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PubMed1988

[Evolutionary significance of the presence in mobile genetic elements of regulatory sites reacting to the environment. Regulatory site as a trigger].

A mathematical model of the Markov's process type describing the duplicative transposition of mobile genetic elements (MGE) has been developed. The possible role of MGE containing regulatory sites activated under unfavourable conditions has been considered. An analysis of the model has shown that there may be such regimes of environmental changes (sharp but random changes of the environment parameters) when sufficiently reliable survival of population is dependent on such MGE.

Animals↗
PubMed2026

RePo index: a multidimensional framework to quantify genetic resilience in data-limited amphibian faunas.

This study explores the resilience of Chilean amphibians to environmental disturbances through an integrative approach that combines ecological, demographic, bibliometric, and molecular information. A total of 58 species distributed across 14 genera and 9 families were evaluated via the resilience potential (RePo) index, which incorporates eleven criteria grouped into five dimensions: distribution, population trends, emerging diseases, evolutionary history, and genetic records. The results revealed high ecological vulnerability: 83% of the species were classified as non resilient (45% with no resilience and 38% with low resilience), and none reached the high-resilience category. At the family level, Telmatobiidae presented the lowest resilience values, whereas Leptodactylidae presented the highest. At the genus level, Insuetophrynus was identified as the most vulnerable taxon, with no molecular records and an extremely restricted distribution. In contrast, species such as Rhinella spinulosa and Pleurodema thaul presented moderate resilience, suggesting greater adaptive potential and relevance for functional studies. From a bibliometric perspective, a bias toward classical research topics (distribution, physiology, and taxonomy) was detected, with limited representation of integrative approaches such as genetic conservation or climate change. The conceptual modularity in the literature was low (Q = 0.1328), indicating weak thematic differentiation and little integration of omics tools. Most species lack transcriptomic and genomic data, severely limiting the assessment of their adaptive mechanisms. In this context, the RePo index has emerged as an integrative tool useful for operationalizing concepts such as evolutionarily significant units (ESUs) and management units (MUs), which are essential for evidence-based conservation. Finally, this study highlights the need to incorporate high-throughput sequencing (HTS) technologies and to participate in international initiatives, such as the Amphibian Genomics Consortium, as a strategic path forward for advancing adaptive conservation of Chilean amphibians.

Animals↗
PubMed2005

Conservation of functional domains and limited heterogeneity of HIV-1 reverse transcriptase gene following vertical transmission.

BACKGROUND: The reverse transcriptase (RT) enzyme of human immunodeficiency virus type 1 (HIV-1) plays a crucial role in the life cycle of the virus by converting the single stranded RNA genome into double stranded DNA that integrates into the host chromosome. In addition, RT is also responsible for the generation of mutations throughout the viral genome, including in its own sequences and is thus responsible for the generation of quasi-species in HIV-1-infected individuals. We therefore characterized the molecular properties of RT, including the conservation of functional motifs, degree of genetic diversity, and evolutionary dynamics from five mother-infant pairs following vertical transmission. RESULTS: The RT open reading frame was maintained with a frequency of 87.2% in five mother-infant pairs' sequences following vertical transmission. There was a low degree of viral heterogeneity and estimates of genetic diversity in mother-infant pairs' sequences. Both mothers and infants RT sequences were under positive selection pressure, as determined by the ratios of non-synonymous to synonymous substitutions. Phylogenetic analysis of 132 mother-infant RT sequences revealed distinct clusters for each mother-infant pair, suggesting that the epidemiologically linked mother-infant pairs were evolutionarily closer to each other as compared with epidemiologically unlinked mother-infant pairs. The functional domains of RT which are responsible for reverse transcription, DNA polymerization and RNase H activity were mostly conserved in the RT sequences analyzed in this study. Specifically, the active sites and domains required for primer binding, template binding, primer and template positioning and nucleotide recruitment were conserved in all mother-infant pairs' sequences. CONCLUSION: The maintenance of an intact RT open reading frame, conservation of functional domains for RT activity, preservation of several amino acid motifs in epidemiologically linked mother-infant pairs, and a low degree of genetic variability following vertical transmission is consistent with an indispensable role of RT in HIV-1 replication in infected mother-infant pairs.

