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PubMed2006

Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family.

BACKGROUND: The medical community requires computational tools that distinguish missense genetic differences having phenotypic impact within the vast number of sense mutations that do not. Tools that do this will become increasingly important for those seeking to use human genome sequence data to predict disease, make prognoses, and customize therapy to individual patients. RESULTS: An approach, termed DETECTER, is proposed to identify sites in a protein sequence where amino acid replacements are likely to have a significant effect on phenotype, including causing genetic disease. This approach uses a model-dependent tool to estimate the normalized replacement rate at individual sites in a protein sequence, based on a history of those sites extracted from an evolutionary analysis of the corresponding protein family. This tool identifies sites that have higher-than-average, average, or lower-than-average rates of change in the lineage leading to the sequence in the population of interest. The rates are then combined with sequence data to determine the likelihoods that particular amino acids were present at individual sites in the evolutionary history of the gene family. These likelihoods are used to predict whether any specific amino acid replacements, if introduced at the site in a modern human population, would have a significant impact on fitness. The DETECTER tool is used to analyze the cystic fibrosis transmembrane conductance regulator (CFTR) gene family. CONCLUSION: In this system, DETECTER retrodicts amino acid replacements associated with the cystic fibrosis disease with greater accuracy than alternative approaches. While this result validates this approach for this particular family of proteins only, the approach may be applicable to the analysis of polymorphisms generally, including SNPs in a human population.

Amino Acid Substitution↗
PubMed1996

Evolutionary patterns in ontogenetic transformation: from laws to regularities.

The concept of heterochrony derives from classical approaches to the study of ontogeny and phylogeny. Under the influence of landmark books by deBeer (1930) and Gould (1977), the traditional theories have been revised to fit into the conceptual framework of modern genetics and evolutionary theory. The current scheme, however, suffers from a problem of lack of precise definitions. The term heterochrony is now used to refer to a developmental process as well as to an evolutionary pattern. That is, it refers to a microevolutionary process of adaptation, operating in local populations under selection and to a macroevolutionary pattern based on undefined internal laws of form. Such conceptually contradictory frameworks are a source of confusion and of empirical misuse of concepts. We propose to reduce the dependence of current thinking about heterochrony on the concept of "timing" and instead focus on the organization of sequences of developmental events in ontogeny. Although Haeckelian views have been rejected, most experts would agree that some subtle parallelism between ontogeny and phylogeny does occur. This relationship deserves renewed attention and urodeles are particularly suited to study it due to their variable patterns of ontogeny and complex life cycles. Current reductionist attempts to apply the morphological terminology and postulates of classical heterochrony concepts to cellular and molecular (genetic) aspects of morphogenesis are problematic. Molecular heterochrony requires a linear or strictly hierarchical structure of gene regulation of development. In addition, isomorphism between genetic mutations and morphological changes would be required for the existing terminology to apply. Finally, we caution against a broad interpretation of heterochronic processes at the molecular level, since the approach may end up permitting the meaningless interpretation of any developmental change as heterochrony.

Animals↗
PubMed1982

Critical examination of postulated cladistic relationships among species of flour beetles (genus Tribolium, Tenebrionidae, Coleoptera).

Cytological considerations have led to the hypothesis that Tribolium confusum (CF) evolved from an ancestor similar to T. castaneum (CS) by translocation of an autosome to the X chromosome, and that T. destructor (DEST) was derived from CF. T. brevicornis (BREV) is regarded as the most primitive on morphological grounds. Electrophoretic analyses of 19 strains of CS, 7 of CF, and 1 each of DEST and BREV do not support this postulated evolutionary pathway. CF and CS are much more similar to BREV than they are to each other. (Comparisons of morphological mutations in CS and CF also indicate that the two species are not similar genetically.) DEST and CF are very dissimilar electrophoretically. It is likely that the species evolved independently from an ancestral stock which may be represented by BREV. Recognition of gene homology in different species is the keystone for all attempts at constructing genetically meaningful evolutionary pathways. The difficulties involved in doing so are pointed out.

