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Evolutionary psychology and genetic variation: non-adaptive, fitness-related and adaptive.

Behavioural variation across individuals can be substantial. A broad generalization emerging from three decades of behavioural genetic studies is that most psychological individual differences have moderate broad heritabilities (30-60%). There are at least three possible scenarios for this genetic variation. First, it may be adaptively neutral and not subject to selection. Second, it may be related to fitness despite selection. Third, it may be maintained by selection for alternative adaptations. Some authors favour the first of these possibilities, but the latter two cannot be ruled out. First, temporally varying selection pressures (e.g. pathogens) can maintain fitness-related genetic variance in a population despite current selection pressures. Moreover, direct and indirect evidence on humans support the notion that some phenotypic variance is fitness related. Second, while adaptive alternatives are unlikely to be found at a level of highly complex design, frequency dependent selection can maintain variation at finer, quantitative levels. One potential example is discussed. Because of their particular relevance to evolutionary psychology, fitness-related and adaptive genetic variance deserve further attention.

Adaptation, Psychological↗

Genetic Variation and Evolutionary Characteristics of Coxsackievirus B1: F3 Subtype Associated With Hand, Foot and Mouth Disease in China.

Coxsackievirus B1 (CV-B1) is primarily associated with meningitis but can also cause localized outbreaks of hand, foot, and mouth disease (HFMD). This study analyzed the genetic diversity of the VP1 gene in 39 strains of the CVB1 virus isolated from HFMD children across 15 provinces in China between 2010 and 2024, as well as 179 strains from 17 countries. Based on the average nucleotide difference of VP1 gene, we classified CVB1 virus into six genotypes A to F, Notably, genotype F is newly classified. Since 2010, genotype F guadually replaced genotype E as the dominant genotype in China and has further subdivided into three subtypes: F1, F2, and F3, with F3 being the most prevalent subtype in China currently. We specifically study the mild and severe cases within the F3 subtype. Temperature-sensitivity experiments revealed no differences between mild and severe cases of the F3 subtype, and they all belong to temperature-sensitive strains. Interestingly, we found that mild cases of the F3 subtype did not involve recombination, whereas all severe cases of the F3 subtype showed recombination with Coxsackievirus B4 (CVB4). CVB4 has consistently been the primary pathogen responsible for severe neonatal illnesses, suggesting that recombination between the F3 subtype and CVB4 may be associated with the development of severe HFMD. These findings provide fundamental scientific data for further investigation into the epidemiology and genetic characteristics of variants of Coxsackievirus B1 in China.

Humans↗

Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations.

Translation is carried out by the ribosome and several associated protein factors through three consecutive steps: initiation, elongation, and termination. Termination remains the least understood of them, partly because of the nonuniversality of the factors involved. To get some insights on the evolution of eukaryotic translation termination, we have compared the phylogeny of the release factors eRF1 and eRF3 to that of the elongation factors EF-1alpha and EF-2, with special focus on ciliates. Our results show that these four translation proteins have experienced different modes of evolution. This is especially evident for the EF-1alpha, EF-2, and eRF1 ciliate sequences. Ciliates appear as monophyletic in the EF-2 phylogenetic tree but not in the EF-1alpha and eRF1 phylogenetic trees. This seems to be mainly because of phylogeny reconstruction artifacts (the long-branch attraction) produced by the acceleration of evolutionary rate of ciliate EF-1alpha and eRF1 sequences. Interaction with the highly divergent actin found in ciliates, or on the contrary, loss of interaction, could explain the acceleration of the evolutionary rate of the EF-1alpha sequences. In the case of ciliate eRF1 sequences, their unusually high evolutionary rate may be related to the deviations in the genetic code usage found in diverse ciliates. These deviations involve a relaxation (or even abolition) of the recognition of one or two stop codons by eRF1. To achieve this, structural changes in eRF1 are needed, and this may affect its evolutionary rate. Eukaryotic translation seems to have followed a mosaic evolution, with its different elements governed by different selective pressures. However, a correlation analysis shows that, beneath the disagreement shown by the different translation proteins, their concerted evolution can still be made apparent when they are compared with other proteins that are not involved in translation.

Animals↗

Community heritability measures the evolutionary consequences of indirect genetic effects on community structure.