Journal Article↗
PubMed2003

Genetic differences within and between species of deep-sea crabs (chaceon) from the North Atlantic Ocean.

The deep-sea red crab Chaceon quinquedens is a commercially important crustacean on the Atlantic continental shelf and slope of North America. To assess genetic subdivision in C. quinquedens, we examined the nucleotide sequence of the mitochondrial 16S rDNA gene and the internal transcribed spacers (ITS) of the nuclear ribosomal repeat in samples from southern New England and the Gulf of Mexico. We compared those data to sequences from two congeners, a sympatric species from the Florida coast, C. fenneri, and an allopatric eastern Atlantic species, C. affinis. The 16S rDNA data consisted of 379 aligned nucleotides obtained from 37 individuals. The greatest genetic difference among geographical groups or nominal species was between C. quinquedens from southern New England and C. quinquedens from the Gulf of Mexico. Haplotypes from these two groups had a minimum of 10 differences. All 11 C. fenneri samples matched the most common haplotype found in C. quinquedens from the Gulf of Mexico, and this haplotype was not detected in C. quinquedens from southern New England. The three haplotypes of C. affinis were unique to that recognized species, but those haplotypes differed only slightly from those of C. fenneri and C. quinquedens from the Gulf of Mexico. Based on 16S rDNA and ITS data, genetic differences between C. quinquedens from southern New England and the Gulf of Mexico are large enough to conclude that these are different fishery stocks. Our results also indicate that the designation of morphological species within the commercially important genus Chaceon is not congruent with evolutionary history. The genetic similarity of C. affinis from the eastern Atlantic and C. quinquedens from the Gulf of Mexico suggests these trans-Atlantic taxa share a more recent common history than the two populations of "C. quinquedens" that we examined.

Animals↗
PubMed2004

Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.

Epistatic gene interactions are believed to be a major factor in the genetic architecture of evolutionary diversification. In Arabidopsis thaliana, the FRI and FLC genes mechanistically interact to control flowering time, and here we show that this epistatic interaction also contributes to a latitudinal cline in this life history trait within the species. Two major FLC haplogroups (FLC(A) and FLC(B)) are associated with flowering time variation in A. thaliana in field conditions, but only in the presence of putatively functional FRI alleles. Significant differences in latitudinal distribution of FLC haplogroups in Eurasia and North Africa also depend on the FRI genotype. There is significant linkage disequilibrium between FRI and FLC despite their location on separate chromosomes. Although no nonsynonymous polymorphisms differentiate FLC(A) and FLC(B), vernalization induces the expression of an alternatively spliced FLC transcript that encodes a variant protein with a radical amino acid replacement associated with the two FLC haplogroups. Numerous polymorphisms differentiating the FLC haplogroups also occur in intronic regions implicated in the regulation of FLC expression. The features of the regulatory gene interaction between FRI and FLC in contributing to the latitudinal cline in A. thaliana flowering time are consistent with the maintenance of this interaction by epistatic selection. These results suggest that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification.

Alternative Splicing↗
PubMed1998

Root pattern: shooting in the dark?

Root pattern formation takes place in the embryo and is propagated through subsequent growth and development of the seedling root meristem. Pattern is maintained by positional cues and in some cases by local cell interactions. Such interactions are involved in the balance between cell division and differentiation in cells neighbouring the quiescent centre. This balancing act also occurs in the shoot in which the genetic circuitry underpinning this phenomenon has been characterised. The common genetic mechanism of patterned cell differentiation in the epidermis between the root and shoot extends these parallels further. Given that these shared mechanisms exist, it is tempting to speculate that they reflect the fact that roots may be derived, shoot structures. Alternatively such mechanisms may reflect an evolutionary convergence of genetic mechanism.

Body Patterning↗
PubMed1995

A speed limit for evolution.

