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PubMed2005

Genes, causation and intentionality.

I want to exhibit the deeper metaphysical reasons why some common ways of describing the causal role of genes in development and evolution are problematic. Specifically, I show why using the concept of information in an intentional sense in genetics is inappropriate, even given a naturalistic account of intentionality. Furthermore, I argue that descriptions that use notions such as programming, directing or orchestrating are problematic not for empirical reasons, but because they are not strictly causal. They are intentional. By contrast, other notions that are part of the received view in genetics and evolutionary theory are defensible if understood correctly, in particular the idea that genes are the main replicators in evolution. The paper concludes that dropping all intentional or intentionally laden concepts does not force us to accept the so-called causal parity thesis, at least not in its stronger form.

Animals↗

PubMed2006

Molecular characterization of the HIV-1 gag nucleocapsid gene associated with vertical transmission.

BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) plays a pivotal role in the viral lifecycle: including encapsulating the viral genome, aiding in strand transfer during reverse transcription, and packaging two copies of the viral genome into progeny virions. Another gag gene product, p6, plays an integral role in successful viral budding from the plasma membrane and inclusion of the accessory protein Vpr within newly budding virions. In this study, we have characterized the gag NC and p6 genes from six mother-infant pairs following vertical transmission by performing phylogenetic analysis and by analyzing the degree of genetic diversity, evolutionary dynamics, and conservation of functional domains. RESULTS: Phylogenetic analysis of 168 gag NC and p6 genes sequences revealed six separate subtrees that corresponded to each mother-infant pair, suggesting that epidemiologically linked individuals were closer to each other than epidemiologically unlinked individuals. A high frequency (92.8%) of intact open reading frames of NC and p6 with patient and pair specific sequence motifs were conserved in mother-infant pairs' sequences. Nucleotide and amino acid distances showed a lower degree of viral heterogeneity, and a low degree of estimates of genetic diversity was also found in NC and p6 sequences. The NC and p6 sequences from both mothers and infants were found to be under positive selection pressure. The two important functional motifs within NC, the zinc-finger motifs, were highly conserved in most of the sequences, as were the gag p6 Vpr binding, AIP1 and late binding domains. Several CTL recognition epitopes identified within the NC and p6 genes were found to be mostly conserved in 6 mother-infant pairs' sequences. CONCLUSION: These data suggest that the gag NC and p6 open reading frames and functional domains were conserved in mother-infant pairs' sequences following vertical transmission, which confirms the critical role of these gene products in the viral lifecycle.

Acquired Immunodeficiency Syndrome↗

PubMed1999

Strategic and genetic models of evolution.

A new model which allows both for the effect of behavioural patterns on productive matings and for parental investment in the survival of offspring to maturity is considered. This combines ideas from genetics and evolutionary game theory, and provides a more realistic formulation to describe mating behaviour than the traditional 'battle of the sexes' model. Allowing individuals to migrate leads to spatial versions of both models. The saddle point method is used to obtain the speed of first spread of new genes/strategies in both spatial systems.

Biological Evolution↗

PubMed2003

Genetic diversity of serum proteins in three subpopulations of the Maria Gond tribe of Madhya Pradesh, India.

The phenotype and allele frequency distribution of group specific component (GC), transferrin (TF), alpha-1-antitrypsin (PI) and apolipoprotein E (APOE) was determined by isoelectric focusing of plasma samples from three subpopulations (Bison Horn Maria of the Kuakonda and Tokapal Block, and Abuj Maria of the Abujmar Hills of the Orchha block) of the Maria Gond tribe of Madhya Pradesh, India. A considerable level of allele frequency variation was observed in these subpopulations, which highlighted social and geographical isolation among them. The average heterozygosity for these IEF subtype systems was high (29-39%) and the gene diversity among these subpopulation groups was of low to moderate range (1.4%). The overall analysis showed that these polymorphisms are useful anthropological markers for micro-evolutionary and genetic structure studies.

Apolipoproteins E↗

PubMed1989

Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus.

At the extremes of its natural distribution, populations of the common killifish Fundulus heteroclitus experience a difference of more than 15 degrees C in mean annual temperature. These populations are virtually fixed for two different codominant alleles at the heart-type lactate dehydrogenase locus (Ldh-B) which code for allozymes with different and adaptive kinetic responses to temperature. Two populations near the extremes of the species range (i.e., Maine and Georgia) were further studied for thermal adaptation at this locus. In the absence of any kinetic differences one would predict that to maintain a constant reaction velocity, 2 to 3 times as much enzyme would be required for each 10 degrees C decrease in environmental temperature. Consistent with this adaptive strategy and in addition to the adaptive kinetic characteristics, the LDH-B4 enzyme (EC 1.1.1.27) concentration and its mRNA concentration were approximately twice as great in the northern population as in the southern population. Acclimation experiments allow us to conclude that these differences are due to a combination of fixed genetic traits (evolutionary adaptation) and plastic responses to temperature (physiological acclimation). Furthermore, our calculations show that the LDH-B4 reaction velocities are essentially equivalent for these two populations, even though they live in significantly different thermal environments.