The evolutionary analysis of community organization is considered a major frontier in biology. Nevertheless, current explanations for community structure exclude the effects of genes and selection at levels above the individual. Here, we demonstrate a genetic basis for community structure, arising from the fitness consequences of genetic interactions among species (i.e., interspecific indirect genetic effects or IIGEs). Using simulated and natural communities of arthropods inhabiting North American cottonwoods (Populus), we show that when species comprising ecological communities are summarized using a multivariate statistical method, nonmetric multidimensional scaling (NMDS), the resulting univariate scores can be analyzed using standard techniques for estimating the heritability of quantitative traits. Our estimates of the broad-sense heritability of arthropod communities on known genotypes of cottonwood trees in common gardens explained 56-63% of the total variation in community phenotype. To justify and help interpret our empirical approach, we modeled synthetic communities in which the number, intensity, and fitness consequences of the genetic interactions among species comprising the community were explicitly known. Results from the model suggest that our empirical estimates of broad-sense community heritability arise from heritable variation in a host tree trait and the fitness consequences of IGEs that extend from tree trait to arthropods. When arthropod traits are heritable, interspecific IGEs cause species interactions to change, and community evolution occurs. Our results have implications for establishing the genetic foundations of communities and ecosystems.

Animals↗

Asymmetry--where evolutionary and developmental genetics meet.

The mechanisms responsible for the fine tuning of development, where the wildtype phenotype is reproduced with high fidelity, are not well understood. The difficulty in approaching this problem is the identification of mutant phenotypes indicative of a defect in these fine-tuning control mechanisms. Evolutionary biologists have used asymmetry as a measure of developmental homeostasis. The rationale for this was that, since the same genome controls the development of the left and right sides of a bilaterally symmetrical organism, departures from symmetry can be used to measure genetic or environmental perturbations. This paper examines the relationship between asymmetry and resistance to organophosphorous insecticides in the Australian sheep blowfly, Lucilia cuprina. A resistance gene, Rop-1, which encodes a carboxylesterase enzyme, also confers a significant increase in asymmetry. Continued exposure of resistant populations to insecticide has selected a dominant suppressor of the asymmetry phenotype. Genetic evidence indicates that the modifier is the L. cuprina Notch homologue.

Animals↗

Genetic variation and evolutionary stability of the FMR1 CGG repeat in six closed human populations.

In an attempt to understand the allelic diversity and mutability of the human FMR1 CGG repeat, we have analyzed the AGG substructure of this locus within six genetically-closed populations (Mbuti pygmy, Baka pygmy, R. surui, Karitiana, Mayan, and Hutterite). Most alleles (61/92 or 66%) possessed two AGG interspersions occurring with a periodicity of one AGG every nine or ten CGG repeats, indicating that this pattern is highly conserved in all human populations. significant differences in allele distribution were observed among the populations for rare variants possessing fewer or more AGG interruptions than the canonical FMR1 CGG repeat sequence. Comparisons of expected heterozygosity of the FMR1 CGG repeat locus with 30 other microsatellite loci, demonstrated remarkably similar levels of polymorphism within each population, suggesting that most FMR1 CGG repeat alleles mutate at rates indistinguishable from other microsatellite loci. A single allele (1 out of 92) was identified with a large uninterrupted tract of pure repeats (42 pure CGG triplets). Retrospective pedigree analysis indicated that this allele had been transmitted unstably. Although such alleles mutate rapidly and likely represent evolving premutations, our analysis suggests that in spite of the estimated frequency of their occurrence, these unstable alleles do not significantly alter the expected heterozygosity of the FMR1 CGG repeat in the human population.

Biological Evolution↗

Evidence for evolutionary stasis and genetic drift by genetic analysis of two equine influenza H3 viruses isolated in France.

The amino acid sequences of the HA(1) portion of the haemagglutinin of two equine A(H3N8) influenza viruses isolated in France in 1993 and 1998 were analysed to determine their evolutionary relationship with 51 other HA(1) amino acid sequences available in databanks. Our data show that the French strain isolated in 1993 belongs to a group of phylogenetically related viruses branched on the main trunk, illustrating the main lineage of evolution of the equine-2 H3 sequences before its split into two distinct lineages in the late 1980s. By contrast, the 1998 French isolate appears to belong to the more recent 'Eurasian' lineage. These data suggest that equine-2 strains antigenically related to old prototype viruses may cocirculate with the more recent 'Eurasian' and 'American' lineages. In conclusion, it may be necessary to include both strains representative of recent equine influenza variants and an older prototype strain in the current equine influenza vaccines.