An upper bound on the speed of evolution is derived. The bound concerns the amount of genetic information which is expressed in observable ways in various aspects of the phenotype. The genetic information expressed in some part of the phenotype of a species cannot increase faster than a given rate, determined by the selection pressure on that part. This rate is typically a small fraction of a bit per generation. Total expressed genetic information cannot increase faster than a species-specific rate--typically a few bits per generation. These bounds apply to all aspects of the phenotype, but are particularly relevant to cognition. As brains are highly complex, we expect large amounts of expressed genetic information in the brain--of the order of 100 kilobytes--yet evolutionary changes in brain genetic information are only a fraction of a bit per generation. This has important consequences for cognitive evolution. The limit implies that the human brain differs from the chimpanzee brain by at most 5 kilobytes of genetic design information. This is not enough to define a Language Acquisition Device, unless it depends heavily on pre-existing primate symbolic cognition. Subject to the evolutionary speed limit, in changing environments a simple, modular brain architecture is fitter than more complex ones. This encourages us to look for simplicity in brain design, rather than expecting the brain to be a patchwork of ad hoc adaptations. The limit implies that pure species selection is not an important mechanism of evolutionary change.

Animals↗
PubMed2005

Widespread evidence for non-additive genetic variation in Cloninger's and Eysenck's personality dimensions using a twin plus sibling design.

Studies using the classical twin design often conclude that most genetic variation underlying personality is additive in nature. However, studies analyzing only twins are very limited in their ability to detect non-additive genetic variation and are unable to detect sources of variation unique to twins, which can mask non-additive genetic variation. The current study assessed 9672 MZ and DZ twin individuals and 3241 of their siblings to investigate the environmental and genetic architecture underlying eight dimensions of personality: four from Eysenck's Personality Questionnaire and four from Cloninger's Temperament and Character Inventory. Broad-sense heritability estimates from best-fitting models were two to three times greater than the narrow-sense heritability estimates for Harm Avoidance, Novelty Seeking, Reward Dependence, Persistence, Extraversion, and Neuroticism. This genetic non-additivity could be due to dominance, additive-by-additive epistasis, or to additive genetic effects combined with higher-order epistasis. Environmental effects unique to twins were detected for both Lie and Psychoticism but accounted for little overall variation. Our results illustrate the increased sensitivity afforded by extending the classical twin design to include siblings, and may provide clues to the evolutionary origins of genetic variation underlying personality.

Australia↗
PubMed2000

Evolution of the mitochondrial genetic system: an overview.

Mitochondria, semi-autonomous organelles possessing their own genetic system, are commonly accepted to descend from free-living eubacteria, namely hydrogen-producing alpha-proteobacteria. The progressive loss of genes from the primitive eubacterium to the nucleus of the eukaryotic cell is strongly justified by the Muller rachet principle, which postulates that asexual genomes, like mitochondrial ones, accumulate deleterious and sublethal mutations faster than sexual genomes, like the nucleus. According to this principle, the mitochondrial genome would be doomed to death; instead, we observe that the mitochondrial genome has a variable size and structure in the different organisms, though it contains more or less the same set of genes. This is an example of genetic conservation versus structural diversity. From an evolutionary point of view the genetic system of organelles is clearly under strong selective pressure and for its survival it needs to utilize strategies to slow down or halt the ratchet. Anyway, the mitochondrial genome changes with time, and the rate of evolution is different for both diverse regions of the mtDNA and between lineages, as demonstrated in the case of mammalian mt genomes. We report here our data on the evolution of the mitochondrial DNA in mammals which demonstrate the suitability of mtDNA as a molecular tool for evolutionary analyses.

Animals↗
PubMed2006

Molecular evolution of 5' flanking regions of 87 candidate genes for atherosclerotic cardiovascular disease.

