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PubMedDate not supplied

Concerted evolution and developmental integration in modular butterfly wing patterns.

Developing organisms are thought to be modular in organization so that traits in different modules evolve independently whereas traits within a module change in a concerted manner. The eyespot pattern in Bicyclus anynana butterflies provides an ideal system where morphological modularity can be dissected and different levels of genetic integration analyzed. Several lines of evidence show that all eyespots in an individual butterfly are genetically integrated, suggesting that the whole pattern, rather than the separate eyespots, should be considered as a single character. However, despite the strong genetic correlations between the two eyespots on the dorsal forewing of B. anynana, there is great potential for independent changes. Here we use laboratory lines selected in different directions for the size of those eyespots to study correlated responses in the whole eyespot pattern. We show clear changes in eyespot size across all wing surfaces, which depend on eyespot position along the anterior-posterior axis. There are also changes in the number of extra eyespots and in eyespot color composition but no changes in eyespot position relative to wing margin. Our analysis of eyespot pattern modularity is discussed in the light of what is known about the cellular and genetic mechanisms of eyespot formation and the great potential for evolutionary diversification in butterfly wing patterns.

Analysis of Variance↗
PubMed2004

Human centromere repositioning "in progress".

Centromere repositioning provides a potentially powerful evolutionary force for reproductive isolation and speciation, but the underlying mechanisms remain ill-defined. An attractive model is through the simultaneous inactivation of a normal centromere and the formation of a new centromere at a hitherto noncentromeric chromosomal location with minimal detrimental effect. We report a two-generation family in which the centromeric activity of one chromosome 4 has been relocated to a euchromatic site at 4q21.3 through the epigenetic formation of a neocentromere in otherwise cytogenetically normal and mitotically stable karyotypes. Strong epigenetic inactivation of the original centromere is suggested by retention of 1.3 megabases of centromeric alpha-satellite DNA, absence of detectable molecular alteration in chromosome 4-centromereproximal p- and q-arm sequences, and failure of the inactive centromere to be reactivated through extensive culturing or treatment with histone deacetylase inhibitor trichostatin A. The neocentromere binds functionally essential centromere proteins (CENP-A, CENP-C, CENP-E, CENP-I, BUB1, and HP1), although a moderate reduction in CENP-A binding and sister-chromatid cohesion compared with the typical centromeres suggests possible underlying structural/functional differences. The stable mitotic and meiotic transmissibility of this pseudodicentric-neocentric chromosome in healthy individuals and the ability of the neocentric activity to form in a euchromatic site in preference to a preexisting alphoid domain provide direct evidence for an inherent mechanism of human centromere repositioning and karyotype evolution "in progress." We discuss the wider implication of such a mechanism for meiotic drive and the evolution of primate and other species.

Autoantigens↗
PubMed2003

Variation in Ginkgo biloba L. leaf characters across a climatic gradient in China.

Fossil leaves assigned to the genus Ginkgo are increasingly being used to reconstruct Mesozoic and Tertiary environments based on their stomatal and carbon isotopic characteristics. We sought to provide a more secure basis for understanding variations seen in the plant fossil record by determining the natural variability of these properties of sun and shade leaf morphotypes of Ginkgo biloba trees under the present atmospheric CO2 concentration and a range of contemporary climates in three Chinese locations (Lanzhou, Beijing, and Nanjing). Climate had no major effects on leaf stomatal index (proportion of leaf surface cells that are stomata) but did result in more variable stomatal densities. The effects of climate and leaf morphotype on stomatal index were rather conserved (<1%) and much less than the response of trees to recent CO2 increases. Leaf carbon isotope discrimination (delta) was highest for trees in Nanjing, which experience a warm, moist climate, whereas trees in the most arid site (Lanzhou) had the lowest delta values. Interestingly, the variation in delta shown by leaf populations of trees from China and the United Kingdom was very similar to that of fossil Ginkgo cuticles dating to the Mesozoic and Tertiary, which suggests to us that the physiology of leaf carbon uptake and regulation of water loss in Ginkgo has remained highly conserved despite the potential for evolutionary change over millions of years.

Biological Evolution↗
PubMed1984

Genetic recombination can generate altered restriction specificity.