Acid Phosphatase↗
PubMed2004

Deciphering the swordtail's tale: a molecular and evolutionary quest.

The power of sexual selection to influence the evolution of morphological traits was first proposed more than 130 years ago by Darwin. Though long a controversial idea, it has been documented in recent decades for a host of animal species. Yet few of the established sexually selected features have been explored at the level of their genetic or molecular foundations. In a recent report, Zauner et al.1 describe some of the molecular features associated with one of the best characterized of sexually selected traits, the male-specific tail "sword" seen in certain species of the fish genus Xiphophorus. Zauner et al. find that the msxC gene, a gene previously implicated in fin development from work in zebrafish, is dramatically and specifically upregulated in the development of the ventral caudal fin rays, which give rise to the sword, in males. The results provide the first molecular insight into the development of this sexually selected trait while prompting new questions about the structure of the entire genetic network that underlies this trait. To fully understand the molecular-genetic and evolutionary history of this network, however, it will be essential to determine whether sword-development is a basal or derived trait in Xiphophorus.

Animals↗
PubMed2006

Contraselectable streptomycin susceptibility determinant for genetic manipulation and analysis of Helicobacter pylori.

Many Helicobacter pylori genetic studies would benefit from an ability to move DNA sequences easily between strains by transformation and homologous recombination, without needing to leave a conventional drug resistance determinant at the targeted locus. Presented here is a two-gene cassette that can be selected both (i) against, due to a Campylobacter jejuni rpsL gene (dominant streptomycin susceptibility in cells also carrying an rpsL-str(r) allele), and (ii) for, due to an erm gene (erythromycin resistance). This rpsL,erm cassette's utility was assessed by using it to replace four gene loci (mdaB, frxA, fur, and nikR) in four streptomycin-resistant [Str(r)] strain backgrounds (derivatives of 26695, SS1, X47, and G27MA). The resultant 16 strains (phenotypically erythromycin resistant [Erm(r)] and Str(s)) were each transformed with wild-type genomic DNAs, and Str(r) derivatives were selected. The desired Erm(s) Str(r) isolates were obtained at frequencies that ranged from 17 to 96% among Str(r) transformants, with the Erm(s) yield apparently depending on the strain background and genome location of the targeted locus. The ease of isolating unmarked transformants described here should be valuable for many H. pylori molecular genetic and evolutionary analyses.

Alleles↗
PubMed2025

Genomic analysis of xerophyte Salweenia species provides insights into the alpine dry-warm valleys divergence and survival history.

Salweenia species are evergreen shrubs capable of preventing desertification and maintaining the health of alpine dry-warm ecosystems in the Hengduan Mountains. However, both the narrowly distributed S. bouffordiana and its more widespread close relative S. wardii are endemic and endangered. Furthermore, their small population sizes render each of these species at risk of extinction. To infer how past climate changes have shaped the evolutionary history of these species, we developed a chromosome-level S. bouffordiana genome (788 Mb) and compared the two species' evolutionary histories, genetic loads and the genomic adaptions to local environmental conditions using whole-genome resequencing data. Our findings reveal a sharp population decline from the Pliocene to the Quaternary. However, populations of S. bouffordiana then started to recover before declining further, while S. wardii populations continued to decline until recently. Abundant homozygous-derived variants accumulated in the two species, particularly in S. bouffordiana, while the species with the most heterozygous variants was S. wardii. Accumulated extensive inbreeding effects but possessed few LOF mutations and few highly deleterious variants in the S. bouffordiana that have experienced the most severe demographic bottlenecks, most likely because of purging effects. This accelerating decline cascade will likely be detrimental to the consequences for the species' future viability and adaptive potential. Overall, this study improves our understanding of the evolutionary history of Salweenia shrubs tolerant to extreme environments and offers a genetic resource for future breeding and conservation efforts.

