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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↗
PubMed2000

Genetic compatibility, mate choice and patterns of parentage: invited review.

There is growing interest in the possibility that genetic compatibility may drive mate choice, including gamete choice, particularly from the perspective of understanding why females frequently mate with more than one male. Mate choice for compatibility differs from other forms of choice for genetic benefits (such as 'good genes') because individuals are expected to differ in their mate preferences, changing the evolutionary dynamics of sexual selection. Recent experiments designed to investigate genetic benefits of polyandry suggest that mate choice on the basis of genetic compatibility may be widespread. However, in most systems the mechanisms responsible for variation in compatibility are unknown. We review potential sources of variation in genetic compatibility and whether there is any evidence for mate choice driven by these factors. Selfish genetic elements appear to have the potential to drive mate compatibility mate choice, though as yet there is only one convincing example. There is abundant evidence for assortative mating between populations in hybrid zones, but very few examples where this is clearly a result of selection against mating with genetically less compatible individuals. There are also numerous cases of inbreeding avoidance, but little evidence that mate choice or differential fertilization success driven by genetic compatibility occurs between unrelated individuals. The exceptions to this are a handful of situations where both the alleles causing incompatibility and the alleles involved in mate choice are located in a chromosome region where recombination is suppressed. As yet there are only a few potential sources of genetic compatibility which have clearly been shown to drive mate choice. This may reflect limitations in the potential for the evolution of mate choice for genetic compatibility within populations, although the most promising sources of such incompatibilities have received relatively little research.

Animals↗
PubMed2001

Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki).

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness.

Animals↗
PubMed2003

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout.

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

Animals↗
PubMed2003

Effects of Wolbachia on mtDNA variation in two fire ant species.

Wolbachia are endosymbiotic bacteria that infect arthropods. As they are maternally transmitted, the spread of Wolbachia variants within host populations may affect host mtDNA evolution. We sequenced a portion of the mitochondrial cytochrome oxidase I gene from numerous individuals of two Wolbachia-infected fire ant species, Solenopsis invicta and S. richteri, to determine how these bacteria influence patterns of mtDNA variation. As predicted, there was a strong association between Wolbachia strain and host mtDNA lineage within and between these fire ant species. However, there was no consistent association between the presence of Wolbachia and a reduction in mtDNA diversity. Moreover, patterns of mtDNA variation within Wolbachia-infected populations did not differ consistently from neutral expectations, despite our prediction that strong positive selection acting on Wolbachia influences the evolutionary dynamics of other cytoplasmic genomes. Specifically, while values of Tajima's D consistently were less than zero for all six samples of fire ants harbouring Wolbachia, MacDonald-Kreitman tests suggested that the patterns of variation were different from those expected under neutrality in only two of the samples. We conclude that these neutrality tests do not unambiguously reveal a clear effect of Wolbachia infection on patterns of mtDNA variation and substitution in fire ants. Finally, consistent with an earlier study, our data revealed the presence of two divergent mtDNA haplotype lineages and Wolbachia strains within S. invicta. Recognition of these two lineages has important consequences for interpreting patterns of mtDNA evolution and genetic differentiation between conspecific social forms of this species.

Animals↗
PubMed2003

Disjunct distribution of highly diverged mitochondrial lineage clade and population subdivision in a marine bivalve with pelagic larval dispersal.

Mitochondrial DNA sequence data for 295 individuals of the marine bivalve Macoma balthica (L.) were collected from 10 sites across the European distribution, and from Alaska. The data were used to infer population subdivision history and estimate current levels of gene flow. Inferred historical biogeography was expected to be congruent with colonization of the Atlantic Ocean from the Pacific Ocean after the opening of the Bering Strait 3.5 Ma. In addition, the last glacial maximum, about 18000 years ago, was expected to have been responsible for most of the present-day distribution of molecular variation within Europe, because the area must have been recolonized after confinement to France and the south of the British Isles during the last glacial maximum. Current gene flow was hypothesized to be high, because the larvae of M. balthica spend 2-5 weeks drifting in the water column. The geographical distribution of one highly diverged haplotype clade was found to be disjunct and was encountered exclusively in samples from the Baltic Sea and Alaska. A molecular clock calibration for marine bivalve cytochrome-c-oxidase I dates this clade as having split off from the other haplotypes 9.8-39 Ma. Multiple colonizations of the Atlantic Ocean from the Pacific by M. balthica may explain the strong differences found between Baltic Sea and other European populations of this species. The sympatric occurrence of the highly diverged mitochondrial lineages in western parts of the Baltic Sea points to secondary admixture. With the use of coalescent analysis, population divergence times for French vs. other non-Baltic European populations ('Atlantic population assemblage') were estimated at a minimum of about 110000 years ago, well before the last glacial maximum 18000 years ago. Signatures of population divergence of M. balthica that appear to have originated during the Pleistocene have thus survived the last glacial maximum. Some of the populations within the Atlantic assemblage are currently isolated, while others appear to be connected by gene flow. Apparently, populations of this species can remain highly subdivided in spite of the potential for high gene flow, implying that their population and evolutionary dynamics can be independent.