A recombinant strain, isolated following the transduction of an Escherichia coli recipient carrying the Salmonella typhimurium (SB) specificity genes with DNA from a donor having the Salmonella potsdam (SP) specificity, was shown [Bullas, L.R., Colson, C. & Van Pel, A. (1976) J. Gen. Microbiol. 95, 166-172] to have neither SB nor SP specificity but to encode a novel restriction specificity, SQ. The heteroduplex analysis of the hsdS (specificity) genes of the SB and SP restriction and modification systems described here identifies a conserved sequence of around 100 base pairs flanked by two nonhomologous regions each of approximately 500 base pairs. This organization parallels that previously deduced from the DNA sequences of the hsdS genes of the related E. coli K-12, B, and D restriction systems. The present heteroduplex analyses further show that the hsdS gene conferring the SQ specificity derives one nonhomologous region from the SB gene and the other from the SP gene, as predicted from genetic exchange within the conserved sequence. This finding supports the idea that two domains of an hsdS polypeptide, which are different for each specificity, may correlate with two regions of the DNA sequence recognized. It has been shown that the recognition sequences for E. coli K-12 and B each consist of two short oligonucleotide sequences interrupted by a nonspecific sequence. A similar organization is suggested for the Salmonella specificity systems, providing the potential for evolutionary diversification of restriction specificities as a result of recombination within the conserved sequence of the hsdS gene.

Bacteriophage lambda↗
PubMed1991

Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Published data on allele frequencies at isozyme loci in inbreeding and outbreeding plant species were analyzed to examine intraspecific variation in gene diversity and effective population size (Ne). Compared with outbreeders, inbreeding species showed markedly greater variation among populations in average values of Nei's gene diversity statistic. Effective population size was estimated by assuming that the variation observed at isozyme loci is selectively neutral. Inbreeding species showed greater levels of variation in Ne than did outbreeders, although the upper range of Ne was similar in the two classes of species. The results suggest that there may be considerable genetic variation and potential for evolutionary change in some but not all populations of inbreeders. Moreover, these findings are important with respect to the conservation of genetic resources. In particular, that the amount of intraspecific variation in population genetic diversity and Ne differs between inbreeding and outbreeding species should be taken into account in sampling efforts designed to optimize the diversity of germplasm collections.

Journal Article↗
PubMedDate not supplied

Heritability of brain size and surface features in rhesus macaques (Macaca mulatta).

The extent of heritability for overall brain size and regional cortical surface features such as sulcus lengths is important for demonstrating a genetic component to the observed phenotypic differences among individuals and for evaluating the potential for evolutionary change in response to selection. Although the genetics of brain size has been extensively considered, the detailed morphology of the cortical surface has not previously been subjected to genetic analysis. We estimated the heritability of brain size and cortical sulcus lengths using 438 endocranial casts taken from skeletons of rhesus macaques (Macaca mulatta) from the Cayo Santiago population. Estimates were obtained both by mother-offspring regression and symmetric-differences-squared (SDS) methods. Brain size, measured as cranial capacity, was highly and significantly heritable in this population, confirming results of previous studies with laboratory mice. Overall, cortical sulcus lengths were also heritable, with 35% of the sulci significantly heritable at the 5% level in the mother-offspring analysis. The average mother-offspring heritability estimate, 0.31, was the same as the average heritability obtained previously from a series of 56 cranial metric characters. The SDS analyses generally corresponded to the findings based on mother-offspring regressions, although the significance test appeared more conservative. Both gross and detailed morphology of the brain are heritable.

Animals↗
PubMed1995

Outcrossing rates and correlated matings in a predominantly selfing freshwater snail.

We estimated outcrossing rates and correlated matings in a natural population of the hermaphroditic freshwater snail Ancylus fluviatilis, using progeny arrays and polymorphic allozyme markers. This design circumvents drawbacks of earlier studies, and yields maximum likelihood estimates of outcrossing rates at both the individual and population level. Adult snails were sampled during the spring breeding period, allowing for prior copulations and sperm transfer under natural conditions. Once in the laboratory, they were kept isolated for 21 days and laid egg capsules, and emerging hatchlings from 42 families were scored for five polymorphic loci. 87 of 848 offspring exhibited non-maternal alleles, representing a minimum population-level outcrossing of 10.3%. Maximum likelihood estimates are in the range 13-15%. Importantly, there is significant among-family heterogeneity, as only 16 of 42 families are estimated to have outcrossed, in accord with high estimates of correlated selfing within progeny arrays. Moreover, the high proportion of full sibs among outcrossed sibs suggests a limited extent of multiple paternity. Our data reveal important heterogeneity in the mating system of an animal hermaphrodite, and indicate the potential for evolutionary change in the breeding system.

