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PubMed1999

Periodicity in marine phosphorus burial rate.

There have been arguments both for and against a periodicity of 26-33 million years (Myr) in terrestrial and extraterrestrial records. The best way to identify such periodicity is the analysis of geomarine evolutionary records. We have analysed the marine sedimentary phosphorus burial rate (PBR), as fluctuations in this rate are strong indicators of the coupling of climate, continental weathering and ocean primary productivity. We find a statistically significant harmonic component of 33 +/- 3 Myr against the estimated robust background noise spectrum, supporting the idea that geomarine processes are cyclic.

Evolution, Planetary↗
PubMed2006

A Cretaceous symmetrodont therian with some monotreme-like postcranial features.

A new spalacotheriid mammal preserved with a complete postcranium and a partial skull has been discovered from the Yixian Formation of Liaoning, China. Spalacotheroid symmetrodonts are relatives to modern therians (combined group of marsupials and placentals) and are characterized by many skeletal apomorphies of therians. But unlike the closely related spalacotheroids and living therians, this new mammal revealed some surprisingly convergent features to monotremes in the lumbar vertebrae, pelvis and hindlimb. These peculiar features may have developed as functional convergence to locomotory features of monotremes, or the presence of lumbar ribs in this newly discovered mammal and their absence in its close relatives might be due to evolutionary developmental homoplasy. Analysis including this new taxon suggests that spalacotheroids evolved earlier in Eurasia and then dispersed to North America, in concordance with prevailing geodispersal patterns of several common mammalian groups during the Early Cretaceous period.

Animals↗
PubMed2005

Isofemale lines in Drosophila: an empirical approach to quantitative trait analysis in natural populations.

Founding isofemale lines from wild collected females is a basic tool for investigating the genetic architecture of Drosophila natural populations. The method permits the analysis of quantitative traits under laboratory conditions, with a much broader scope than the mere evidence of a significant genetic heterogeneity among lines. Genetic variability is generally demonstrated by a significant coefficient of intraclass correlation, but several experimental precautions are needed and explained here. The relationship between classical (additive) heritability and intraclass correlation is not straightforward, presumably because the genetic bottlenecks due to the initiation of the lines unravel a significant, nonadditive genetic variance due to dominance and epistatic effects. It is thus suggested to consider intraclass correlation as a specific genetic parameter that enables comparisons between different traits, different populations or different environments. The use of isofemale lines is, however, not restricted to the calculation of an intraclass correlation. It can be used to estimate genetic correlations among traits or environments. The method is also convenient for the analysis of phenotypic plasticity in relation to an environmental gradient. A precise description of the response curves (the reaction norms) is possible, distinguishing trait parameters and plasticity parameters. A fairly general conclusion is that, for a given trait, mean value and plasticity are genetically independent. It is also possible to analyze traits, which, like sexual dimorphism, must be measured on different individuals, and even to demonstrate their genetic variability. In many cases, further empirical and theoretical analyses are possible and needed. It is argued that, in the future, isofemale lines will have an increasing significance among the various techniques appropriate to the analysis of quantitative evolutionary genetics in a diversity of species.

Animals↗
PubMed1996

Antibody reactivity profiles following immunization with diverse peptides of the PERB11 (MIC) family.

PERB11 (MIC) is a gene family possessing multiple copies located within the MHC. Structurally, PERB11 is related to the MHC class I, neonatal IgG Fc receptor (FcRn) and Zn-alpha 2-glycoprotein molecules. The MHC class I family is complex in terms of its genomic arrangement, expression and function, and available evidence suggests that the PERB11 family may be similarly complex. We have adopted an approach to study the expression of such complex gene families by immunizing with multiple peptides and by screening the resulting antibodies against a large range of tissues. The amino acid sequences of PERB11.1 and PERB11.2 as well as those of other related molecules were analysed and compared. Peptides were chosen for immunization based upon (i) loop formation within the equivalent known structure of the MHC class I molecules; (ii) immunogenicity by computer analysis; and (iii) evolutionary relationships. Antibodies in serum from immunized rabbits bound to three out of six peptides used for immunization. ELISA and immunoprecipitation demonstrated binding both to the peptides and to the PERB11.2 recombinant protein. By immunofluorescent staining of various tissues of several species, the three antisera generated overlapping profiles of activity. These included reactions with kidney, small and large intestine, oesophagus, testis, ovary and human neutrophils. This is the first description of antibodies induced by the PERB11 peptides. The extreme complexity of these profiles requires further investigation, but may be explained in terms of antibodies against diverse products of the PERB11 gene family and/or related molecules.