Alaska↗
PubMed2003

Incongruent nuclear and mitochondrial phylogeographic patterns in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae).

Phylogeographic analyses have mostly been based on single-gene genealogies but it is unclear how conclusions from such studies depend on the choice of gene markers. We conducted a nested geographical clade analysis [A.R. Templeton, E. Routman and C.A. Phillips (1995) Genetics 140: 767-782] based on nuclear rDNA internal transcribed spacer region 2 (ITS2) sequences in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae), and compared the inferences with an updated version of previously published results using mitochondrial cytochrome oxidase II (COIl) sequences. Inferences from ITS2 suggest that patterns of marker distribution are mostly explained by restricted gene flow with isolation by distance. In contrast, COII revealed a history of geographical structure resulting from episodic population contiguous-range expansions. Both markers also show different genealogical patterns, which are associated to the effects of genetic introgression in a putative hybrid zone between two major lineages in the complex. Altogether, these differences are attributed to distinct population and/or evolutionary dynamics of the markers, and offer a more accurate phylogeographic description for the T. goettingensis complex.

Animals↗
PubMed2006

Evolutionary changes of metabolic networks and their biosynthetic capacities.

The metabolic networks of different species show a large variety in their structural design. In this work, the evolution of functional properties of metabolism in relation with metabolic network structure is investigated. The metabolism of ancestral species is inferred from the metabolism of contemporary species using a Bayesian network model for metabolism evolution. Subsequently, these networks are analysed with the recently developed method of network expansion. This method allows for a structural analysis of metabolic networks as well as a quantification of network functions in terms of their synthesising capacities when they are provided with certain external resources. The evolutionary dynamics of one particular network function: the metabolic expansion of glucose is investigated.

Adaptation, Physiological↗
PubMed2002

Absence of p16INK4a and truncation of ARF tumor suppressors in chickens.

The INK4b-ARF-INK4a locus on human chromosome 9p21 (Human Genome Organization designation CDKN2B-CDKN2A), and the corresponding locus on mouse chromosome 4, encodes three distinct products: two members of the INK4 cyclin-dependent kinase inhibitor family and a completely unrelated protein, ARF, whose carboxyl-terminal half is specified by the second exon of INK4a but in an alternative reading frame. As INK4 proteins block the phosphorylation of the retinoblastoma gene product and ARF protects p53 from degradation, the locus plays a key role in tumor suppression and the control of cell proliferation. To gain further insights into the relative importance of INK4a and ARF in different settings, we have isolated and characterized the equivalent locus in chickens. Surprisingly, although we identified orthologues of INK4b and ARF, chickens do not encode an equivalent of INK4a. Moreover, the reading frame for chicken ARF does not extend into exon 2, because splicing occurs in a different register to that used in mammals. The resultant 60-aa product nevertheless shares functional attributes with its mammalian counterparts. As well as indicating that the locus has been subject to dynamic evolutionary pressures, these unexpected findings suggest that in chickens, the tumor-suppressor functions of INK4a have been compensated for by other genes.

Amino Acid Sequence↗
PubMed2004

Imprint of evolution on protein structures.

We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence duplication and subsequent point mutations. A new gene's ability to fold into a stable and unique structure is tested each time through direct kinetic folding simulations. Where possible, the algorithm accepts the new sequence and structure and thus a "new protein structure" is born. During the course of each run, this model evolutionary algorithm provides several thousand new proteins with diverse structures. Analysis of evolved structures shows that later evolved structures are more designable than seed structures as judged by recently developed structural determinant of protein designability, as well as direct estimate of designability for selected structures by thermodynamic sampling of their sequence space. We test the significance of this trend predicted on lattice models on real proteins and show that protein domains that are found in eukaryotic organisms only feature statistically significant higher designability than their prokaryotic counterparts. These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.