Animals↗
PubMed2003

The Arabidopsis basic/helix-loop-helix transcription factor family.

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.

Amino Acid Sequence↗
PubMed2005

Allele-specific assay reveals functional variation in the chalcone synthase promoter of Arabidopsis thaliana that is compatible with neutral evolution.

Promoters are thought to play a major role in adaptive evolution, yet little is known about the regulatory diversity within species, where microevolutionary processes take place. To investigate the potential for evolutionary change in the promoter of a gene, we examined nucleotide and functional variation of the Chalcone Synthase (CHS) cis-regulatory region in Arabidopsis thaliana. CHS is the branch point enzyme of a biosynthetic pathway that leads to the production of secondary metabolites influencing the interaction between the plant and its environment. We found that nucleotide diversity in the intergenic region encompassing the CHS promoter (pi=0.003) is compatible with neutral expectations. To quantify functional variation specifically as a result of cis-regulation of CHS mRNA levels, we developed an assay using F1 individuals in which distinct promoter alleles are compared within a common trans-regulatory background. We examined functional cis-regulatory variation in response to different stimuli representing a variety of CHS transcriptional environments (dark, light, and insect feeding). We observed extensive functional variation, some of which appeared to be independent of the trans-regulatory background. Comparison of functional and nucleotide diversity suggested a candidate point mutation that may explain cis-regulatory differences in light response. Our results indicate that functional changes in promoters can arise from a few mutations, pointing to promoter regions as a fundamental determinant of functional genetic variation.

Acyltransferases↗
PubMed2004

Natural selection, evolvability and bias due to environmental covariance in the field in an annual plant.

Estimates of the form and magnitude of natural selection based on phenotypic relationships between traits and fitness measures can be biased when environmental factors influence both relative fitness and phenotypic trait values. I quantified genetic variances and covariances, and estimated linear and quadratic selection coefficients, for seven traits of an annual plant grown in the field. For replicates of 50 paternal half-sib families, coefficients of selection were calculated both for individual phenotypic values of the traits and for half-sib family mean values. The potential for evolutionary response was supported by significant heritability and phenotypic directional selection for several traits but contradicted by the absence of significant genetic variation for fitness estimates and evidence of bias in phenotypic selection coefficients due to environmental covariance for at least two of the traits analysed. Only studies of a much wider range of organisms and traits will reveal the frequency and extent of such bias.

Analysis of Variance↗
PubMed1991

Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis.

There is strong inferential evidence for recent horizontal gene transfer of the P (mobile) element to Drosophila melanogaster from a species of the Drosophila willistoni group. One potential vector of this transfer is a semiparasitic mite, Proctolaelaps regalis DeLeon, whose morphology, behavior, and co-occurrence with Drosophila are consistent with the properties necessary for such a vector. Southern blot hybridization, polymerase chain reaction (PCR) amplification, and DNA sequencing showed that samples of P. regalis associated with a P strain of D. melanogaster carried P element sequences. Similarly, Drosophila ribosomal DNA sequences were identified in P. regalis samples that had been associated with Drosophila cultures. These results have potentially important evolutionary implications, not only for understanding the mechanisms by which genes may be transferred between reproductively isolated species, but also for improved detection of some host-parasite and predator-prey relationships.

Animals↗
PubMed1985

A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance.

A human DNA sequence (p12f2), derived from a partial Y-chromosome genomic library and showing homology with the X and Y chromosomes and with an undetermined number of autosomes, detected two Y-specific restriction fragment length variants on male DNA that had been digested with Taq I and Eco RI. These variants may have been generated through a deletion-insertion mechanism and their pattern of holoandric transmission indicates that they represent a two-allele Y-linked polymorphism (RFLP). By means of DNA from patients with inborn deletions in chromosome Y, this polymorphic DNA site was mapped to the interval Yq11.1-Yq11.22. The frequency of the rarest allele was about 35 percent in Algerian and Sardinian human males, whereas it was only 4 percent among Northern Europeans. The p12f2 probe also detected Y-specific DNA fragments in the gorilla and chimpanzee. In view of the monosomy of the Y chromosome in mammalian species, Y-linked RFLP's may prove to be more useful than autosomal or X-linked markers in estimating genetic distances within and between species.