Genome, Plant↗
PubMed2000

Cloning and primary structure of putative cytosolic and mitochondrial malate dehydrogenase from the mollusc Nucella lapillus (L.).

The evolutionary history of the malate dehydrogenase (MDH) gene family [NAD-dependent MDH; EC 1.1.1.37 and NAD(P)-dependent MDH; EC 1.1.1.82] has received much attention. MDHs have also featured extensively as electrophoretic markers in population genetics and evolutionary ecology, and in many cases, intraspecific variation in MDH has been correlated with environmental variables. However, while the amino acid residues essential for MDH function are known, no studies have examined intraspecific nucleotide variation despite evidence indicating that natural selection may be operating on this locus. This study presents two sets of degenerate oligonucleotide PCR primers to facilitate the cloning of cytosolic MDH (cMDH) and mitochondrial MDH (mMDH) from a broad range of animals (cMDH) and animals and plants (mMDH). These primers were used to obtain putative cMDH and mMDH cDNAs from the mollusc Nucella lapillus. The N. lapillus cMDH cDNA was found to encode a putative cMDH protein of 334aa and 36kDa, while the mMDH cDNA encoded a putative mature mMDH protein of 315aa and 33kDa. The putative amino acid sequences of the two compartmentalised N. lapillus MDHs are presented and compared to other known MDH sequences.

Amino Acid Sequence↗
PubMed2006

Physiological anthropology: past and future.

Environmental studies in adaptive human biology by North American anthropologists have a history of strong investigative research. From both laboratory and field work, we have gained major insights into human response to physical and social challenges. While these results were considered by most professionals to belong within evolutionary biology, in fact the intellectual structure sprang almost entirely from physiological equilibrium models. Consequently, physiological process itself was the focus. Further, most of the physiological patterns were not linked directly to important outcomes such as work output, reproductive success or survival. About 1975, American physiological anthropologists, led by Paul Baker, turned to studies of health, change and stress response. These studies were strong, but were still neither genetic nor evolutionary in intellectual structure. Evolutionary human biology was taken over by a new body of theory now called "behavior ecology", positing that selfish genes control human behavior to promote their own reproduction. This was paralleled by strong use of evolutionary theory in some areas of molecular biology. However, although physiological anthropologists have not focused on evolution, we have been developing powerful causal models that incorporate elements of physiology, morphology, physical environment and cultural behavior. In these "proximate" biocultural models, it is of little importance whether outcomes such as work or energy management are genetically based. Our future offers two major challenges. First, we must confirm causal links between specific physiological patterns and outcomes of practical importance to individuals and societies. Second, if we are to take our place in evolutionary biology, the one overarching theory of life on earth, we must understand the heritability of physiological traits, and determine whether they play a role in survival and reproduction.

Adaptation, Physiological↗
PubMed2006

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

BACKGROUND: Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. RESULTS: Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. CONCLUSION: The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

Conservation of Natural Resources↗
PubMed1979

Evolutionary conservation of large chromosomal segments reflected in mammalian gene maps.

Conservation of genetic linkage over long periods of time is exemplifted. Comparisons are made between chromosomal regions in different species as well as within two species, man and the house mouse. Homologous regions are defined and the phenomenon of differential silencing of genes is described. The importance of conservation of particular sequences of genes is discussed in relation to medical genetics, animal breeding, evolutionary theory and genetic regulation.

Animals↗
PubMed1982

Genetic mapping in mammals: chromosome map of domestic cat.

A genetic map of 31 biochemical loci located on 17 feline syntenic (linkage) groups has been derived by somatic cell genetic analysis of cat-rodent hybrids. Most of these syntenic groups have been assigned to one of the 19 feline chromosomes. Comparative linkage analysis of the feline biochemical loci and homologous human loci revealed considerable conservation of linkage associations between the primates and the Felidae (order Carnivora). Many of these same linkage groups have not been conserved in the murine genome. The genetic and evolutionary implications of comparative mapping analysis among mammalian species are discussed.