Amino Acid Sequence↗

Evolving evolutionary algorithms using linear genetic programming.

A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

Algorithms↗

An evolutionary relationship between genetic variation and phenotypic fluctuation.

The relevance of phenotype fluctuations among clones (i.e., organisms with identical genes) to evolution has recently been recognized both theoretically and experimentally. By considering the stability of the distributions of genetic variations and phenotype fluctuations, we derive a general inequality between the phenotype variance due to genetic differences and the intrinsic phenotype variance of clones. For a given mutation rate, an approximately linear relationship between the two is obtained which elucidates the consistency between the fundamental theorem of natural selection by Fisher and the evolutionary fluctuation-response relationship (fluctuation dissipation theorem) proposed recently. A general condition for the error catastrophe is also derived as the violation of the inequality, which sets up the limit to the speed of stable evolution. All of these theoretical results are confirmed by a numerical evolution experiment of a cell that consists of a catalytic reaction network. Based on the relationships proposed here, relevance of the phenotypic plasticity to evolution as well as the genetic assimilation is discussed.

Animals↗

Nemo: an evolutionary and population genetics programming framework.

UNLABELLED: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. AVAILABILITY: The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

Biological Evolution↗

Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: studies of infected donor-recipient clusters.

Six donor-recipient clusters of hepatitis C virus (HCV)-infected individuals were studied. For five clusters the period of infection of the donor could be estimated, and for all six clusters the time of infection of the recipients from the donor via blood transfusion was also precisely known. Detailed phylogenetic analyses were carried out to investigate the genomic evolution of the viral quasispecies within infected individuals in each cluster. The molecular clock analysis showed that HCV quasispecies within a patient are evolving at the same rate and that donors that have been infected for longer time tend to have a lower evolutionary rate. Phylogenetic analysis based on the split decomposition method revealed different evolutionary patterns in different donor-recipient clusters. Reactivity of antibody against the first hypervariable region (HVR1) of HCV in donor and recipient sera was evaluated and correlated to the calculated evolutionary rate. Results indicate that anti-HVR1 reactivity was related more to the overall level of humoral immune response of the host than to the HVR1 sequence itself, suggesting that the particular sequence of the HVR1 peptides is not the determinant of reactivity. Moreover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quasispecies in the patients and the strength of the immune response to HVR1 epitopes. Rather, the results seem to imply that genetic drift is less dependent on immune pressure than on the rate of evolution and that the genetic drift of HCV is independent of the host immune pressure.

Blood Donors↗

Regional genetic structuring and evolutionary history of the impala Aepyceros melampus.

Samples of 162 impala antelope (Aepyceros melampus) from throughout its distribution range in sub-Saharan Africa were surveyed using eight polymorphic microsatellite loci. Furthermore, 155 previously published mitochondrial DNA (mtDNA) sequences from the same localities were reanalyzed. Two subspecies of impala are presently recognized--the isolated black-faced impala (Aepyceros melampus petersi) in southwest Africa and the common impala (Aepyceros melampus melampus) abundant in southern and east Africa. All tests performed indicated significant genetic differentiation at the subspecific level. Furthermore, individual-based analyses split the common impala subspecies into two distinct genetic groups, conforming with regional geographic affiliation to southern or east Africa. This was supported by assignment tests, genetic distance measures, pairwise theta values, and analysis of molecular variance. We suggest that the presence of such previously unknown regional structuring within the subspecies reflects a pattern of colonization from a formerly large panmictic population in southern Africa toward east Africa. This scenario was supported by a progressive decline in population diversity indices toward east Africa and a significant increase in the quantity theta/(1 - theta). Both microsatellite and mtDNA data indicated a genetic distinctiveness of the Samburu population in Kenya.

Animals↗

Reverse engineering genetic networks using evolutionary computation.