Base Sequence↗
PubMed2004

Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group.

BACKGROUND: DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes. RESULTS: The genome sequences of two Xanthomonas species were used as the basis for phylogenetic analyses of genes related to DNA repair that were found duplicated. Although 16S rRNA phylogenetic analyses confirm their classification at the basis of the gamma proteobacteria subdivision, differences were found in the origin of the various genes investigated. Except for lexA, detected as a recent duplication, most of the genes in more than one copy are represented by two highly divergent orthologs. Basically, one of such duplications is frequently positioned close to other gamma proteobacteria, but the second is often positioned close to unrelated bacteria. These orthologs may have occurred from old duplication events, followed by extensive gene loss, or were originated from lateral gene transfer (LGT), as is the case of the uvrD homolog. CONCLUSIONS: Duplications of DNA repair related genes may result in redundancy and also improve the organisms' responses to environmental challenges. Most of such duplications, in Xanthomonas, seem to have arisen from old events and possibly enlarge both functional and evolutionary genome potentiality.

DNA Repair↗
PubMed2001

Richness of Colchic vegetation: comparison between refugia of south-western and East Asia.

BACKGROUND: The Colchis is one of the species-rich refugia and a centre of biological diversity in western Eurasia. We analysed patterns of richness, endemism and invasions in relation to taxonomy (family membership), life form, certain habitats in the Colchis, and compared them to patterns found for Japan. RESULTS: We found that in the Colchis perennials are significantly over-represented in endemic species, and that they typically occur on limestone soils and in alpine tall herbaceous vegetation. The Asteraceae produce significantly large number of both endemic and alien species, whereas the Poaceae are over-represented in alien species but under-represented in endemics. Likewise, the Apiaceae are over-represented in endemics, whereas the Euphorbiaceae are over-represented in alien species. Similar patterns have been found in Yakushima, Japan. The Morisita-Horn index of similarity between these two sites was 0.83 (based on family size). Although the flora of Adjara comprised of fewer families than the flora of Yakushima, the largest families are richer in species in the flora of Adjara than in the flora of Yakushima. CONCLUSIONS: Floristic analysis of refugia of western Eurasia and their comparison with geographically distant areas can provide useful data for plant ecological and evolutionary studies. Potentially, such studies can produce testable hypotheses on plant migrations and on their historical geography. For example, the data presented in this study indicate that more severe conditions in the Pleistocene and geographical isolation of the Colchis may be responsible for the higher relative importance of adaptive radiation in the shaping of its modern flora.

Biodiversity↗
PubMed2003

Demographic and genetic structures of two partially isolated communities of Santa Catarina Island, southern Brazil.

The objectives of this study were to analyze the population structure and genetic variability of two communities, Costa da Lagoa (CLG) and São João do Rio Vermelho (SJRV), located on Santa Catarina Island in southern Brazil. The two populations descend from Azores Archipelago immigrants (Portuguese), with a minor contribution of sub-Saharan Africans and Amerindians. To estimate the relative contribution of the different ethnic groups to the current gene pool of the two communities, values of admixture were obtained using the weighted least-squares method based on allelic frequencies of the loci ABO, RHD-RHCE, GPA-GPB (MNSs), HBB, HP, TF, CP, AK, and ACP1. The origins of the studied populations can be quantified as follows: for CLG, sub-Saharan Africans (A) = 17.3%, Iberian Europeans (P) = 75.0%, and Southern Amerindians (I) = 7.7%; for SJRV, A = 48.8%, P = 44.5%, and I = 6.7%. Because haplotype frequencies of the GPA-GPB loci in SJRV were unusual, possibly as a consequence of random genetic drift, the values of admixture were recalculated after exclusion of GPA-GPB, as follows: A = 28.0%; P = 53.3%, and I = 18.7%. The total diversity (HT) was estimated as 42.29%, of which 99.6% can be attributed to the intrapopulational variability (HS). The interpopulational genetic variation (or standard distance, DST) corresponds to 0.19%, while the gene differentiation coefficient is 0.28%, indicative of low genetic difference. These results led to the conclusion that random genetic drift may have had an important effect on the Costa da Lagoa community, while presently gene flow might be the predominant evolutionary factor potentially capable of changing allele frequencies in SJRV.