Animals↗
PubMed2001

The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence?

This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the compositions of the major clades in the phylogenies based on these two markers were similar, there were several important differences. This, in combination with the fact that many species were not monophyletic, suggests either that introgressive hybridization is occurring or that lineage sorting is incomplete. The molecular tree topologies bear little similarity to the results of a recent cladistic analysis based on skeletal morphology and are at odds with the fossil record. We hypothesize that these conflicting results may be due to the same morphology having evolved independently more than once in Acropora and/or the occurrence of extensive interspecific hybridization and introgression in combination with morphology being determined by a small number of genes. Our results indicate that many Acropora species belong to a species complex or syngameon and that morphology has little predictive value with regard to syngameon composition. Morphological species in the genus often do not correspond to genetically distinct evolutionary units. Instead, species that differ in timing of gamete release tend to constitute genetically distinct clades.

Animals↗
PubMed2005

Hybridization dynamics between sympatric species of trout: loss of reproductive isolation.

Although reinforcement should enhance reproductive barriers in sympatric species, sympatric trout species do hybridize. Using mitochondrial and nuclear species markers, we investigated hybridization directionality, hybrid mating biases, and selection against hybrids in 13 sympatric cut-throat and rainbow trout populations on Vancouver Island, Canada. Approximately 50% of the genotyped fish were hybrid (F1 or higher-order) and populations ranged from very recent (all F1 hybrids) to extremely advanced higher-order hybridization. Overall, interbreeding was reciprocal, although some populations showed directional hybridization. Pronounced cytonuclear disequilibrium in post-F1 hybrids indicated a remarkable mating bias not previously reported, which is most likely because of behavioural reproductive preferences. Selection against hybrids was observed in only two populations, indicative of extrinsic selection. Two populations were 'hybrid swarms', with a complete loss of reproductive isolation. The complex hybridization dynamics in this system represent a valuable natural experiment of the genetic and evolutionary implications of recent and on-going interspecific hybridization.

Animals↗
PubMed1986

Genetic studies of low abundance human plasma proteins. II. Population genetics of coagulation factor XIIIB.

Plasma samples from a large number of different ethnic groups, consisting of U.S. whites, U.S. blacks, Eskimos from Kodiak and St. Lawrence Island, Aleuts of the Pribilof Islands, and three Amerindian groups from Canada and Mexico have been analyzed by isoelectric focusing followed by immunoblotting to determine the magnitude of genetic variation at the F XIIIB structural locus. The synthesis of published data and our new data demonstrate remarkable variation in the distribution of the three common alleles at this locus and establishes F XIIIB as an extremely informative marker for population differentiation and evolutionary studies. Genetic distance analysis based on this variation separates Caucasian, black, and Mongoloid populations into three distinct clusters.

Blood Proteins↗
PubMed2003

How the analysis of genetic mutations can help us to solve basic problems in gerontology? II. Life extending genetic modifications in budding yeast S. cereviseae, fruit fly D. melanogaster and laboratory mice M. musculus.

Most studies of aging are conducted in humans and domestic or laboratory animals, i.e. in conditions where artificial environment protection is applied, This yields changes in physiology and behavior, which set up organism's state unobserved in wild life. This state may be less adequate to the evolutionary adjusted genetic construction of an organism, which generates a hypothesis that in natural niches the aging rate can be lower and stress resistance can be higher than in captivity despite the fact that life expectancy in habitat is essentially lower than that in laboratory conditions due to high external mortality. Direct test of this hypothesis is difficult because of problems related to reconstruction of natural environment conditions in the laboratory. Substantial life-extending effect of some mutated genes can serve as indirect test of the hypothesis. We propose that in some cases genetic mutations can distort reaction of an organism on environmental cues and change control parameters of its life cycle. As a result such mutants in laboratory may partly demonstrate life traits similar to those observed in natural environment, e.g. associated with high stress resistance and low rate of aging. These features combined with low external mortality in laboratory conditions may lead to significant extension in the life span of mutants. Recently we considered 56 life-extending gene modifications in nematode C. elegans (Adv. Gerontol., 2003, Vol. 11), scattered in many publications. In this paper we consider pertinent life-extending gene modifications corresponded to the budding yeast S. cerevisease (29 genes), fruit fly D. melanogaster (22 genes) and laboratory mice M. musculus (8 genes).