Algorithms↗
PubMed2002

Redundancy, antiredundancy, and the robustness of genomes.

Genetic mutations that lead to undetectable or minimal changes in phenotypes are said to reveal redundant functions. Redundancy is common among phenotypes of higher organisms that experience low mutation rates and small population sizes. Redundancy is less common among organisms with high mutation rates and large populations, or among the rapidly dividing cells of multicellular organisms. In these cases, one even observes the opposite tendency: a hypersensitivity to mutation, which we refer to as antiredundancy. In this paper we analyze the evolutionary dynamics of redundancy and antiredundancy. Assuming a cost of redundancy, we find that large populations will evolve antiredundant mechanisms for removing mutants and thereby bolster the robustness of wild-type genomes; whereas small populations will evolve redundancy to ensure that all individuals have a high chance of survival. We propose that antiredundancy is as important for developmental robustness as redundancy, and is an essential mechanism for ensuring tissue-level stability in complex multicellular organisms. We suggest that antiredundancy deserves greater attention in relation to cancer, mitochondrial disease, and virus infection.

Biological Evolution↗
PubMed2005

Experiments investigating cooperative types in humans: a complement to evolutionary theory and simulations.

Unlike other species, humans cooperate in large, distantly related groups, a fact that has long presented a puzzle to biologists. The pathway by which adaptations for large-scale cooperation among nonkin evolved in humans remains a subject of vigorous debate. Results from theoretical analyses and agent-based simulations suggest that evolutionary dynamics need not yield homogeneous populations, but can instead generate a polymorphic population that consists of individuals who vary in their degree of cooperativeness. These results resonate with the recent increasing emphasis on the importance of individual differences in understanding and modeling behavior and dynamics in experimental games and decision problems. Here, we report the results of laboratory experiments that complement both theory and simulation results. We find that our subjects fall into three types, an individual's type is stable, and a group's cooperative outcomes can be remarkably well predicted if one knows its type composition. Reciprocal types, who contribute to the public good as a positive function of their beliefs about others' contributions, constitute the majority (63%) of players; cooperators and free-riders are also present in our subject population. Despite substantial behavioral differences, earnings among types are statistically identical. Our results support the view that our human subject population is in a stable, polymorphic equilibrium of types.

Algorithms↗
PubMed2005

Punishing and abstaining for public goods.

The evolution of cooperation within sizable groups of nonrelated humans offers many challenges for our understanding. Current research has highlighted two factors boosting cooperation in public goods interactions, namely, costly punishment of defectors and the option to abstain from the joint enterprise. A recent modeling approach has suggested that the autarkic option acts as a catalyzer for the ultimate fixation of altruistic punishment. We present an alternative, more microeconomically based model that yields a bistable outcome instead. Evolutionary dynamics can lead either to a Nash equilibrium of punishing and nonpunishing cooperators or to an oscillating state without punishers.

Altruism↗
PubMed2007

Transcriptional regulation of protein complexes within and across species.

Yeast two-hybrid and coimmunoprecipitation experiments have defined large-scale protein-protein interaction networks for many model species. Separately, systematic chromatin immunoprecipitation experiments have enabled the assembly of large networks of transcriptional regulatory interactions. To investigate the functional interplay between these two interaction types, we combined both within a probabilistic framework that models the cell as a network of transcription factors regulating protein complexes. This framework identified 72 putative coregulated complexes in yeast and allowed the prediction of 120 previously uncharacterized transcriptional interactions. Several predictions were tested by new microarray profiles, yielding a confirmation rate (58%) comparable with that of direct immunoprecipitation experiments. Furthermore, we extended our framework to a cross-species setting, identifying 24 coregulated complexes that were conserved between yeast and fly. Analyses of these conserved complexes revealed different conservation levels of their regulators and provided suggestive evidence that protein-protein interaction networks may evolve more slowly than transcriptional interaction networks. Our results demonstrate how multiple molecular interaction types can be integrated toward a global wiring diagram of the cell, and they provide insights into the evolutionary dynamics of protein complex regulation.