Adaptation, Physiological↗

PubMed2003

The evolution of mate choice and mating biases.

We review the current status of three well-established models (direct benefits, indirect benefits and sensory drive) and one newcomer (antagonistic chase-away) of the evolution of mate choice and the biases that are expressed during choice. We highlight the differences and commonalities in the underlying genetics and evolutionary dynamics of these models. We then argue that progress in understanding the evolution of mate choice is currently hampered by spurious distinctions among models and a misguided tendency to test the processes underlying each model as mutually exclusive alternatives. Finally, we suggest potentially fruitful directions for future theoretical and empirical research.

Animals↗

PubMed2004

Fast and high precision algorithms for optimization in large-scale genomic problems.

There are several very difficult problems related to genetic or genomic analysis that belong to the field of discrete optimization in a set of all possible orders. With n elements (points, markers, clones, sequences, etc.), the number of all possible orders is n!/2 and only one of these is considered to be the true order. A classical formulation of a similar mathematical problem is the well-known traveling salesperson problem model (TSP). Genetic analogues of this problem include: ordering in multilocus genetic mapping, evolutionary tree reconstruction, building physical maps (contig assembling for overlapping clones and radiation hybrid mapping), and others. A novel, fast and reliable hybrid algorithm based on evolution strategy and guided local search discrete optimization was developed for TSP formulation of the multilocus mapping problems. High performance and high precision of the employed algorithm named guided evolution strategy (GES) allows verification of the obtained multilocus orders based on different computing-intensive approaches (e.g., bootstrap or jackknife) for detection and removing unreliable marker loci, hence, stabilizing the resulting paths. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on simulated data of multilocus genetic maps up to 1000 points per linkage group.

Algorithms↗

PubMedDate not supplied

Vertebrate dentitions at the origin of jaws: when and how pattern evolved.

New evidence shows that teeth evolved with a greater degree of independence from jaws than previously considered. Pharyngeal denticles occur in jawless fish and also in early gnathostomes and precede jaw teeth in phylogeny. Many of these denticles form joined polarized sets on each branchial arch; these resemble whorl-shaped tooth sets on the jaws of stem and crown gnathostomes and are proposed as homologous units. Therefore, the source of patterning of these pharyngeal denticle and tooth sets is conserved from jawless conditions. It is proposed that developmental regulatory systems, responsible for all such tooth patterns on the jaws, are co-opted from the pharyngeal region and not from the skin as classically understood. This strongly implicates embryonic endoderm as opposed to ectoderm in the genetic control of dentition patterning. New interpretations of ontogenetic data on patterning dentitions of extant sharks are proposed, together with those of osteichthyan fish. Two entirely fossil groups, placoderms and acanthodians, at the base of gnathostome phylogeny are reassessed on the basis of a new model. It is concluded that within stem group and crown group gnathostomes several different strategies, unique to each taxon, were adopted to produce different developmental models of dentition patterning from pharyngeal denticles. One shared developmental pattern is that of initiation from primordial tooth sites, independently in each dentate zone of the jaws. The new model is proposed as a framework for data on evolutionary developmental genetics.

Animals↗

PubMed2006

Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group.

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group.

Animals↗

PubMed1996

The medicalization of race: scientific legitimization of a flawed social construct.

The term "race" has many definitions, ranging from a family unit to a species, but in common and medical usage, defining "race" has meant separating Homo sapiens into three to six groups. This division of Homo sapiens into race taxons started in the 18th century, when the sciences of genetics and evolutionary biology were not yet invented. These disciplines have since shown that human race taxonomy has no scientific basis. Race categories are social constructs, that is, concepts created from prevailing social perceptions without scientific evidence. Despite modern proof that race is arbitrary biological fiction, racial taxons are still used widely in medical teaching, practice, and research. Human diversity is inconsistently taught in medical schools and erratically presented in medical texts. Race taxons have been "medicalized"; that is, race groupings have been legitimized by their use in medical literature and practice as acceptable descriptive labels that are integral to the proper diagnosis and treatment of disease in humans. Assumptions about disease that are made because a race has been assigned can result in important negative consequences for individual patients and inaccurate genetic inferences for populations. In contrast, ethnicity is a concept that incorporates social, religious, linguistic, dietary, and other variables to identify individual persons and populations. Ethnicity may be able to impart clinical clues to diagnosis if the clinician taking the history is well informed and open minded. Ethnic boundaries are dynamic and imprecise, and a strict methodical approach to ethnicity that is equal to the approach required for the study of other variables is necessary if the concept of ethnicity is to be clinically useful.