Inter-individual variation in quantitative traits as well as in disease susceptibility may be due to differences in the level and spatio-temporal pattern of gene expression. An evolutionary model of genetic variation in cis-regulatory regions may help identify loci of interest for the study of the genetic basis of complex diseases such as atherosclerotic cardiovascular disease (ASCVD). We studied the molecular evolution of 87 candidate genes for ASCVD to detect signatures of selection in 5' flanking regions. Resequenced data for these genes were available in 24 African-Americans, 23 European-Americans, and 1 chimpanzee (Pan troglodytes). Statistical tests of evolutionary neutrality (Tajima's D and Fay and Wu's H) were performed using coalescent simulations under a standard neutral model and a population structure model to differentiate selection from human demographic history. Evidence suggestive of selection was present in 5' flanking regions of 15 genes. A modified McDonald-Kreitman test was used to compare the ratio of putative functional and non-functional sites between and within species in 5' flanking regions. A significant excess or deficit of fixed changes over polymorphisms was noted in 16 genes. Of the 26 genes showing deviation from evolutionary neutrality based on the above two tests, 13 genes showed an unusual haplotype pattern in 5' flanking regions, providing supportive evidence of selection. These results indicate that selection may play a role in establishing variation in 5' flanking regions of a subset of candidate genes for ASCVD and motivate further studies of these loci in determining inter-individual susceptibility to ASCVD.

5' Flanking Region↗
PubMed2004

Molecular evolution in space and through time: mtDNA phylogeography of the Olive Sunbird (Nectarinia olivacea/obscura) throughout continental Africa.

This study constitutes the first investigation of the phylogeographic structure of a forest bird distributed throughout the montane and lowland forest biomes of Africa. The key objective was to investigate the importance of Pleistocene climatic cycles on avian diversification across Africa. The Olive Sunbird is a relatively large polytypic sunbird widely distributed throughout evergreen, montane and coastal forests in Africa. Recently, it was split into two species, the Eastern Olive Sunbird (Nectarinia olivacea) and the Western Olive Sunbird (Nectarinia obscura), based on morphological grounds. Analyses of a 395bp fragment of the mtDNA NADH subunit 3 gene with flanking tRNA sequences, from 196 individuals of N. olivacea and 86 from N. obscura indicate that genetic divergence levels are low (1.0-2.4%) across some 9000km, from Ghana in the northwest of Africa to KwaZulu-Natal in eastern South Africa. Neither currently recognized Olive Sunbird species were monophyletic using either parsimony or likelihood tree-building methods. Phi(ST) values suggested that there was less variation partitioned among species than between most neighboring regions. Genetic diversity within the N. olivacea/obscura complex was dominated by three star-like phylogenies linked to each other by a single mutational step and two subnetworks (IV and V) separated from the core star-like phylogenies (subnetworks I, II, and III) by five to six mutational steps. The dominant evolutionary mechanism shaping genetic variation within the N. olivacea/obscura complex as identified by nested-clade analyses, appears to be one of range expansion possibly out of East Africa associated with a period of forest expansion during the mid-Pleistocene, some 1.1-0.7 million years ago. Mismatch profiles suggested that secondary contact has occurred between eastern and western lineages within the Ufipa Escarpment and possibly Zimbabwe, as well as between eastern lineages in the Kenyan Highlands and northern Eastern Arc Mts.

Africa↗
PubMedDate not supplied

[Individual development and lessons of evolutionism].

The present crisis of evolutionism was predictable initially, since the preformational model of development expressed in the idea of discrete heredity contradicts the systemic properties of ontogenesis. Correspondingly, the principle of selection of inherited factors cannot explain evolution. The synthetic theory based on this principle contains insoluble contradictions in its key notions. According to the alternative epigenetic theory based on the integrity of living organization, heredity is a product of selection and expresses teleonomic direction of development to a stable final state. Unification of the genetic concept of evolution with recognition of the integrity of development is principally impossible. The cause of dominance of genetic views on evolution consists in the correspondence of the mechanistic tradition of the 18-19th centuries, rather than in their logistic substantiation. For the same reason, the biology as a whole is characterized by identification of specific linear dependences with the laws of evolution. Following this path in search for "new evolutionary synthesis" invites a priori its failure. Evolutionary interpretation of genetic generalizations is only possible on the basis of their description in terms of development.

Biological Evolution↗
PubMed2004

Studying the effect of environmental change on biotic evolution: past genetic contributions, current work and future directions.

