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PubMed1991

Reassessing 'hereditary' interethnic differences in anemia status.

The widely accepted hypothesis that significant differences in hemoglobin levels exist between African Americans and European Americans is critically evaluated. Most studies implying hereditary interethnic differences are derived from analyses of national cross-sectional surveys or smaller nonprobability samples. Yet those studies give inadequate consideration to the important nutritional and genetic variables that must be controlled for in acceptable comparative assessments of the heritable component of anemia. Missing but vital nutritional variables include reliable parameters of intake, absorption, and utilization of nutrients, and preexisting nutrient stores. Actual measures of confounding genetic conditions such as alpha-thalassemia and hemoglobin variants are also absent, although pronounced within-group diversity has been observed in both macroethnic groups. The likelihood that significant interethnic differences exist in the structural genes coding for hemoglobin level is nil given our species' molecular genetics and evolutionary history. Common recent African origins for all modern humans, as suggested by the fossil and molecular data, as well as our close biochemical affinities with chimpanzees and gorillas, suggest that biologically significant differences among populations of contemporary humans are unlikely. When the proper control of relevant epigenetic and genetic variables is maintained, the reported discrepancies tend to disappear.

Africa↗
PubMed2005

Genetic variability in the three genomes of Nasonia: nuclear, mitochondrial and Wolbachia.

Nasonia consists of three closely related species of parasitoid wasps that are all infected with the endosymbiotic bacteria Wolbachia, a reproductive parasite common in arthropods. This situation presents the opportunity to compare patterns of variation in three associated genomes, Wolbachia and the nuclear and mitochondrial genomes of its host. Furthermore, although Nasonia wasps are emerging as a model for evolutionary and genetic studies, little is known about their genetic variability. Using amplified fragment length polymorphisms (AFLPs), all three species present a relatively high level of nuclear polymorphism and have different patterns of variation, with one of the species, Nasonia giraulti, being divided into two divergent subgroups. In each species, the mitochondrial pattern of variation is different from the nuclear pattern, possibly due to genetic hitchhiking of the mitochondria during (cytoplasmically inherited) Wolbachia sweeps. Mitochondria in Nasonia show a synonymous substitution rate approximately 10-15-fold higher than nuclear genes, probably reflecting an elevated mitochondrial mutation rate that is among the highest found in insects. Finally, all three species are doubly infected with their own strains of Wolbachia, one each from the two major supergroups (A and B). Sequence analysis reveals that each of the three Nasonia species acquired their A and B bacteria independently by horizontal transfer events from other insects with the exception of B type Wolbachia in N. longicornis and N. giraulti, which were acquired prior to speciation and then codiverged with the host. This represents one of the few clear-cut examples of codivergence of Wolbachia during host speciation.

Animals↗
PubMedDate not supplied

[R. Goldschmidt and J. Huxley: creative parallelisms].

The comparative analysis of scientific heritage of Richard Goldschmidt and Julian Huxley shows convincingly the resemblance of these two scientists' views over the core problems of evolutionary theory, genetics and development biology. They both contributed to developing a triad "genetics--development--evolution". The problem of a relative growth of animals was the central point in both Goldschmidt's and Huxley's works. Huxley developed a formula of the allometric growth (law of constant differential growth) while Goldschmidt was the first to draw up the broad interpretation of the consequences of that phenomenon. Both scientists belonged to initiators of development genetics and used the "non-morganian" genetics in their efforts of solving problems of macroevolution. Goldschmidt tended toward an idea of an important role of macromutation in the process of macroevolution, though Huxley adhered to more moderate views. But at the same time the concept of preadaptive mutations proposed by Huxley was close to Goldschmidt's idea of macromutants. It is shown that both scientists analyzed profoundly the changes in early stages of embryogenesis in respect to macroevolution. It is not likely to be reasonable to oppose firmly Goldschmidt's saltationism to the evolutionary synthesis of Huxley. They developed the larger biological problems in a similar way, and undoubtedly their works in the field helped to enrich the development of the views over genetics and evolution. The open-minded analysis of Goldschmidt's and Huxley's concepts leads to creating modern and up-to-date views over the theory of evolution where seemingly incompatible things go together rather well and supplement each other. Evo-Devo rediscovered Goldshmidt's Biology and Huxley's Synthesis.