Amino Acid Sequence↗
PubMed1997

Lack of concordance between mtDNA gene flow and population density fluctuations in the bank vole.

The genetic structure of bank voles Clethrionomys glareolus was determined from analyses of mitochondrial DNA (mtDNA) sequences, and compared with previous data on geographical synchrony in population density fluctuations. From 31 sample sites evenly spaced out along a 256-km transect in SE Norway a total of 39 distinct mtDNA haplotypes were found. The geographical distribution of the haplotypes was significantly non-random, and a cladistic analysis of the evolutionary relationship among haplotypes shows that descendant types were typically limited to a single site, whereas the ancestral types were more widely distributed geographically. This geographical distribution pattern of mtDNA haplotypes strongly indicates that the range and amount of female dispersal is severely restricted and insufficient to account for the previously observed synchrony in population density fluctuations. We conclude that geographical synchrony in this species must be caused by factors that are external to the local population, such as e.g. mobile predators.

Animals↗
PubMed1999

Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK.

The relationships among 207 squirrels from 12 locations in the UK and three in mainland Europe were examined using mitochondrial DNA (mtDNA) control region sequence. Twenty-six haplotypes were detected, many of which were population specific. Eighty per cent of the populations analysed contained two or more haplotypes. Hierarchical analysis of molecular variance showed the majority of genetic variation to be partitioned among populations. Genetic diversity varied considerably within the UK, and conformed to no obvious geographical trend. The populations in Argyll and Spadeadam Forest showed the highest levels of variation in the UK. However, the greatest genetic diversity was seen in Bavaria, southern Germany where six unique alleles were detected in a sample of 10 individuals. Phylogenetic analysis revealed no evolutionary divergence between UK and mainland European haplotypes. We conclude that, within the UK, the genetic patterns observed are most likely to be explained by the effects of genetic drift which has occurred since the isolation of populations during the past few hundred years, hence we cannot detect any underlying phylogeographic pattern. Therefore, the use of larger, geographically distinct populations within the UK for augmentation of small isolated populations is unlikely to pose problems of genetic incompatibility. Further, the role that demographic factors may have in complicating the application of current genetically based management unit criteria is likely to need further attention.

Animals↗
PubMed2002

Diversity and evolution of the green fluorescent protein family.

The family of proteins homologous to the green fluorescent protein (GFP) from Aequorea victoria exhibits striking diversity of features, including several different types of autocatalytically synthesized chromophores. Here we report 11 new members of the family, among which there are 3 red-emitters possessing unusual features, and discuss the similarity relationships within the family in structural, spectroscopic, and evolutionary terms. Phylogenetic analysis has shown that GFP-like proteins from representatives of subclass Zoantharia fall into at least four distinct clades, each clade containing proteins of more than one emission color. This topology suggests multiple recent events of color conversion. Combining this result with previous mutagenesis and structural data, we propose that (i) different chromophore structures are alternative products synthesized within a similar autocatalytic environment, and (ii) the phylogenetic pattern and color diversity in reef Anthozoa is a result of a balance between selection for GFP-like proteins of particular colors and mutation pressure driving the color conversions.

Base Sequence↗
PubMed2000

Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab.