Animals↗
PubMed2000

The evolution of the G matrix: selection or drift?

The evolution of quantitative characters can be described by the equation Deltaz=GP-1S where Deltaz is the vector of mean responses, G is the matrix of additive genetic variances and covariances, P is the matrix of phenotypic variances and covariances and S is the vector of selection differentials. This equation can be used to predict changes in trait values or to retrospectively estimate the selection gradient and is thus a central equation of evolutionary quantitative genetics. Genetic variances and covariances will be reduced by stabilizing selection, directional selection and drift, and increased by mutation. Changes in trait values resulting from directional selection that are comparable with differences observed among species are readily obtainable in short geological time spans (<5000 generations) with selection intensities so small that they would have an insignificant effect on the G matrix (of course it is possible that such changes came about by strong selection over a few generations, followed by long periods of stasis; there is insufficient evidence to presently distinguish these two possibilities). On the other hand, observed effective population sizes are sufficiently small that considerable changes in G can be expected from drift alone. The action of drift can be distinguished from selection because the former produces a proportional change in G whereas the latter, in general, will not. A survey of studies examining variation in G suggests that the null hypothesis that most of the variation can be attributed to drift rather than selection cannot be rejected. However, more research on the predicted statistical distribution of G as a result of selection and/or drift is required and further development of statistical tests to distinguish these two forces needs to be made.

Animals↗
PubMed2006

Progress and challenges in studies of the evolution of development.

Plant evolutionary developmental genetics (EDG) has made considerable progress over the last decade. This is in part due to the accumulation of large amounts of sequence data that have provided robust organismal phylogenies and, increasingly, broad assessments of molecular evolution. Attempts to use primary sequence data to identify genes that have changed function in evolutionary time have not been as successful as initially hoped. The coding sequences of most genes, which are more amenable to statistical analysis than are regulatory sequences, are generally under purifying selection, as would be expected if much evolutionary change is the result of changes in cis-regulatory sequences. Sequence-based analysis of the regulatory sequences themselves remains difficult. Comparative studies of gene expression have been useful to identify genes whose developmental role may have changed in evolutionary time and will be critical to the future development of EDG. Such studies can be used to test hypotheses of gene function. Transformation experiments are often illuminating, but can be hard to interpret, particularly if genes from multiple species are all placed into a single heterologous system such as Arabidopsis. The ideal experiment would be a gene swap or promoter swap between two species, but this awaits development of good transformation systems. The immediate need for EDG is studies of gene expression on a massive scale, far broader than any studies undertaken to date.

Botany↗
PubMed2003

Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus.

Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the "biometric method" for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, fully homozygous inbred lines. The second is that all genetic variation is attributable to deleterious mutations maintained in mutation-selection balance. I explicitly test this hypothesis using likelihood ratios. Of the three deleterious mutation models tested, the first two are rejected for all characters. The failure of these models is due to an excess of additive genetic variation relative to the expectation under mutation-selection balance. The third model is not rejected for either of two log-transformed male fitness traits. However, this model imposes only "weak conditions" and is not sufficiently detailed to provide estimates for mutational parameters. The implication is that, if biometric methods are going to yield useful parameter estimates, they will need to consider mutational models more complicated than those typically employed in experimental studies.

Analysis of Variance↗