Animals↗
PubMed2006

Genetic models of homosexuality: generating testable predictions.

Homosexuality is a common occurrence in humans and other species, yet its genetic and evolutionary basis is poorly understood. Here, we formulate and study a series of simple mathematical models for the purpose of predicting empirical patterns that can be used to determine the form of selection that leads to polymorphism of genes influencing homosexuality. Specifically, we develop theory to make contrasting predictions about the genetic characteristics of genes influencing homosexuality including: (i) chromosomal location, (ii) dominance among segregating alleles and (iii) effect sizes that distinguish between the two major models for their polymorphism: the overdominance and sexual antagonism models. We conclude that the measurement of the genetic characteristics of quantitative trait loci (QTLs) found in genomic screens for genes influencing homosexuality can be highly informative in resolving the form of natural selection maintaining their polymorphism.

Alleles↗
PubMed2005

Eae19, a new locus on rat chromosome 15 regulating experimental autoimmune encephalomyelitis.

Multiple sclerosis (MS) and its animal model, myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis (MOG-EAE), share a complex genetic predisposition with contributions from the major histocompatibility complex class II genes and many other genes. Linkage mapping in F(2) crosses between the susceptible DA rat strain and the resistant ACI or BN rat strains in various models of autoimmune neuroinflammation have repeatedly displayed suggestive linkage to a region on rat chromosome 15. A direct study of this region was undertaken in congenic strains by transferring resistant ACI alleles to the susceptible DA background. Phenotypic analysis demonstrated lower maximal and cumulative EAE scores in the DA.ACI-D15Rat6-D15Rat71 (C15), DA.ACI-D15Rat6-D15Rat48, D15Rat126-D15Rat71 (C15R3b), and DA.ACI-D15Rat23-D15rat71 (C15R4) strains compared to the parental DA rat strain. Linkage analysis was then performed in a (DA x PVG.AV1)F(7) advanced intercross line, resulting in a LOD score of 4.7 for the maximal EAE score phenotype at the peak marker D15Rat71 and a confidence interval of 13 Mb, overlapping with the congenic fragment defined by the C15R3b and the C15R4 strains. Thus, a new MOG-EAE locus with the designation Eae19 is identified on rat chromosome 15. There are 32 confirmed or predicted genes in the confidence interval, including immune-responsive gene 1 and neuronal ceroid lipofuscinose gene 5. Definition of loci such as Eae19 enables the characterization of genetically regulated, evolutionary conserved disease pathways in complex neuroinflammatory diseases.

Animals↗
PubMed1999

Sperm competition between Drosophila males involves both displacement and incapacitation.

Females in almost all animal groups copulate with multiple males. This behaviour allows different males to compete for fertilization and gives females the opportunity to mediate this competition. In many animals and most insects, the second male to copulate with a female typically sires most of her offspring. In Drosophila melanogaster, this second-male sperm precedence has long been studied but, as in most species, its mechanism has remained unknown. Here we show, using labelled sperm in doubly mated females, that males can both physically displace and incapacitate stored sperm from earlier-mating males. Displacement occurs only if the second male transfers sperm to the female, and in only one of her three sperm-storage organs. Incapacitation can be caused by either fertile or spermless second males, but requires extended intervals between matings. Sperm from different males are not 'stratified' in the storage organs but mix freely. Many animal species may have multiple mechanisms of sperm competition like those observed here, and revealing these mechanisms is necessary to understand the genetic and evolutionary basis of second-male sperm precedence in animals.

Animals↗
PubMed2004

Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium.