During the past decade, the plant disease called scab or Fusarium head blight of wheat and barley has reached epidemic proportions in North America and elsewhere in the world. Scab is an economically devastating plant disease, not only because it causes significant reduction in seed yields and quality, but also because infested seeds are often contaminated with trichothecene and estrogenic mycotoxins that pose a serious threat to animal health and food safety. To test whether the primary etiological agent of scab, the fungus Fusarium graminearum, is panmictic throughout its range, allelic genealogies were constructed from six single-copy nuclear genes from strains selected to represent the global genetic diversity of this pathogen. Excluding one hybrid strain, all six genealogies recovered the same seven biogeographically structured lineages, suggesting that they represent phylogenetically distinct species among which gene flow has been very limited during their evolutionary history. Parsimony analysis of the combined data set comprising 7,120 aligned nucleotide characters resolved most relationships among the seven lineages of the F. graminearum clade and related fusaria included in the study. Phylogenetic evidence is also presented for introgressive hybridization and intragenic recombination among lineages of the F. graminearum clade in nature.

Biological Evolution↗
PubMed1979

Rapid evolution of animal mitochondrial DNA.

Mitochondrial DNA was purified from four species of higher primates (Guinea baboon, rhesus macaque, guenon, and human) and digested with 11 restriction endonucleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with respect to the origin and direction of DNA replication, revealed that the species differ from one another at most of the cleavage sites. The degree of divergence in nucleotide sequence at these sites was calculated from the fraction of cleavage sites shared by each pair of species. By plotting the degree of divergence in mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the curve. The value obtained, 0.02 substitutions per base pair per million years, was compared with the value for single-copy nuclear DNA. The rate of evolution of the mitochondrial genome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10. This high rate may be due, in part, to an elevated rate of mutation in mitochondrial DNA. Because of the high rate of evolution, mitochondrial DNA is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.

Animals↗
PubMed1990

A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism.

Different alleles undergoing strong symmetric balancing selection show a simple genealogical structure (allelic genealogy), similar to the gene genealogy described by the coalescence process for a sample of neutral genes randomly drawn from a panmictic population at equilibrium. The only difference between the two genealogies lies in the different time scales. An approximate scaling factor for allelic genealogy relative to that of neutral gene genealogy is [square root of S/(2M)].[In[S/(16 pi M2)]]-3/2, where M = Nu and S = 2Ns (N, effective population size; u, mutation rate to selected alleles per locus per generation; s, selection coefficient). The larger the value of square root of S/M (greater than or equal to 100), the larger the scaling factor. These findings, supported by simulation results, allow one to apply the theoretical results of the coalescence process directly to the allelic genealogy. Combined with the trans-species evolution of the major histocompatibility complex polymorphism for which balancing selection is believed to be responsible, allelic genealogy predicts that the number of breeding individuals in the human population could not be as small as 50-100 at any time of its evolutionary history. The analysis appears to contradict the founder principle as being important in recent mammalian evolution.

Alleles↗
PubMed1996

Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex.

The pivotal role of G proteins in sensory, hormonal, inflammatory, and proliferative responses has provoked intense interest in understanding how they interact with their receptors and effectors. Nonetheless, the locations of the receptors and effector binding sites remain poorly characterized, although nearly complete structures of the alphabetagamma heterotrimeric complex are available. Here we apply evolutionary trace (ET) analysis [Lichtarge, O., Bourne, H. R. & Cohen, F. E. (1996) J. Mol. Biol. 257, 342-358] to propose plausible locations for these sites. On each subunit, ET identifies evolutionarily selected surfaces composed of residues that do not vary within functional subgroups and that form spatial clusters. Four clusters correctly identify subunit interfaces, and additional clusters on Galpha point to likely receptor or effector binding sites. Our results implicate the conformationally variable region of Galpha in an effector binding role. Furthermore the range of predicted interactions between the receptor and Galphabetagamma, is sufficiently limited that we can build a low resolution and testable model of the receptor-G protein complex.

Amino Acid Sequence↗
PubMed2001

Directed evolution of ampicillin-resistant activity from a functionally unrelated DNA fragment: A laboratory model of molecular evolution.

