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PubMed2003

Haplotype analysis in population genetics and association studies.

Several studies of haplotype structures in the human genome in various populations have been published recently. Such knowledge may provide valuable information on human evolutionary history and lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. In this review, we summarize the current understanding of haplotype structure, diversity, and distribution in the human genome, with a focus on statistical issues in using haplotypes for studies of population genetics and evolutionary history, as well as to identify genetic variants underlying complex human traits.

Evolution, Molecular↗
PubMed2000

Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers.

Despite the urgent need to conserve domesticated plant genetic resources, and developing 'on farm' strategies of conservation, the impact of traditional farming practices and of their interaction with ecological factors on the structure and evolutionary dynamics of the genetic variability of crop populations has been little documented. We assessed the genetic variability of 31 varieties of cassava (M. esculenta Crantz) traditionally grown by Makushi Amerindians from Guyana, using AFLP markers. We used a sample of 38 varieties from an ex situ core collection as a reference. Accessions of wild cassava were also included. While clonality of the varieties was expected due to the vegetative propagation of cassava, 21 varieties presented intravarietal polymorphism. Among the varieties from a single site in Guyana, genetic diversity was the same as that in the accessions from the core collection. We suggest that incorporation of volunteer seedlings, produced by sexual reproduction, into the stock of varieties grown by the Makushi plays a major role in explaining both intravarietal polymorphism and the high level of genetic diversity. No correspondence was found between the structure of molecular diversity and variation observed for agronomic traits that are targets for selection by cultivators. As found in previous studies, all wild forms of cassava clustered together and separately from the cultivated varieties in a Neighbour-Joining dendrogram. These results are consistent with the hypothesis of a limited domestication event in a restricted area, followed by rapid diffusion of cultivated phenotypes and convergent evolution. Our results show that local varieties are an important source of genetic diversity, and highlight the importance of the interaction between human and ecological factors in the dynamics of this diversity.

Evolution, Molecular↗
PubMed2004

The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand.

Dengue represents a major public health problem in Thailand, with all four viral serotypes co-circulating. Dengue virus serotype 4 (DENV-4) is the least frequently sampled serotype, although one that is often associated with hemorrhagic fever during secondary infection. To determine the evolutionary forces shaping the genetic diversity of DENV-4, and particularly whether its changing prevalence could be attributed to instances of adaptive evolution in the viral genome, we undertook a large-scale molecular epidemiological analysis of DENV-4 in Bangkok, Thailand, using both E gene and complete coding region sequences. This analysis revealed extensive genetic diversity within a single locality at a single time, including the discovery of a new and divergent genotype of DENV-4, as well as a pattern of continual lineage turnover. We also recorded the highest average rate of evolutionary change for this serotype, at 1.072 x 10(-3) nucleotide substitutions per site, per year. However, despite this abundant genetic variation, there was no evidence for adaptive evolution in any gene, codon, or lineage of DENV-4, with the highest rate of nonsynonymous substitution observed in NS2A. Consequently, the rapid turnover of DENV-4 lineages through time is most likely the consequence of a high rate of deleterious mutation in the viral genome coupled to seasonal fluctuations in the size of the vector population.

Adolescent↗
PubMed1988

Motor training and physical fitness: possible short- and long-term influences on the development of individual differences in behavior.

Individual differences in the behavior of young and adult animals have been documented in diverse species. Possible sources of such variation are of interest to scientists representing many disciplines, including behavior, genetics, and population and evolutionary biology. Two variables that may be important in the ontogeny and maintenance of behavioral differences are (1) individual physical (aerobic and anaerobic) fitness and (2) possible genetic variations underlying individual abilities to engage in, and to benefit from, motor training early in life. The differential development of aerobic and anaerobic capacities may play a significant role in the ontogeny of individual differences in the performance of various motor skills. There also may be short- and long-term consequences of variations in physical fitness that influence individual abilities to perform energy demanding acts during aggressive encounters, interactions with prey or predators, and courtship and breeding. Genetic studies of a limited number of species indicate that specific genotypes are correlated with individual variations in motor performance, even among conspecifics. Multidisciplinary research concerning possible relationships among the ontogeny of physical fitness, genetics, and variations in behavior is needed. Recent work on the relationship between individual differences in physical fitness and variations in the behavior of adult cold-blooded vertebrates provides a good model for comparative research on warm-blooded species.