Resistance (R) genes of plants are responsible for pathogen recognition and encode proteins that trigger a cascade of responses when a pathogen invades a plant. R genes are assumed to be under strong selection, but there is limited knowledge of the processes affecting R gene diversity in the wild. In this study, DNA sequence variation of Cf-2 homologs was surveyed in populations of Solanum pimpinellifolium, a wild relative of the cultivated tomato. The Cf-2 locus is involved in resistance to strains of the fungus Cladosporium fulvum. At least 26 different Cf-2 homologs were detected in natural populations of S. pimpinellifolium. These homologs differ by single base pair substitutions as well as indels in regions coding for leucine-rich repeats. Molecular population genetic analyses suggest that natural selection has acted heterogeneously on Cf-2 homologs, with selection against amino acid substitutions occurring in the 5' portion of the genes, and possible restricted positive selection in the 3' end. Balancing selection may have maintained haplotypes at the 5' end of the genes. Limited sequence exchange between genes has also contributed to sequence variation. S. pimpinellifolium individuals differ in the number of Cf-2 homologs they contain, obscuring the relationships of orthology and paralogy. This survey of Cf-2 variation in S. pimpinellifolium illustrates the wealth of R gene diversity that exists in wild plant populations, as well as the complexity of interacting genetic and evolutionary processes that generate such diversity.

Evolution, Molecular↗
PubMed2003

Reconciling actual and inferred population histories in the house finch (Carpodacus mexicanus) by AFLP analysis.

The house finch (Carpodacus mexicanus) is a native songbird of western North America that was introduced to the eastern United States and Hawaiian Islands in historic times. As such, it provides an unusually good opportunity to test the ability of molecular markers to recover recent details of a known population history. To investigate this prospect, genetic variation in 172 individuals from 16 populations in the western and eastern United States, southeastern Canada, Hawaiian Islands, and Mexico, as well as genetic variation in the closely related purple finch (Carpodacus purpureus) and Cassin's finch (Carpodacus cassinii) was studied by a semi-automated fluorescence-labeled amplified fragment length polymorphism (AFLP) marker system. A total of 363 markers were generated, of which 258 (71.2%) were polymorphic among species, 166 (61.4%) polymorphic among house finch subspecies, and 157 (60.2%) polymorphic among populations within the frontalis subspecies complex. Heterozygosities and interpopulation divergences revealed by the analysis appeared relatively low at all taxonomic levels, but there are few similar studies in avian populations with which to compare results. Whereas the known population history predicts that both eastern and Hawaiian finches should have been derived from within western populations, tree analysis using both populations and individuals as units suggests weak monophyly of eastern populations and indicates that Hawaiian populations are not clearly derived from California populations. However, the genetic distinctiveness of native and recently founded populations was disclosed by analyses of molecular variance as well as by a model-based assignment approach in which 98%, 94%, and 99% individuals from western, Hawaiian, and eastern regions, respectively, were assigned correctly to their populations without using prior information on population of origin, suggesting that these recent introductions have resulted in detectable differentiation without substantial loss of AFLP diversity. Our results indicate that AFLPs are a useful tool for population genetic and evolutionary studies of birds, particularly as a prelude to finding molecular markers linked to traits subjected to recent adaptive evolution.

Analysis of Variance↗
PubMed2005

Genetic dissection of neurodegeneration and CNS inflammation.

Inflammation and neurodegeneration characterize multiple sclerosis, as well as many other diseases of the central nervous system (CNS). The understanding of the molecular pathways that regulate these processes is of fundamental importance for the development of new therapies. Nerve lesions paradigms in animals can serve as important tools to dissect central features of human CNS disease and by using these models certain key regulators have also been identified. However, our knowledge of how aspects of neurodegeneration and CNS inflammation are regulated on a genomic level is very limited. Such knowledge may help to unravel disease mechanisms. By using a standardized nerve trauma model, ventral root avulsion (VRA), in a series of inbred rat strains we here demonstrate a potent genetic regulation of the degree of neuron death and glial activation. Genome wide mapping of these phenotypes in experimental rat strain crosses identifies several quantitative trait loci (QTLs) controlling nerve lesion-induced nerve cell death, local T cell accumulation and expression of MHC class II on microglia. This approach may lead to the identification of evolutionary conserved genetic polymorphisms in key controlling genes, which can serve as prime candidates for association studies in several human CNS diseases.