Evolutionary geneticists currently face a major scientific opportunity when integrating across the rapidly increasing amount of genetic data and existing biological scenarios based on ecology, fossils or climate models. Although genetic data acquisition and analysis have improved tremendously, several limitations remain. Here, we discuss the feedback between history and genetic variation in the face of environmental change with increasing taxonomic and temporal scale, as well as the major challenges that lie ahead. In particular, we focus on recent developments in two promising genetic methods, those of 'phylochronology' and 'molecular clocks'. With the advent of ancient DNA techniques, we can now directly sample the recent past. We illustrate this amazing and largely untapped utility of ancient DNA extracted from accurately dated localities with documented environmental changes. Innovative statistical analyses of these genetic data expose the direct effect of recent environmental change on genetic endurance, or maintenance of genetic variation. The 'molecular clock' (assumption of a linear relationship between genetic distance and evolutionary time) has been used extensively in phylogenetic studies to infer time and correlation between lineage divergence time and concurrent environmental change. Several studies at both population and species scale support a persuasive relationship between particular perturbation events and time of biotic divergence. However, we are still a way from gleaning an overall pattern to this relationship, which is a prerequisite to ultimately understanding the mechanisms by which past environments have shaped the evolutionary trajectory. Current obstacles include as-yet undecided reasons behind the frequent discrepancy between molecular and fossil time estimates, and the frequent lack of consideration of extensive confidence intervals around time estimates. We suggest that use and interpretation of both ancient DNA and molecular clocks is most effective when results are synthesized with palaeontological (fossil) and ecological (life history) information.

Animals↗
PubMed1998

Analysis of genetic diversity in Chinese sweetpotato [Ipomoea batatas (L.) Lam.] germplasm using DNA amplification fingerprinting.

The genetic diversity and evolutionary relationships in a representative sample of Chinese sweetpotato collection were assessed using the DNA amplification fingerprinting approach. DNA fingerprint profiles were developed for all 42 accessions tested. There were 19-26 bands for each accession and an average of 20.7 such bands were polymorphic. Chinese sweetpotato germplasm tested exhibited a high degree of genetic diversity. Phenetic analysis revealed five major clusters with the following components: (1) landraces from Guangdong Province, (2) landraces from Fujian province, (3) Chinese cultivars, (4) those closely related to Japanese sweetpotato cultivars, and (5) those closely related to the US sweetpotato cv. Nancy Hall. The genetic association observed between accessions was largely consistent with the known pedigree records. The DNA amplification fingerprinting may provide reliable insights into the domestication history of the sweetpotato crop and may be useful in germplasm enhancement.

Base Sequence↗
PubMed2002

Understanding quantitative genetic variation.

Until recently, it was impracticable to identify the genes that are responsible for variation in continuous traits, or to directly observe the effects of their different alleles. Now, the abundance of genetic markers has made it possible to identify quantitative trait loci (QTL)--the regions of a chromosome or, ideally, individual sequence variants that are responsible for trait variation. What kind of QTL do we expect to find and what can our observations of QTL tell us about how organisms evolve? The key to understanding the evolutionary significance of QTL is to understand the nature of inherited variation, not in the immediate mechanistic sense of how genes influence phenotype, but, rather, to know what evolutionary forces maintain genetic variability.

Animals↗
PubMed2026

The genetic control of rapid genome content divergence in Arabidopsis thaliana.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1043 resequenced Arabidopsis thaliana genomes using a novel K-mer-based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 candidate trans-acting loci associated with repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, and DNA methylation regulation. The results are consistent with purifying selection acting against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Arabidopsis↗
PubMed2004

Evolutionary medicine.

Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

Adaptation, Biological↗
PubMed2002

Brain and cognitive evolution: forms of modularity and functions of mind.

Genetic and neurobiological research is reviewed as related to controversy over the extent to which neocortical organization and associated cognitive functions are genetically constrained or emerge through patterns of developmental experience. An evolutionary framework that accommodates genetic constraint and experiential modification of brain organization and cognitive function is then proposed. The authors argue that 4 forms of modularity and 3 forms of neural and cognitive plasticity define the relation between genetic constraint and the influence of developmental experience. For humans, the result is the ontogenetic emergence of functional modules in the domains of folk psychology, folk biology, and folk physics. The authors present a taxonomy of these modules and review associated research relating to brain and cognitive plasticity in these domains.

Animals↗