Animals↗
PubMed2004

Genotypic variation among lineages of Trypanosoma cruzi and its geographic aspects.

Isozyme analysis with 18 enzyme loci was conducted on 146 isolates of Trypanosoma cruzi from Mexico, Guatemala, Colombia, Ecuador, Peru, Brazil, Bolivia, Paraguay and Chile. Forty-four different MLGs (groups of isolates with identical multilocus genotypes) were identified and a phylogeny was constructed. The phylogenetic tree consisted of two main groups (T. cruzi I, T. cruzi II), and the latter was further divided into two subgroups (T. cruzi IIa, T. cruzi IIb-e). Evidence of hybridization between different MLGs of T. cruzi II was found, which means that genetic exchanges seem to have occurred in South American T. cruzi. On the other hand, the persistence of characteristic T. cruzi I and T. cruzi II isozyme patterns in single small villages in Bolivia and Guatemala suggested that genetic exchange is very rare between major lineages. A significant difference in genetic diversity was shown between T. cruzi I and T. cruzi II from several indices of population genetics. Two possibilities could explain this genetic variation in the population: differences in evolutionary history and/or different tendencies to exchange genetic material. Broad-scale geographic distributions of T. cruzi I and T. cruzi IIb-e were different; T. cruzi I occurred in Central America and south to Bolivia and Brazil, while T. cruzi IIb-e occurred in the central and southern areas of South America, overlapping with T. cruzi I in Brazil and Bolivia.

Animals↗
PubMed2005

Speciation through the learning of habitat features.

Learning of environmental features can influence both mating behaviour and the location where young are produced. This may lead to speciation in three steps: (i) colonization of a new habitat, (ii) genetic divergence of the two groups by adaptation to the habitats, and (iii) a decrease of genetic mixing between the lineages (similar to reinforcement). In a previous paper we showed that steps (i) and (ii) occur readily for a wide range of fixed mating and habitat preferences. Here, we study whether this can ultimately lead to speciation through selective changes in these preferences. We show that this indeed occurs, and, furthermore, it is very general: for a large class of models there is selection toward producing young more frequently in the natal habitat. Once habitat preference is strong, there is selection toward stronger assortative mating. Even when steps (i) and (ii) initially fail, genetic divergence may succeed at a later evolutionary stage, after which a decrease of genetic mixing completes speciation. Our results show that speciation by the learning of habitat features is an extremely effective mechanism.

Animals↗
PubMed2005

Human-induced dwarfing of Himalayan snow lotus, Saussurea laniceps (Asteraceae).

Because evolutionary processes such as genetic drift and natural selection play a crucial role in determining the response that species will have to human-induced disturbances, there is increasing interest in the evolutionary aspects of conservation biology. Harvesting select individuals in natural plant populations can bring about unforeseen impacts that may negatively affect fitness. We analyzed how human harvesting affects two congeners known as snow lotus. Over a period of 100 years, there was a negative trend in plant height (r2= 0.4361, P < 0.001) for the intensely collected and rare species, Saussurea laniceps, but not in the less intensely collected species, Saussurea medusa. Additionally, S. laniceps were significantly smaller in areas of high harvest than in areas with low harvest (Z = 4.91, P < 0.0001), but this was not so for S. medusa. Humans can unconsciously drive evolution and must be considered when managing threatened species.

Biological Evolution↗
PubMed2025

aPhyloGeo: a Python application for correlating genetic and climatic conditions.

MOTIVATION: Environmental variation and its influence on genetic diversity is a central topic in evolutionary biology and phylogeography. Accurate correlations between genetic and climatic datasets to understand the genetic adaptations of different species to specific environments. It requires integrated and reproducible workflows. RESULTS: We developed aPhyloGeo, an open-source and multiplatform application implemented in Python, for investigating correlations between genetic variation and environmental data within a phylogenetic framework. The workflow integrates multiple analytical steps, including sequence alignment, sliding window phylogenetic inference, and statistical approaches such as the Mantel test and the Procrustean randomization test. These analyses enable the identification of mutation hotspots that exhibit strong associations with environmental variables. In addition, aPhyloGeo supports multicore data processing and provides a fully reproducible pipeline for evaluating localized relationships between genomic variation and climatic distributions. AVAILABILITY AND IMPLEMENTATION: aPhyloGeo is freely available on GitHub at: https://github.com/tahiri-lab/aPhyloGeo, as both a PyPI package and as Python scripts for Linux, macOS, and Windows.

