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PubMed2004

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.

Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.

Amino Acid Sequence↗
PubMed1993

A molecular approach to estimating the human deleterious mutation rate.

We propose a method of measuring the human genomic deleterious mutation rate based on comparison of the rate of evolution per nucleotide per generation of neutral sequences, microN, with the overall rate of evolution of unique sequence DNA, microO. Data on microN, which are based on pseudogenes, permit an estimate of the total zygotic (twice the genomic) mutation rate, UT = 2 microNn = 2(2 x 10(-8)(3 x 10(9)) approximately 10(2), where n is the number of nucleotides per genome. Data on microO can be obtained by comparison of representative samples of relatively short homologous sequences from the genomes of Homo and a related species. The fraction of the genome that is controlled by negative selection is fS = (microN - microO)/microN and the deleterious zygotic mutation rate, the expected number of new deleterious alleles carried by a zygote, is US = UTfS. If fS > 0.01, US > 1, which would have important implications for human genetics and evolutionary biology.

Biological Evolution↗
PubMed2006

Isolation by resistance.

Despite growing interest in the effects of landscape heterogeneity on genetic structuring, few tools are available to incorporate data on landscape composition into population genetic studies. Analyses of isolation by distance have typically either assumed spatial homogeneity for convenience or applied theoretically unjustified distance metrics to compensate for heterogeneity. Here I propose the isolation-by-resistance (IBR) model as an alternative for predicting equilibrium genetic structuring in complex landscapes. The model predicts a positive relationship between genetic differentiation and the resistance distance, a distance metric that exploits precise relationships between random walk times and effective resistances in electronic networks. As a predictor of genetic differentiation, the resistance distance is both more theoretically justified and more robust to spatial heterogeneity than Euclidean or least cost path-based distance measures. Moreover, the metric can be applied with a wide range of data inputs, including coarse-scale range maps, simple maps of habitat and nonhabitat within a species' range, or complex spatial datasets with habitats and barriers of differing qualities. The IBR model thus provides a flexible and efficient tool to account for habitat heterogeneity in studies of isolation by distance, improve understanding of how landscape characteristics affect genetic structuring, and predict genetic and evolutionary consequences of landscape change.

Biological Evolution↗
PubMed2000

Gene genealogies and population variation in plants.

Early in the development of plant evolutionary biology, genetic drift, fluctuations in population size, and isolation were identified as critical processes that affect the course of evolution in plant species. Attempts to assess these processes in natural populations became possible only with the development of neutral genetic markers in the 1960s. More recently, the application of historically ordered neutral molecular variation (within the conceptual framework of coalescent theory) has allowed a reevaluation of these microevolutionary processes. Gene genealogies trace the evolutionary relationships among haplotypes (alleles) with populations. Processes such as selection, fluctuation in population size, and population substructuring affect the geographical and genealogical relationships among these alleles. Therefore, examination of these genealogical data can provide insights into the evolutionary history of a species. For example, studies of Arabidopsis thaliana have suggested that this species underwent rapid expansion, with populations showing little genetic differentiation. The new discipline of phylogeography examines the distribution of allele genealogies in an explicit geographical context. Phylogeographic studies of plants have documented the recolonization of European tree species from refugia subsequent to Pleistocene glaciation, and such studies have been instructive in understanding the origin and domestication of the crop cassava. Currently, several technical limitations hinder the widespread application of a genealogical approach to plant evolutionary studies. However, as these technical issues are solved, a genealogical approach holds great promise for understanding these previously elusive processes in plant evolution.

Journal Article↗
PubMed1997

Genetic factors in reproduction and their evolutionary significance.

PROBLEM: The reproductive process is a major driving force in human evolution. An evolutionary perspective was brought to bear on some aspects of reproduction and its aberrations, and, conversely, some of the insights of modern reproductive genetics were used to investigate problems in evolution. METHOD: The data used were obtained from the literature in evolution, anthropology, archeology, linguistics, and genetics. RESULTS: The evolutionary line leading to modern humans diverged from that leading to the chimpanzees approximately 5-7 million years ago (Mya). Archaic Homo sapiens emerged ca. 0.3 Mya, and modern Homo sapiens and the development of language ca. 0.1 Mya; thus, modern humans occupy approximately 2% of the evolutionary history of the hominid line. During all of this time, the ancestors of modern humans were migratory hunter-gatherers. It was only during the Neolithic transition ca. 0.01 Mya (approximately 0.2% of hominid evolutionary history) that agriculture was developed, and with it a settled lifestyle that allowed a more stable existence and the development of a different reproductive pattern. Various estimates indicate that the human population increased from 0.05 million at the time of the emergence of modern Homo sapiens to 6,000 million at the present time (120,000-fold increase). CONCLUSIONS: These evolutionary considerations were used to explore three areas: (1) the extinction of the Neanderthals, who coexisted for ca. 65,000 years with modern humans; (2) the relatively low and stable rate of human conceptions (20-35% of ova fertilized naturally or fertilized in vitro); and (3) the long postnatal period required for the full maturation of the immune response. From these considerations, a broad view of the human reproductive process was obtained that may provide some insight into the rationale for the development of effective reproductive technologies.