This paper proposes an improved evolutionary method for constructing the underlying network structure and inferring effective kinetic parameters from the time series data of gene expression using decoupled S-system formalism. We employed Trigonometric Differential Evolution (TDE) as the optimization engine of our algorithm for capturing the dynamics in gene expression data. A more effective fitness function for attaining the sparse structure, which is the hallmark of biological networks, has been applied. Experiments on artificial genetic network show the power of the algorithm in constructing the network structure and predicting the regulatory parameters. The method is used to evaluate interactions between genes in the SOS signaling pathway in Escherichia coli using gene expression data.

Algorithms↗

Genetic analysis of evolutionary relationships among deer (subfamily Cervinae).

The evolutionary relationships among 10 taxa of deer from the four genera of the subfamily Cervinae (Cervus, Elaphurus, Axis, and Dama) were examined by a comparison of their electrophoretic types for 22 proteins. We analyzed the data using both phenetic and cladistic methods and found that the genera of the Cervinae were not monophyletic. The genus Cervus was split into two distinct groups with red deer, wapiti (C. elaphus ssp.), and sika (C. nippon) in one clade and sambar (C. unicolor) and rusa (C. timorensis) in another. There was a close genetic relationship between the genus Elaphurus and the red deer, wapiti, sika group, whereas sambar and rusa were more similar to members of the genera Dama and Axis than to the other members of their own genus. These findings contrast with the taxonomy of the species that is based largely on studies of comparative morphology. Our samples (n = 5) showed fixed allelic differences between wapiti and red, wapiti and sika, and red and sika samples at 3, 6, and 7 loci, respectively. Analysis of these protein loci in a wider range of C. elaphus and C. nippon subspecies could resolve debate over the evolutionary relationships of these taxa.

Animals↗

Evolutionary analysis of genetic variation observed in citrus tristeza virus (CTV) after host passage.

We have studied the genetic variability in two genes (p18 and p20) from two groups of Citrus tristeza virus (CTV) isolates. One group (isolates T385, T317, T318, and T305) was derived from a Spanish source by successive host passages while the other (isolates T388 and T390) was obtained after aphid transmission from a Japanese source. A total of 274 sequences were obtained for gene p18 and 451 for p20. In the corresponding phylogenetic trees, sequences derived from the severe isolates (T318, T305, and T388) clustered together and separately from those derived from mild or moderate isolates (T385, T317, and T390), regardless of their geographic origin. Hierarchical analyses of molecular variance showed that up to 53% of the total genetic variability in p18 and up to 87% of the variation in p20 could be explained by differences in the pathogenicity features of the isolates. Neutrality tests revealed that different selection forces had been acting between isolates and between genes, with purifying selection being suggested for p18 from isolates T385 and T390 and for p20 from isolates T385, T317, and T388, and balancing selection for p18 from isolates T318, T305, and T388 and for p20 from isolates T318 and T390. Furthermore, several models of codon selection were observed, with purifying selection being the most notable one, compatible with low effective population size of the virus populations resulting from transmission bottlenecks. We found no evidence of recombination playing a significant role during p18 and p20 evolution in these isolates. These results suggest that hosts can be an important evolutionary factor for CTV isolates.

Animals↗

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

Animals↗

Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids.

Evolutionary studies suggest that 200-250 million years ago an aphid ancestor was infected with a free-living eubacterium. The latter became established within aphid cells. Host and endosymbiont (genus Buchnera) became interdependent and unable to survive without each other. The growth of Buchnera became integrated with that of the aphids, which acquired the endosymbionts from their mothers before birth. Speciation of host lineages was paralleled by divergence of associated endosymbiont lineages, resulting in parallel evolution of Buchnera and aphids. Present day Buchnera retains many of the properties of its free-living ancestor, containing genes for proteins involved in DNA replication, transcription, and translation, as well as chaperonins and proteins involved in secretion, energy-yielding metabolism, and amino acid biosynthesis. Some of these processes are also observed in isolated endosymbiont cells. Genetic and physiological studies indicate that Buchnera can synthesize methionine, cysteine, and tryptophan and supply these amino acids to the aphid host. In the case of some fast-growing species of aphids, the overproduction of tryptophan by Buchnera involves plasmid-amplification of the gene coding for anthranilate synthase, the first enzyme of the tryptophan biosynthetic pathway. These recent studies provide a beginning in our understanding of Buchnera and its role in the endosymbiosis with aphids.

Animals↗