Software↗
PubMedDate not supplied

[Use of ISSR-markers for determination of convergent evolutionary relations in Fagus genus].

Genetic relationships between members of Fagus genus were assessed using ISSR markers and amplification. The taxonomic status of Fagus sylvatica L. and Fagus orientalis LYPSKY. species in Ukraine has been ascertained more precisely. Intraspecies mean genetic distances were compared according to Nei & Li and respective dendrogram was constructed with the complete joining method.

DNA, Plant↗
PubMed2005

Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.

The evolutionary mechanisms that operate on genetic variation within transcriptional regulatory sequences are not well understood. We present here an evolutionary analysis of an exceptionally well characterized cis-regulatory region, the endo16 promoter of the purple sea urchin. Segregating variation reveals striking differences in the intensity of negative selection among regulatory modules, reflecting their distinct functional roles. Surprisingly, transcription-factor-binding sites are as polymorphic and as likely to contain fixed differences as flanking nucleotides. Whereas nucleotides in protein-binding sites in the most proximal regulatory module exhibit reduced variation, those in other modules tend to be more polymorphic than putatively nonfunctional nucleotides. Two unrelated large insertions at the same position within the promoter are segregating at low frequencies; one is a strong ectodermal repressor that contains 16 verified transcription-factor-binding sites. These results demonstrate that a simple relationship between conservation and function does not exist within this cis-regulatory region and highlight significant population heterogeneity in the fine structure of a well understood promoter.

Animals↗
PubMed2006

Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus.

Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.

Base Sequence↗
PubMed1991

Behavioral pathway to evolutionary change.

The extreme malleability or plasticity of cells early in their development is mirrored to a certain, if lesser, degree in the psychological, behavioral, and neural functioning of developing organisms. The early developmental adaptability of organisms has significance for our understanding of evolution. It is the purpose of the present article to make a case for the extra-genetic or, better, the supra-genetic developmental basis of evolutionary change through the genesis of novel behavioral phenotypes. To make things as clear as possible, I contrast this developmental approach to evolution with the population-genetic model of the modern synthesis. I should say at the outset that the present theory can be integrated with the population-genetic model, with the exception of the radically different role ascribed to genes in the two viewpoints.

Adaptation, Biological↗
PubMed2005

Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity.

CYP2D6 is of great importance for the metabolism of clinically used drugs and about 20-25% of those are metabolised by this enzyme. In addition, the enzyme utilises hydroxytryptamines as endogenous substrates. The polymorphism of the enzyme results in poor, intermediate, efficient or ultrarapid metabolisers (UMs) of CYP2D6 drugs. It is plausible that the UM genotype, where more than one active gene on one allele occurs, is the outcome of selective dietary selection in certain populations in North East Africa. The UM phenotype affects 5.5% of the population in Western Europe. A hypothesis for the evolutionary basis behind selection for CYP2D6 gene duplications is presented in relation to selection for Cyp6 variants in insecticide resistant Drosophila strains. The polymorphism of CYP2D6 significantly affects the pharmacokinetics of about 50% of the drugs in clinical use, which are CYP2D6 substrates. The consequences of the polymorphism at ordinary drug doses can be either adverse drug reactions or no drug response. Examples are presented where CYP2D6 polymorphism affects the efficacy and costs of drug treatment. Predictive CYP2D6 genotyping is estimated by the author to be beneficial for treatment of about 30-40% of CYP2D6 drug substrates, that is, for about 7-10% of all drugs clinically used, although prospective clinical studies are necessary to evaluate the exact benefit of drug selection and dosage based on the CYP2D6 genotype.

Animals↗
PubMed1983

The human histocompatibility system: anthropological considerations.

