the pollinators of functionally dioecious figs are not monophyletic. However, pollinator relationships were generally congruent with host phylogeny and support a revised classification of Ficus. Ancestral changes in pollinator ovipositor length also correlated with changes in fig breeding systems. In particular, the relative elongation of the ovipositor was associated with the repeated loss of functionally dioecious pollination. The concerted evolution of interacting morphologies may bias estimates of phylogeny based on female head characters, but homoplasy is not so strong in other morphological traits. The lesser phylogenetic utility of morphology than of mtDNA is not due to rampant convergence in morphology but rather to the greater number of potentially informative characters in DNA sequence data; patterns of nucleotide substitution also limit the utility of mtDNA findings. Nonetheless, inferring the ancestral associations of fig pollinators from the best-supported phylogeny provided strong evidence of host conservatism in this highly specialized mutualism.

Animals↗
PubMed2005

A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (chiroptera).

Bats (Order Chiroptera), the only mammals capable of powered flight and sophisticated laryngeal echolocation, represent one of the most species-rich and ubiquitous orders of mammals. However, phylogenetic relationships within this group are poorly resolved. A robust evolutionary tree of Chiroptera is essential for evaluating the phylogeny of echolocation within Chiroptera, as well as for understanding their biogeographical history. We generated 4 kb of sequence data from portions of four novel nuclear intron markers for multiple representatives of 17 of the 18 recognized extant bat families, as well as the putative bat family Miniopteridae. Three echolocation-call characters were examined by mapping them onto the combined topology: (1) high-duty cycle versus low-duty cycle, (2) high-intensity versus low-intensity call emission, and (3) oral versus nasal emission. Echolocation seems to be highly convergent, and the mapping of echolocation-call design onto our phylogeny does not appear to resolve the question of whether echolocation had a single or two origins. Fossil taxa may also provide insight into the evolution of bats; we therefore evaluate 195 morphological characters in light of our nuclear DNA phylogeny. All but 24 of the morphological characters were found to be homoplasious when mapped onto the supermatrix topology, while the remaining characters provided insufficient information to reconstruct the placement of the fossil bat taxa with respect to extant families. However, a morphological synapomorphy characterizing the Rhinolophoidea was identified and is suggestive of a separate origin of echolocation in this clade. Dispersal-Vicariance analysis together with a relaxed Bayesian clock were used to evaluate possible biogeographic scenarios that could account for the current distribution pattern of extant bat families. Africa was reconstructed as the center of origin of modern-day bat families.

Amino Acid Sequence↗
PubMed2002

Evolution of Tetrahymena ribozyme mutants with increased structural stability.

Determining how large RNA molecules stabilize their tertiary structures is critical for understanding how they perform their biological functions. Here we use in vitro selection to identify active variants of the Tetrahymena ribozyme with increased stability. The mutant pool converged to a single family that shared nine mutations; an RNA representing the consensus sequence was structurally more stable by 10.5 degrees C and catalytically active at elevated temperatures. Remarkably, of the nine altered sites, most are already known to be involved in tertiary interactions, and the stabilizing mutations primarily improve the packing interactions in the molecular interior. The wild type ribozyme and the selected mutants provide pairs of mesophilic and thermophilic homologs for studying the origin of their thermal stability.

Animals↗
PubMed2001

Evolutionary radiations and convergences in the structural organization of mammalian brains.

The sizes of mammalian brain components seem to be mostly related to the sizes of the whole brain (and body), suggesting a one-dimensional scale of encephalization. Previous multivariate study of such data concludes that evolutionary selection for enlargement of any one brain part is constrained to selection for a concerted enlargement of the whole brain. However, interactions between structurally related pairs of brain parts confirm reports of differential change in brain nuclei, and imply mosaic rather than concerted evolution. Here we analyse a large number of variables simultaneously using multi-dimensional methods. We show that the relative proportions of different systems of functionally integrated brain structures vary independently between different mammalian orders, demonstrating separate evolutionary radiations in mammalian brain organization. Within each major order we identify clusters of unrelated species that occupy similar behavioural niches and have convergently evolved similar brain proportions. We conclude that within orders, mosaic brain organization is caused by selective adaptation, whereas between orders it suggests an interplay between selection and constraints.

Adaptation, Physiological↗
PubMed1999

Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes.

Mammalian secretory ribonucleases (RNases 1) form a family of extensively studied homologous proteins that were already used for phylogenetic analyses at the protein sequence level previously. In this paper we report the determination of six ribonuclease gene sequences of Artiodactyla and two of Cetacea. These sequences have been used with ruminant homologues in phylogenetic analyses that supported a group including hippopotamus and toothed whales, a group of ruminant pancreatic and brain-type ribonucleases, and a group of tylopod sequences containing the Arabian camel pancreatic ribonuclease gene and Arabian and Bactrian camel and alpaca RNase 1 genes of unknown function. In all analyses the pig was the first diverging artiodactyl. This DNA-based tree is compatible to published trees derived from a number of other genes. The differences to those trees obtained with ribonuclease protein sequences can be explained by the influence of convergence of pancreatic RNases from hippopotamus, camel, and ruminants and by taking into account the information from third codon positions in the DNA-based analyses. The evolution of sequence features of ribonucleases such as the distribution of positively charged amino acids and of potential glycosylation sites is described with regard to increased double-stranded RNA cleavage that is observed in several cetacean and artiodactyl RNases which may have no role in ruminant or ruminant-like digestion.

Amino Acid Sequence↗