Africa↗
PubMed2002

In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migration.

Eosinophil migration from circulation is controlled, in part, by chemokines through a family of G-protein-coupled chemokine receptors (CCR). Studies of human eosinophils have demonstrated that signaling through CCR3 receptors is a prominent pathway leading to chemotaxis, although several other receptor-ligand interactions also appear to mediate eosinophil recruitment. The availability of genetically unique strains of mice permits a reductionist approach to assess the signaling pathways in experimental models of human disease. However, despite similarities in these pathways between mice and humans, significant species differences exist, complicating the translation of results from animal models to humans. Purified mouse eosinophils were used in this study to investigate the chemokine receptor expression and the activities of 18 chemokines. Mouse eosinophils isolated from IL-5 transgenic mice expressed transcripts encoding the chemokine receptors CCR1, CCR2, CCR3, CCR5, CCR8, CXCR2, and CXCR4, but not CCR4. Mouse eosinophils also migrated in response to human and mouse eotaxin-1 and -2, but not human eotaxin-3. In addition, the induced migration of mouse eosinophils by TARC, MIP-1beta, and KC suggests that unidentified receptor-ligand interactions contribute to eosinophil recruitment. It is interesting that the potent chemoattractant of human eosinophils, RANTES, was unable to mediate mouse eosinophil migration. Furthermore, despite the ability of MIP-1alpha to bind receptors on purified mouse eosinophils, it was only able to induce significant eosinophil migration in a mixed splenocyte population and was unable to induce migration of highly purified eosinophils. Collectively, these observations reveal physiologically relevant distinctions in mechanisms mediating human and mouse eosinophil migration that potentially reflect evolutionary disparities between these species.

Amino Acid Sequence↗
PubMed2004

Birds in a bush: five genes indicate explosive evolution of avian orders.

All recent studies of bird phylogeny have produced poorly resolved relationships among the orders of Neoaves, the lineage that includes most modern birds. This "bush" result suggests the possibility of an explosive and potentially unresolvable evolutionary radiation. However, simultaneous radiations of multiple lineages are thought to be rare or nonexistent in nature and difficult to corroborate empirically because lack of phylogenetic resolution can also be caused by analytical artifacts. Here we examine the predictions of the explosive radiation hypothesis for five independent genetic datasets for Neoaves. We propose a methodology for testing for polytomies of evolutionary lineages, perform likelihood-ratio tests to compare trees with zero-length branches to more resolved trees, compare topologies between independent gene trees, and propose a power test for the SOWH test. The evidence of (1) extremely short (in some cases zero-length) branches for interordinal relationships across independent gene trees and (2) topological incongruence among gene trees suggests that the bird tree includes essentially simultaneous radiation of multiple lineages. This result explains why a robust phylogeny of birds has not been produced despite much effort on the part of avian systematists.

Animals↗
PubMed2006

Inferring functional linkages between proteins from evolutionary scenarios.

Identifying potential protein interactions is of great importance in understanding the topologies of cellular networks, which is much needed and valued in current systematic biological studies. The development of our computational methods to predict protein-protein interactions have been spurred on by the massive sequencing efforts of the genomic revolution. Among these methods is phylogenetic profiling, which assumes that proteins under similar evolutionary pressures with similar phylogenetic profiles might be functionally related. Here, we introduce a method for inferring functional linkages between proteins from their evolutionary scenarios. The term evolutionary scenario refers to a series of events that occurred in speciation over time, which can be reconstructed given a phylogenetic profile and a species tree. Common evolutionary pressures on two proteins can then be inferred by comparing their evolutionary scenarios, which is a direct indication of their functional linkage. This scenario method has proven to have better performance compared with the classical phylogenetic profile method, when applied to the same test set. In addition, predicted results of the two methods are found to be fairly different, suggesting the possibility of merging them in order to achieve a better performance. We analyzed the influence of the topology of the phylogenetic tree on the performance of this method, and found it to be robust to perturbations in the topology of the tree. However, if a completely random tree is incorporated, performance will decline significantly. The evolutionary scenario method was used for inferring functional linkages in 67 species, and 40,006 linkages were predicted. We examine our prediction for budding yeast and find that almost all predicted linkages are supported by further evidence.

Computational Biology↗