The human histocompatibility system (HLA) is a linked complex of genes on human chromosomes 6. Many of the loci in this region are highly polymorphic. This endows the system with unique differentiating powers, both in terms of the population genetics of the reconstruction of evolutionary trees to assess biological divergences (or affinities) in human populations, and in terms of detecting the genetic component of the many diseases which show an association with certain variants (alleles) of the HLA system. Different racial groups often exhibit different HLA disease associations; that is, a different allele is associated with the disease in different populations, although in some cases the same allele is associated with the disease in all populations. The classical example of this latter situation is the association of B27 with ankylosing spondylitis. This disease will be used as an example to illustrate how population observations allow inferences to be made regarding the evolutionary histories of the HLA-associated diseases, as well as the genetic mechanisms of the diseases.

Chromosomes, Human, 6-12 and X↗
PubMed2002

Potential genetic variance and the domestication of maize.

Since Darwin, there has been a long and arduous struggle to understand the source and maintenance of natural genetic variation and its relationship to phenotype. The reason that this task is so difficult is that it requires integration of detailed, and as yet incomplete, knowledge from several biological disciplines, including evolutionary, population, and developmental genetics. In this 'post-genomic' era, it is relatively easy to identify differences in the DNA sequence between individuals. However, the task remains to delineate how this abundant genetic diversity actually contributes to phenotypic diversity. This necessitates tackling the problem of hidden genetic variation. Genetic polymorphisms can be conditionally cryptic, but have the potential to contribute to phenotypic variation in particular genetic backgrounds or under specific environmental conditions. A recent paper by Lauter and Doebley highlights the contribution of hidden genetic variation to traits characterizing the morphological evolution of modern maize from its wild grass-like progenitor teosinte.1 This work is the first to demonstrate hidden variance for selected (agronomically 'adaptive') traits in a well-characterized model for morphological evolution.

DNA↗
PubMed2007

Peopling of South Asia: investigating the caste-tribe continuum in India.

In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.

Animals↗
PubMed2005

How to use molecular marker data to measure evolutionary parameters in wild populations.

Estimating the genetic basis of phenotypic traits and the selection pressures acting on them are central to our understanding of the evolution and conservation of wild populations. However, obtaining such evolutionary-related parameters is not an easy task as it requires accurate information on both relatedness among individuals and their breeding success. Polymorphic molecular markers are very useful in estimating relatedness between individuals and parentage analyses are now extensively used in most taxa. The next step in the application of molecular data to wild populations is to use them to derive estimates of evolutionary-related parameters for quantitative traits, such as quantitative genetic parameters (e.g. heritability, genetic correlations) and measures of selection (e.g. selection gradients). Despite their great appeal and potential, the optimal use of molecular tools is still debated and it remains unclear how they should best be used to obtain reliable estimates of evolutionary parameters in the wild. Here, we review the methods available for estimating quantitative genetic and selection parameters and discuss their merits and shortcomings, to provide a tool that summarizes the potential uses of molecular data to obtain such parameters in wild populations.

Biological Evolution↗
PubMed1996

Modelling phenotypic plasticity. II. Do genetic correlations matter?

Predictions of the evolutionary trajectory of reaction norms and interpretation of empirical results are usually based on two mathematically equivalent ways of partitioning phenotypic variance into its genetic, environmental, and interaction components: the genotype by environment interaction estimated by means of an analysis of variance, or the interenvironment genetic correlation (i.e. the genetic correlation between the expressions of the same trait in two environments). Both these quantities are supposed to indicate the amount of genetic variability for plasticity in natural population. I point out that not only are the qualitative predictions based on these statistical methods sometimes in conflict with each other, but that both may fail to predict rates of evolution and equilibria under some circumstances, because they ignore the details of the genetic machinery. It is shown that, ultimately, the only way to predict reliably the evolution of plasticity is actually to know its specific genetic basis and the genotypic constitution of the population, however inconvenient this may be from both theoretical and empirical standpoints. The discussion is framed in terms of a simple one-locus two-allele model that mimics the real case of the pennant/vestigial system describing plasticity of wing length to temperature in Drosophila melanogaster.

Alleles↗