To establish an experimental system to directly observe molecular evolution, a DNA fragment that confers ampicillin resistance on Escherichia coli was cloned from an archaeal genomic DNA. The activity of this clone was enhanced by 50 rounds of directed evolution by using DNA shuffling. Analysis of the evolved DNA fragments shows that two genetic regions have coevolved: One region, which has no obvious ORF, is essential for the activity, whereas the other, which appears to encode a protein, is not essential but enhances the activity of the former region. Analysis of the evolutionary intermediates shows that negative mutations are effectively removed while beneficial mutations accumulate and illustrates how a protein has evolved over the course of the evolution experiments. Although the mechanism of the activity remains unclear, the evolved DNA fragments also confer resistance to other drugs that inhibit bacterial cell-wall synthesis. The present system would serve as an experimental model to study evolutionary dynamics in the laboratory and provide the concept of screening natural libraries to obtain starting materials for directed evolution.

Ampicillin↗
PubMed2005

Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors.

Germ cell nuclear factor (GCNF) is an orphan nuclear receptor that plays important roles in development and reproduction, by repressing the expression of essential genes such as Oct4, GDF9, and BMP15, through binding to DR0 elements. Surprisingly, whereas recombinant GCNF binds to DR0 sequences as a homodimer, endogenous GCNF does not exist as a homodimer but rather as part of a large complex termed the transiently retinoid-induced factor (TRIF). Here, we use evolutionary trace (ET) analysis to design mutations and peptides that probe the molecular basis for the formation of this unusual complex. We find that GCNF homodimerization and TRIF complex formation are DNA-dependent, and ET suggests that dimerization involves key functional sites on both helix 3 and helix 11, which are located on opposing surfaces of the ligand binding domain. Targeted mutations in either helix of GCNF disrupt the formation of both the homodimer and the endogenous TRIF complex. Moreover, peptide mimetics of both of these ET-determined sites inhibit dimerization and TRIF complex formation. This suggests that a novel helix 3-helix 11 heterotypic interaction mediates GCNF interaction and would facilitate oligomerization. Indeed, it was determined that the endogenous TRIF complex is composed of a GCNF oligomer. These findings shed light on an evolutionarily selected mechanism that reveals the unusual DNA-binding, dimerization, and oligomerization properties of GCNF.

Adaptor Proteins, Vesicular Transport↗
PubMed2004

Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome.

The peridinin-pigmented plastids of dinoflagellates are very poorly understood, in part because of the paucity of molecular data available from these endosymbiotic organelles. To identify additional gene sequences that would carry information about the biology of the peridinin-type dinoflagellate plastid and its evolutionary history, an analysis was undertaken of arbitrarily selected sequences from cDNA libraries constructed from Lingulodinium polyedrum (1012 non-redundant sequences) and Amphidinium carterae (2143). Among the two libraries 118 unique plastid-associated sequences were identified, including 30 (most from A. carterae) that are encoded in the plastid genome of the red alga Porphyra. These sequences probably represent bona fide nuclear genes, and suggest that there has been massive transfer of genes from the plastid to the nuclear genome in dinoflagellates. These data support the hypothesis that the peridinin-type plastid has a minimal genome, and provide data that contradict the hypothesis that there is an unidentified canonical genome in the peridinin-type plastid. Sequences were also identified that were probably transferred directly from the nuclear genome of the red algal endosymbiont, as well as others that are distinctive to the Alveolata. A preliminary report of these data was presented at the Botany 2002 meeting in Madison, WI.

Animals↗
PubMed2005

Plant population dynamics, pollinator foraging, and the selection of self-fertilization.