Animals↗
PubMed2005

Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche.

An understanding of the mutational and evolutionary mechanisms underlying the emergence of novel genes is critical to studies of phenotypic and genomic evolution. Here we describe a new example of a recently formed chimeric fusion gene that occurs in Drosophila guanche, D. madeirensis, and D. subobscura. This new gene, which we name Adh-Twain, resulted from an Adh mRNA that retrotransposed into the Gapdh-like gene, CG9010. Adh-Twain is transcribed; its 5' promoters and transcription patterns appear similar to those of CG9010. Population genetic and phylogenetic analyses suggest that the amino acid sequence of Adh-Twain evolved rapidly via directional selection shortly after it arose. Its more recent history, however, is characterized by slower evolution consistent with increasing functional constraints. We present a model for the origin of this new gene and discuss genetic and evolutionary factors affecting the evolution of new genes and functions.

5' Untranslated Regions↗
PubMed2006

Evolution of hypervariable microsatellites in apomictic polyploid lineages of Ranunculus carpaticola: directional bias at dinucleotide loci.

Microsatellites are widely used in genetic and evolutionary analyses, but their own evolution is far from simple. The mechanisms maintaining the mutational patterns of simple repeats and the typical stable allele-frequency distributions are still poorly understood. Asexual lineages may provide particularly informative models for the indirect study of microsatellite evolution, because their genomes act as complete linkage groups, with mutations being the only source of genetic variation. Here, we study the direction of accumulated dinucleotide microsatellite mutations in wild asexual lineages of hexaploid Ranunculus carpaticola. Whereas the overall number of contractions is not significantly different from that of expansions, the within-locus frequency of contractions, but not of expansions, significantly increases with allele length. Moreover, within-locus polymorphism is positively correlated with allele length, but this relationship is due solely to the influence of contraction mutations. Such asymmetries may explain length constraints generally observed with microsatellites and are consistent with stable, bell-shaped allele-frequency distributions. Although apomictic and allohexaploid, the R. carpaticola lineages show mutational patterns resembling the trends observed in a broad range of organisms, including sexuals and diploids, suggesting that, even if not of germline origin, the mutations in these apomicts may be the consequence of similar mechanisms.

Cell Lineage↗
PubMed1997

A comparison of heuristic search algorithms for molecular docking.

This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein-ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone.

Algorithms↗
PubMed2005

The avian genome uncovered.

Our knowledge of avian genomics has increased rapidly over the past few years, culminating in the recent publication of a draft sequence of the chicken genome, a milestone event in avian genetics and evolutionary biology. Comparative analysis reveals a compact avian genome structure containing a similar number of genes as found in mammals but with shorter intergenic DNA sequences and fewer repeats. Recombination is at a higher rate than in mammals, particularly for microchromosomes. These also differ from macrochromosomes in their GC and gene content, and their substitution rate. The avian genome has remained unusually stable during evolution and contrasts sharply with the frequent chromosomal rearrangements seen in the rodent lineage. Detailed analyses of polymorphism levels in chickens, including a genome-wide screening in three chicken breeds yielding a set of 2.8 million SNP markers, reveal unexpectedly high levels of genetic diversity. As a notable exception, the female-specific W chromosome is very low in diversity, a probable consequence of the effect of selection on non-recombining chromosomes. The chicken genome promises to be a useful resource for ecological and evolutionary studies of other bird species.