Animals↗
PubMedDate not supplied

[Nikolaĭ Vladimirovich Timofeev-Resovskiĭ (1900-1981). (Essay on his life and works)].

The article contains a brief review of the basic works (1925-1981) written by Nikolay V. Timofeeff-Ressovsky--one of the famous geneticist of the elapsing century, the founder of radiobiology and radiation genetics, biocenology and radioecology, a prominent evolutionary biologist. In genetics, his name is associated with the development of fundamental problems of population genetics, phenogenetics, gene interaction and investigations of the role of environmental and genetic factors in expression of different characters. Timofeeff-Ressovsky classical works on mutagenesis process and especially, radiation mutagenesis, promoted penetration of methods and approaches applied in molecular physics and chemistry, into genetic analysis, and accelerated forming of the modern molecular genetics. A special place in the development of population genetics is occupied by the hypothesis of microevolutionary process developed by Nikolay V. Timofeeff-Ressovsky along with other famous biologists in the end of the 30-ies. This hypothesis connected Darwin's evolutionary theory with rapidly developing concepts of genetics. In the last years of his life, Timofeeff-Ressovsky was especially interested in a global problem which was called by him "The Biosphere and Humanity". Here was especially strikingly shown the broadness of his approach to the analysis of the biosphere phenomena in the best traditions of the Russian natural science. In the course of time, the wealth of Nikolay V. Timofeeff-Ressovsky's scientific heritage not only remains valuable, but also takes on more profundity and value.

History, 20th Century↗
PubMed2004

A general theory for the evolutionary dynamics of virulence.

Most theory on the evolution of virulence is based on a game-theoretic approach. One potential shortcoming of this approach is that it does not allow the prediction of the evolutionary dynamics of virulence. Such dynamics are of interest for several reasons: for experimental tests of theory, for the development of useful virulence management protocols, and for understanding virulence evolution in situations where the epidemiological dynamics never reach equilibrium and/or when evolutionary change occurs on a timescale comparable to that of the epidemiological dynamics. Here we present a general theory similar to that of quantitative genetics in evolutionary biology that allows for the easy construction of models that include both within-host mutation as well as superinfection and that is capable of predicting both the short- and long-term evolution of virulence. We illustrate the generality and intuitive appeal of the theory through a series of examples showing how it can lead to transparent interpretations of the selective forces governing virulence evolution. It also leads to novel predictions that are not possible using the game-theoretic approach. The general theory can be used to model the evolution of other pathogen traits as well.

Animals↗
PubMed1993

Genetic imprinting in human evolution: the decisive role of maternal lineage.

The modern study of human evolution must take into account physical anthropology, which examines phenotypic expression, and molecular evolution, which examines genotypic change. Recent independent investigations have shown that the process of genetic imprinting, defined as parental-dependent transmission of genetic traits, plays a pivotal role in human evolution. We draw on data from various scientific disciplines to support the hypothesis that maternal lineage via preferential genetic contribution, plays a decisive role in this regard. This concept is of more than theoretical interest, in that, current human disease states can be better understood and studied in the context of loss of genetically-defined evolutionary advantage.

Biological Evolution↗
PubMedDate not supplied

[Concept of the effect of low doses of ionizing radiation on cells and its possible use in the interpretation of medical-biological consequences].

A concept is proposed where the events induced by low doses of ionizing radiation with low linear energy transfer have different script than those induced by high doses. Its essence consist in the existence of a small fraction (subpopulation) in clonal heterogeneous population whose cells are determined for a specific programmed response induced by a number of action that are potentially able (at high doses) to decrease the survival of the given population. The function of the postulated cell is a deliberate sacrifice necessary for formation of evolutionary reserve. A mechanism of this response is based on an autogeneration of wide-scale genome rearrangements in cells and is not connected with direct influence of genetically hazardous agents on DNA. This leads to arising of a number of genetic variants (evolutionary reserve cells). Selection among them enhancing survival of the population may in the same time lead to harmful consequences for the organism (if there are malfunctions of the immune system). Medical-biological consequences of the effect of low doses are associated with the appearance of such clones and biologically active products secreted from the exposed cells. Mechanisms responsible for the above phenomena are discussed.

Cell Nucleus↗
PubMed2002

Population, evolutionary and genomic consequences of interference selection.