Many flowering plants rely on pollinators, self-fertilization, or both for reproduction. We model the consequences of these features for plant population dynamics and mating system evolution. Our mating systems-based population dynamics model includes an Allee effect. This often leads to an extinction threshold, defined as a density below which population densities decrease. Reliance on generalist pollinators who primarily visit higher density plant species increases the extinction threshold, whereas autonomous modes of selfing decrease and can eliminate the threshold. Generalist pollinators visiting higher density plant species coupled with autonomous selfing may introduce an effect where populations decreasing in density below the extinction threshold may nonetheless persist through selfing. The extinction threshold and selfing at low density result in populations where individuals adopting a single reproductive strategy exhibit mating systems that depend on population density. The ecological and evolutionary analyses provide a mechanism where prior selfing evolves even though inbreeding depression is greater than one-half. Simultaneous consideration of ecological and evolutionary dynamics confirms unusual features (e.g., evolution into extinction or abrupt increases in population density) implicit in our separate consideration of ecological and evolutionary scenarios. Our analysis has consequences for understanding pollen limitation, reproductive assurance, and the evolution of mating systems.

Animals↗
PubMed1997

The novel human HNF-3/fork head-like 5 gene: chromosomal localization and expression pattern.

Analysis of cDNA clones, isolated from a human fetal brain cDNA library, that hybridized with the rat HNF-3 alpha fork head homolog domain revealed the 3.6-kb HFKL5 cDNA. The transcript of HFKL5 is 4.4 kb long and represents a novel member of the HNF-3/fork head transcription factor family. Comparison of the amino acid sequence of the fork head domain reveals a relatively low level of homology to other members of this family of genes, the closest related sequence being rat HFH7 with 68% homology. The HFKL5 cDNA codes for a putative 500-amino-acid protein. Southern analysis revealed that the HFKL5 gene homolog is present as a single copy in the human genome. Zoo Southern analysis showed strong evolutionary conservation of HFKL5 among mammalian and possibly avian species. Expression of HFKL5 in neurons is restricted to the fully differentiated neurons in fetal and adult brain as well as in the parasympathic ganglia of the small intestine. We also observed expression in lymphocytes, kidney tubule cells, and a subset of hepatocytes. The HFKL5 gene homolog was mapped to chromosome 22q13-qter by cell panel hybridization.

Adult↗
PubMed2005

A framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors.

Solving relevant biological problems requires answering complex questions. Addressing such questions traditionally implied the design of time-consuming experimental procedures which most of the time are not accessible to average-sized laboratories. The current trend is to move towards a multidisciplinary approach integrating both theoretical knowledge and experimental work. This combination creates a powerful tool for shedding light on biological problems. To illustrate this concept, we present here a descriptive example of where computational methods were shown to be a key aspect in detecting crucial players in an important biological problem: the dimerization of chemokine receptors. Using evolutionary based sequence analysis in combination with structural predictions two CCR5 residues were selected as important for dimerization and further validated experimentally. The experimental validation of computational procedures demonstrated here provides a wealth of valuable information not obtainable by any of the individual approaches alone.

Amino Acid Sequence↗
PubMed1994

Unraveling selection in the mitochondrial genome of Drosophila.

We examine mitochondrial DNA variation at the cytochrome b locus within and between three species of Drosophila to determine whether patterns of variation conform to the predictions of neutral molecular evolution. The entire 1137-bp cytochrome b locus was sequenced in 16 lines of Drosophila melanogaster, 18 lines of Drosophila simulans and 13 lines of Drosophila yakuba. Patterns of variation depart from neutrality by several test criteria. Analysis of the evolutionary clock hypothesis shows unequal rates of change along D. simulans lineages. A comparison within and between species of the ratio of amino acid replacement change to synonymous change reveals a relative excess of amino acid replacement polymorphism compared to the neutral prediction, suggestive of slightly deleterious or diversifying selection. There is evidence for excess homozygosity in our world wide sample of D. melanogaster and D. simulans alleles, as well as a reduction in the number of segregating sites in D. simulans, indicative of selective sweeps. Furthermore, a test of neutrality for codon usage shows the direction of mutations at third positions differs among different topological regions of the gene tree. The analyses indicate that molecular variation and evolution of mtDNA are governed by many of the same selective forces that have been shown to govern nuclear genome evolution and suggest caution be taken in the use of mtDNA as a "neutral" molecular marker.

Animals↗