Journal Article↗
PubMed2025

Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex.

Eden's whale (Balaenoptera edeni), a poorly understood baleen cetacean, has long been shrouded in taxonomic ambiguity due to limited genomic resources, obscuring its distinction from closely related species and its position within the cetacean Tree of Life. In this paper, we present a high-quality chromosomal-level genome of B. edeni and conduct comparative genomic analyses to address long-standing taxonomic confusion and elucidate speciation of balaenopterids. Our phylogenomic analysis and demographic reconstruction reveal that B. edeni is a distinct sister to Bryde's whale (Balaenoptera brydei), sharing a common ancestor that diverged approximately 7.84 million years ago during the late Miocene. Their genetic divergence exceeds typical intraspecific variation in whales, supporting the reinstatement of B. brydei as a valid species. Chromosomal syntenic analyses suggest that macro-fragment inversions contributed to speciation in balaenopterid whales and uncover unexpected large-scale complex genome rearrangements in Bryde's whale, offering novel insights into cetacean genome evolution. Functional enrichment analysis of inverted regions between B. edeni and Balaenoptera musculus indicates their predominant association with metabolism and biosynthesis, as well as responses to various substances, stress, and stimuli. These genomic resources for B. edeni not only lay a critical foundation for comparative genetic and evolutionary research of cetaceans but also advance our understanding of the taxonomy and evolutionary dynamics of the Bryde's whale complex, with broader implications for baleen whale conservation and biodiversity.

Animals↗
PubMedDate not supplied

Current gene-mapping strategies in experimental models of multiple sclerosis.

Both family-based linkage analyses and population-based association studies have failed to identify disease-regulatory non-human leucocyte antigen genes of importance in multiple sclerosis (MS). Instead, investigators have employed experimental models, which offer major advantages in genetic studies. We summarize the current main methodologies used and the status of both the human and experimental approaches. Why is it important to find genes regulating MS? There is an immense number of cellular and molecular interactions defined in the immunological field and it is very difficult to unravel those that are critical to an inflammatory disease, such as MS, by classical hypothesis-driven research. Unbiased genetics defines evolutionary conserved gene polymorphisms and pathways regulated by these genes, which are central in the pathogenesis. These, in turn, are of interest as therapeutic targets and pharmacogenetic markers.

Animals↗
PubMed2006

Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria.

The field of microbiology has in recent years been transformed by the ever increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics and evolutionary development of bacteria. Among the latter group of microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. In this review we will discuss how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract.

Acclimatization↗
PubMed1998

Counting on comparative maps.

Comparative maps record the history of chromosome rearrangements that have occurred during the evolution of plants and animals. Effective use of these maps in genetic and evolutionary studies relies on quantitative analyses of the patterns of segment conservation. We review the analytical methods that have been developed for characterizing these maps and evaluate their application to existing comparative maps mainly for plants and animals.

Animals↗
PubMed2003

From Eden to a hell of uniformity? Directed evolution in humans.

For the first time during evolution of life on this planet, a species has acquired the ability to direct its own genetic destiny. Following 200,000 years of evolution, modern man now has the technologies not only to eradicate genetic disease but also to prolong life and enhance desired physical and mental traits. These technologies include preimplantation diagnosis, cloning, and gene therapy in the germline on native chromosomes or by adding artificial ones. At first glance, we should all be in favor of eliminating genetic diseases and enhancing genetic traits. Evolutionary considerations, however, uncover hidden dangers and suggest caution against the total embracement of such actions. The first major concern is that the genome will never be a completely reliable crystal ball for predicting human phenotypes. This is especially true for predictions concerning the performance of alleles in future generations whose populations might be subjected to different environmental and social challenges. The second, and perhaps more important, concern is that the end result of germline intervention and genetic enhancement will likely lead to the impoverishment of gene variants in the human population and deprive us of one of our most valued assets for survival in the future, our genetic diversity.

Alleles↗