Weakly selected mutations are most likely to be physically clustered across genomes and, when sufficiently linked, they alter each others' fixation probability, a process we call interference selection (IS). Here we study population genetics and evolutionary consequences of IS on the selected mutations themselves and on adjacent selectively neutral variation. We show that IS reduces levels of polymorphism and increases low-frequency variants and linkage disequilibrium, in both selected and adjacent neutral mutations. IS can account for several well-documented patterns of variation and composition in genomic regions with low rates of crossing over in Drosophila. IS cannot be described simply as a reduction in the efficacy of selection and effective population size in standard models of selection and drift. Rather, IS can be better understood with models that incorporate a constant "traffic" of competing alleles. Our simulations also allow us to make genome-wide predictions that are specific to IS. We show that IS will be more severe at sites in the center of a region containing weakly selected mutations than at sites located close to the edge of the region. Drosophila melanogaster genomic data strongly support this prediction, with genes without introns showing significantly reduced codon bias in the center of coding regions. As expected, if introns relieve IS, genes with centrally located introns do not show reduced codon bias in the center of the coding region. We also show that reasonably small differences in the length of intermediate "neutral" sequences embedded in a region under selection increase the effectiveness of selection on the adjacent selected sequences. Hence, the presence and length of sequences such as introns or intergenic regions can be a trait subject to selection in recombining genomes. In support of this prediction, intron presence is positively correlated with a gene's codon bias in D. melanogaster. Finally, the study of temporal dynamics of IS after a change of recombination rate shows that nonequilibrium codon usage may be the norm rather than the exception.

Animals↗
PubMed1981

Genetic and structural studies on rat kappa chain allotypes.

Several features of the RI-1 system in the rat render it of special interest to the immunogeneticist. First, it remains the only kappa chain marker in a laboratory rodent. Second, the degree of structural divergence between the two known forms is unexpected for the products of allelic genes and raises interesting genetic and evolutionary questions. If they are truly allelic, what is the nature of the selective forces that have produced and maintained this polymorphism? If they are not allelic, what genetic structure and control mechanism can account for their allelic expression? The Australian Rattus group is clearly providing a valuable system for studying the nature of kappa chain diversity and evolution. In addition, the possibility of making laboratory crosses between forms that differ both phenotypically and karyologically provides the opportunity of establishing linkage relationships and chromosomal localization for RI-1 and many other biochemical loci.

Alleles↗
PubMed1994

The phylogeny of tRNA molecules and the origin of the genetic code.

The evolutionary relationships between transfer RNA (tRNA) molecules are analyzed by parsimony algorithms. The position of the topologies expected on the basis of the hypotheses made to explain the origin of the genetic code, on the frequency distribution of all the possible tree topologies of the evolutionary relationships between tRNAs seems to lead to the following conclusion: The hypothesis (Wong, J. T., Proc. Natl. Acad. Sci. USA, 1975, 72: 1909-1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids seems to occupy a statistically significant position on these frequency distributions, thus reflecting a significant part of the tRNA phylogeny.

Base Sequence↗
PubMed2005

Estimating cancer survival and clinical outcome based on genetic tumor progression scores.

MOTIVATION: In cancer research, prediction of time to death or relapse is important for a meaningful tumor classification and selecting appropriate therapies. Survival prognosis is typically based on clinical and histological parameters. There is increasing interest in identifying genetic markers that better capture the status of a tumor in order to improve on existing predictions. The accumulation of genetic alterations during tumor progression can be used for the assessment of the genetic status of the tumor. For modeling dependences between the genetic events, evolutionary tree models have been applied. RESULTS: Mixture models of oncogenetic trees provide a probabilistic framework for the estimation of typical pathogenetic routes. From these models we derive a genetic progression score (GPS) that estimates the genetic status of a tumor. GPS is calculated for glioblastoma patients from loss of heterozygosity measurements and for prostate cancer patients from comparative genomic hybridization measurements. Cox proportional hazard models are then fitted to observed survival times of glioblastoma patients and to times until PSA relapse following radical prostatectomy of prostate cancer patients. It turns out that the genetically defined GPS is predictive even after adjustment for classical clinical markers and thus can be considered a medically relevant prognostic factor. AVAILABILITY: Mtreemix, a software package for estimating tree mixture models, is freely available for non-commercial users at http://mtreemix.bioinf.mpi-sb.mpg.de. The raw cancer datasets and R code for the analysis with Cox models are available upon request from the corresponding author.

Biomarkers, Tumor↗
PubMed1999

Reproductive and genetic evidence for a reticulate evolutionary history of mass-spawning corals.