Animals↗
PubMed2002

Importance of compartment formation for a self-encoding system.

A self-encoding system designed to have strict "compartition" of the molecules, i.e., to contain only a single molecule of DNA in each compartment, was established, and its evolutionary fate was analyzed. The system comprised the Thermus thermophilus DNA polymerase gene as the informational molecule and its protein product replicating the gene as the functional molecule. Imposing strict compartition allows the self-encoding system to last up to at least the tenth generation, whereas the system ceased to work after the third generation when loose compartition initiated with 100 molecules was imposed. These results provide experimental evidence on the importance of compartition for the maintenance of a self-encoding system. In addition, the extent of diversity in self-replication activity of the compartments was found to be another vital difference in the evolutionary dynamics between the strict and loose compartitions. Although the system with strict compartition provides widely diversified activity of the compartments at each generation, the values of the activity diverge only within a small range in the system with loose compartition. When the variety in the activity of a compartment is small, functional selection becomes weak, and to conform Darwinian evolution may become unfeasible. Therefore, strict compartition is essential for the evolvability of a self-encoding system.

Amino Acid Substitution↗
PubMed2002

Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant.

Because of their extremely low nucleotide mutation rates, plant mitochondrial genes are generally not expected to show variation within species. Remarkably, we found nine distinct cytochrome b sequence haplotypes in the gynodioecious alpine plant Silene acaulis, with two or more haplotypes coexisting locally in each of three sampled regions. Moreover, there is evidence for intragenic recombination in the history of the haplotype sample, implying at least transient heteroplasmy of mitochondrial DNA (mtDNA). Heteroplasmy might be achieved by one of two potential mechanisms, either continuous coexistence of subgenomic fragments in low stoichiometry, or occasional paternal leakage of mtDNA. On the basis of levels of synonymous nucleotide substitutions, the average divergence time between haplotypes is estimated to be at least 15 million years. Ancient coalescence of extant haplotypes is further indicated by the paucity of fixed differences in haplotypes obtained from related species, a pattern expected under trans-specific evolution. Our data are consistent with models of frequency-dependent selection on linked cytoplasmic male-sterility factors, the putative molecular basis of females in gynodioecious populations. However, associations between marker loci and the inferred male-sterility genes can be maintained only with very low rates of recombination. Heteroplasmy and recombination between divergent haplotypes imply unexplored consequences for the evolutionary dynamics of gynodioecy, a widespread plant breeding system.

Base Sequence↗
PubMed2003

The early stages of duplicate gene evolution.

Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems. Gene duplicates account for 8-20% of the genes in eukaryotic genomes, and the rates of gene duplication are estimated at between 0.2% and 2% per gene per million years. Duplicate genes are believed to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty, yet very little is known about the early stages of the evolution of duplicated gene pairs. It is unclear, for example, to what extent selection, rather than neutral genetic drift, drives the fixation and early evolution of duplicate loci. Analysis of recently duplicated genes in the Arabidopsis thaliana genome reveals significantly reduced species-wide levels of nucleotide polymorphisms in the progenitor and/or duplicate gene copies, suggesting that selective sweeps accompany the initial stages of the evolution of these duplicated gene pairs. Our results support recent theoretical work that indicates that fates of duplicate gene pairs may be determined in the initial phases of duplicate gene evolution and that positive selection plays a prominent role in the evolutionary dynamics of the very early histories of duplicate nuclear genes.

Arabidopsis↗
PubMed1976

Evolution of continuous variation: direct approach through joint distribution of genotypes and phenotypes.

The evolutionary dynamics of the joint distribution of genotypes and phenotypes is studied. The model, originally devised to study the joint effects of Mendelian and other types of transmissions, provides results of interest also to the theory of direct Mendelian transmission with natural selection. Assuming bivariate normal distributions, it is shown that in the latter case genotypic and phenotypic means and variances, and genotype-phenotype correlation can be expressed recursively as functions of the parameters for the selection, environmental, and mutation variance. Equilibria and rates of approach for these moments are calculated. It is also proved that in the presence of selection the heritability,defined as the ratio of expected genotypic to expected phenotypic variance after selection, is greater than that before selection by a predictable amount and that it can be greater than unity.

Biological Evolution↗