Biomedical Research↗

PubMed2005

Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation.

The ability to obtain large amounts of genomic sequence for organisms and high throughput technology has led to a change in the thrust of research at the level of chromosomes in animals. In the past chromosomal analysis of animals was focused on gross changes such as inversions, translocations, and deletions for both genetic and evolutionary studies. The advent of in situ hybridization technology and the ability to measure genome content size changed both the precision and the scale of studies addressing chromosomal change as a tool in evolutionary biology. This chapter addresses two of the major areas of change that have occurred in chromosomal studies in the past decade -- examination of more refined and genome enabled structural changes in chromosomes and genome size measure. This chapter describes some of the chromosome structure approaches such as fluorescent in situ hybridization (FISH), comparative genomic hybridization (CGH) and other techniques. As well, advances in Genome size measurement and theory are described herein.

Animals↗

PubMed2003

[Illnesses as racial concepts: political and scientific dimensions of a biomedical research program by Cécile and Oskar Vogt between Tiflis and Berlin (1919-1939)].

In the research of Cécile and Oskar Vogt during the 1920s at the Kaiser Wilhelm Institute for Brain Research, the notion of race had a double function. Firstly, it integrated the mapping of brain functions, the classification of psychiatric diseases, genetics, and evolutionary biology. Secondly, it proved useful in attracting funding for the creation of research facilities in Germany and the USSR. After 1933, C. and O. Vogt stopped using the term race for political reasons, but tried to offer their work as a contribution to eugenics. Bernhard Patzig, their collaborator, continued their approach during National Socialism. Distancing his research from Rüdin's statistics on heredity, but working within the paradigm of eugenics, he established the hereditary nature of certain neurological diseases and psychotic disorders such as schizophrenia.

Genetic Diseases, Inborn↗

PubMed2006

A role for genetic accommodation in evolution?

Whether evolutionary change can occur by genetic assimilation, or more generally by genetic accommodation, remains controversial. Here we examine some of the experimental evidence for both phenomena. Several experiments in Drosophila suggest that assimilation is possible, and a new paper shows that a color polyphenism in the tobacco hornworm, Manduca sexta, can evolve by genetic accommodation. We argue that genetic accommodation, including assimilation, is a plausible mechanism in evolution; however, more work is required to test how this mechanism acts and how often it is involved in evolutionary change.

Animals↗

PubMedDate not supplied

Taxonomy of phototrophic green and purple bacteria: a review.

The presently existing classification for the green and purple bacteria comprises physiological-ecological assemblages of phototrophic bacteria with anoxygenic photosynthesis. The taxonomic units of the different levels were based entirely on common phenotypic traits, including morphological, cytological, physiological and biochemical characteristics. Since degrees of resemblance form the basis of the grouping, this classification cannot reflect the genetic or evolutionary relatedness of these bacteria, neither among themselves nor with other bacteria. The advantage of the artificial system, however, is the use of features which can be established in most laboratories and which allow the comparison and identification of newly isolated strains with those already studied and described. The four existing families correspond to the four major recognized, ecophysiological groups, the Chlorobiaceae and Chloroflexaceae among the green bacteria, and the Chromatiaceae and Rhodospirillaceae among the purple bacteria. Our knowledge of all these groups is incomplete; this is reflected by the fact that seven new species have been described during the past three years (6th Newsletter on phot. bacteria, Trüper and Hansen, 1982). The description of the new genus and species Erythrobacter longus (Shiba and Simidu, 1982) is also interesting, as it comprises aerobic chemoorganotrophic marine bacteria which form bacteriochlorophyll a and carotenoids; however, no strains were able to grow phototrophilcally. Significant success is currently being obtained in the different approaches toward elucidating the genetic relationships within and outside of the purple and green bacteria. Detailed studies of the lipopolysaccharides of several species and genera of the Rhodospirillaceae (Weckesser et al., 1979, and more recent paper) have proven to be very useful for the recognition of relationships or dissimilarities between the species of a genus or between different genera. Amino acid sequence studies of cytochromes c from Rhodospirillaceae, other bacteria and eukaryotic organisms (Dickerson, 1980) have led to the recognition of four different groups of cytochrome c molecules (long, medium and two groups of short protein chains). The subdivision of the Rhodospirillaceae into three species groups, each possessing one of the three types of cytochrome c, proved to be in total agreement with the results of oligonucleotide cataloging of the 16 S ribosomal RNA of these bacteria (Gibson et al., 1979). The latter method also revealed that several chemotropic bacteria, including the nitrifying bacteria, are more closely related to certain purple bacteria than different species of the purple bacteria among themselves (Seewaldt et al., 1982).(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteria↗

PubMed2002

Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review.

Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.

Animals↗

PubMedDate not supplied

[Heredity and environment in the genesis, epigenesis and evolution of the orofacial area].

Genetic and evolutionary aspects of the dento-facial complex are described according to the concept of heredity as a force of preservation for the human species, though ruled by natural selection and by mutational changes. Ontogenesis and growth of the oral structures reflect mutual regulations between genes and environmental factors. Therefore, the authors carry out an analysis of environmental and constitutional factors affecting dental and facial development. Three levels are identified: individual morphogenesis and growth; actual heredity of parietal dento-facial traits; role and meaning of teeth, jaws and temporo-mandibular joint during evolution leading to Homo sapiens sapiens. As far as individual development is concerned, genes provide only the input for initial cell proliferation and/or differentiation. Further on, growth and morphogenesis of oro-facial structures takes place by means of cell-to-cell and cell-to-substrate interactions. The final, structural result is due to reciprocal interactions among developing structures: muscles modify bone, teeth alignment influences bony bases alignment, ecc. Each structure is genetically determined (teeth, bones, muscles) and each structure carries out epigenetic regulations on other structures: no structure is secluded from biological function of the organism. The inheritance of oro-facial "traits", then, is hardly valuable. First of all, "traits" actually do not exist: they are the product of complex, multifactorial biological mechanisms. Moreover, facial characteristics are affected by polygenic regulation, each gene often showing pleiotropic effects. It has been calculated that 85-90% of facial dimensions in due to epigenetic modifications. Evolution and phylogenesis give evidence about the deep environmental influence on oro-facial morphology. Apart from certain molecular features regarding tooth structure (several dental proteins are today the same as those of the first Vertebrates who lived 500 millions of years ago), tooth number, form, and size depend upon environmental factors. Therefore, dentistry has the important task to preserve fundamental characteristics of dentition, and to intercept environmental pathogenetic factors, as dentition represents a precious instrument for the survival of the human species.

Biological Evolution↗

PubMed1980

An n locus multiallele model for gene substitution.

We discuss the conceptual conflict between a slow series of gene substitutions as the mechanism of evolutionary change, and the apparent need for rapid and coordinated changes at many loci simultaneously in producing complex adaptations. To improve on the limitations of classical theory and accommodate the enormous amount of variability disclosed by electrophoretic studies, we develop a model that can deal with gene substitution at n loci, with numerous alleles at each locus. Fitness is treated somewhat differently from the usual way by allowing it to vary between zero and the number of offspring an individual of a particular species can produce. As maximum fitnesses, we chose five as typical of large mammals, 100 for insects like Drosophila, and 1000 for very prolific species. When our model is applied to the classical problem of determining the number of generations required to change the gene frequency from 0.0001 to 0.9999 (but for 100 loci rather than one), we find that it requires 22,899 generations when maximum fitness is five, 7,984 generations when maximum fitness is 100 and 5,333 generations when it is 1000. This is something of an improvement over the 300,000 generations calculated by Haldane (1957). By allowing the fitnesses in our model to be explicitly frequency dependent, these results are reduced considerably. In addition, allowing varying proportions of the population to inbreed reduces the number of generations required for the classical problem by as much as 50%. We also point out that, given the large amount of observed genetic variation, evolutionary change may not be so much a matter of classical gene substitution as it is of changing from one array of alleles to another. With our model, the array (0.5, 0.15, 0.2, 0.1, 0.05) can be changed to (0.03, 0.1, 0.2, 0.17, 0.5) at 1000 loci in 6,043, 2,108, or 1,408 generations, depending on whether the maximum fitness is five, 100, or 1000. Finally, we note that it is possible to substitute one array for another while continuously favoring heterozygotes.

Alleles↗

PubMed2002

Genes, interactions, and the development of behavior.

Explaining how genes influence behavior is important to many branches of psychology, including development, behavior genetics, and evolutionary psychology. Presented here is a developmental model linking the immediate consequence of gene activity (transcription of messenger RNA molecules from DNA sequences) to behavior through multiple molecular, cellular, and physiological levels. The model provides a level of detail appropriate to theories of behavioral development that recognizes the molecular level of gene action, dispensing with the metaphorical use of such terms as blueprints, plans, or constraints that has obscured much previous discussion. Special attention is paid to the possible role of immediate-early genes in initiating developmental responses to experience, adding specificity to the claim that neither genes nor experience act alone to shape development.

Behavior↗