Reef-building corals, which reproduce through simultaneous multispecies spawning, are thought to hybridize frequently, and it is hypothesized that they have evolved in repeated rounds of species separation and fusion. We conducted cross-fertilization experiments and molecular analyses with a number of mass-spawning coral species in the genus Acropora. A high rate of interspecific fertilization occurred between some species despite very different morphologies. The hybrid larvae developed normally and contained an allelic sequence transmitted from each parent, suggesting common diploid hybridization. Molecular phylogenetic analyses provided strong evidence for a gene pool shared between the hybridizing species. These reproductive and genetic characteristics are consistent with a species complex formed under the separation/fusion processes predicted for a reticulate evolutionary history.

Animals↗
PubMed2006

An evolutionary view of human recombination.

Recombination has essential functions in mammalian meiosis, which impose several constraints on the recombination process. However, recent studies have shown that, in spite of these roles, recombination rates vary tremendously among humans, and show marked differences between humans and closely related species. These findings provide important insights into the determinants of recombination rates and raise new questions about the selective pressures that affect recombination over different genomic scales, with implications for human genetics and evolutionary biology.

Animals↗
PubMed1998

Study of correlations in segmented DNA sequences: application to structure coupling between exons and introns.

A technique for the study of correlations in segmented DNA sequences is developed. Within this approach the effects of compositional patchiness are separated from the beginning, allowing us to display the refined effects of structural coupling between different segments. The mutual analysis of Fourier structure spectra and pair correlation functions identifies both the main ranges (long, short, or intermediate) and the sources (coincident periodicities, large scale density variations, short-memory coupling, or coherent point mutations) of correlations. A scheme is applied to the study of structural coupling between exons and introns in fragmented genes of eukaryotes. The molecular, genetic, and evolutionary aspects of the features observed are discussed.

Animals↗
PubMed1992

The role of the transposable element hobo in the origin of endemic inversions in wild populations of Drosophila melanogaster.

Evidence from in situ hybridizations of DNA from the transposable element hobo to polytene salivary gland chromosome squashes reveals that hobo occupies both cytological breakpoints of three of four endemic inversions sampled from natural populations of Drosophila melanogaster in the Hawaiian islands. The fourth endemic inversion has a single hobo insert at one breakpoint. Cosmopolitan inversions on the same chromosomes do not show this association. Frequencies of both endemic and cosmopolitan inversions in Hawaiian populations fall in ranges typical for natural populations of D. melanogaster sampled worldwide, suggesting that these results may be typical of other regions besides Hawaii. This appears to be the first direct demonstration that transposable elements are responsible for causing specific rearrangements found in nature; consequently, it is also the first direct demonstration that chromosome rearrangements can arise in nature in a manner predicted by results of hybrid dysgenic crosses in the laboratory. Possible population genetic and evolutionary consequences are discussed.

Animals↗
PubMed2026

Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.

BACKGROUND: Pleione yunnanensis a terrestrial or semi-epiphytic herbaceous plant belonging to the Orchidaceae family, is valued for both its medicinal uses and ornamental appeal. Although its chloroplast genomes have been sequenced, its complete mt genome had not previously been resolved, limiting genetic and evolutionary studies of the species. RESULTS: In this work, we assembled and characterized the first complete mt genome of P. yunnanensis, revealing a structurally complex, multibranched system composed of 14 circular-mapping molecules totaling 468,176 bp with a GC content of 44.32%. The genome encodes 44 annotated genes, including 28 protein-coding genes (PCGs), 15 tRNAs, and one rRNA. The multibranched architecture provides new evidence supporting the dynamic and recombinational nature of plant mt genomes. Repeat analysis uncovered 29 simple sequence repeats (SSRs), 19 tandem repeats, and 118 dispersed repeats, indicating a comparatively lower repeat abundance than that found in closely related orchids with similar mt genome sizes. Codon-usage profiling of PCGs showed a marked bias toward A/T-ending codons. Prediction of RNA editing sites identified 4,708 putative edits across mitochondrial PCGs. Most mitochondrial genes displayed Ka/Ks ratios close to 1.0, suggesting relaxed selective constraints or lineage-specific evolutionary patterns rather than strong positive selection. Moreover, we detected 69 chloroplast-derived homologous fragments, including 15 intact genes, suggesting ongoing plastid-mitochondrial DNA transfer. Phylogenetic reconstruction and collinearity comparisons demonstrated that P. yunnanensis clustered closely with Dendrobium species, including D. amplum and D. hancockii, within the Orchidaceae clade. CONCLUSIONS: This study provides the first complete mt genome of P. yunnanensis, providing a foundational genomic resource for the genus Pleione. The results not only improve our understanding of mt genome structure and evolution in Orchidaceae, but also offer valuable molecular evidence for phylogenetic inference, germplasm identification, and conservation of this endangered medicinal species.

Orchidaceae↗