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PubMed1999

Factors influencing the extent of inbreeding depression: an example from scots pine

Detailed studies suggest that the level of inbreeding depression may vary between populations. In a study of Scots pine from Finland, the level of inbreeding depression was much lower in northern than in southern populations. We have examined theoretically whether population genetic factors, such as the level of selfing, intensity of selection against heterozygotes or homozygotes, level of mutation, a bottleneck, finite population size, or the level of polyembryony could account for this difference. Higher selfing or stronger selection against heterozygotes in the north, both at biologically reasonable levels, appear to produce changes consistent with the observed differences and we consider these to be the most likely explanations. In addition, the differences could have accumulated by these mechanisms over the age of the northern population, approximately 100 generations. Finally, the differences generated by these factors could still be maintained in the face of reasonable levels of gene flow from the south. Such a comprehensive theoretical investigation of this example has given some general insight into the potential influence of these evolutionary factors on the level of inbreeding depression and provides an approach that could be used to understand similar phenomena in other examples.

Journal Article↗
PubMed1999

Mitochondrial restriction fragment length polymorphism (RFLP) and sequence variation among closely related avian species and the genetic characterization of hybrid Dendroica warblers.

To address several interconnected goals, we used mitochondrial DNA (mtDNA) sequences to explore evolutionary relationships among four potentially hybridizing taxa in a North American avian superspecies (Dendroica occidentalis, D. townsendi, D. virens, and D. nigrescens). We first compared the results of a previous restriction fragment length polymorphism (RFLP)-based study with 1453 nucleotides from the mitochondrial cytochrome oxidase subunit I (COI), ATP-synthase 6 (ATPase 6), and ATP-synthase 8 (ATPase 8) genes. Separate phylogenetic analyses of the RFLP and sequence data provided identical and well-supported hierarchical species-level reconstructions that grouped occidentalis and townsendi as sister taxa. We then explored several general features of mitochondrial evolution via a comparison of the RFLP and sequence data sets. Qualitative rate differences that seemed evident in highly autocorrelated comparisons of RFLP vs. sequence pairwise distances were not supported when autocorrelation was removed. We also noted a high variance in corresponding RFLP and sequence distances after the removal of autocorrelation effects. This variance suggests that caution should be used when combining RFLP and sequence-based data in studies that require the large-scale synthesis of divergence estimates drawn from sources employing different molecular techniques. Finally, we used our parallel RFLP and sequence data to design and validate a rapid and inexpensive polymerase chain reaction-RFLP (PCR-RFLP) protocol for determining species-specific mitochondrial haplotypes. This PCR-RFLP technique will be applied in ongoing studies of the occidentalis/townsendi hybrid zone, where the historic and geographical complexity of the interbreeding populations necessitates the genotyping of thousands of individual warblers.

Adenosine Triphosphatases↗
PubMed2000

Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.).

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salar L.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within-river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member-vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life-history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.

Animals↗
PubMed2003

Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis.

The founding of new populations by small numbers of colonists has been considered a potentially important mechanism promoting evolutionary change in island populations. Colonizing species, such as members of the avian species complex Zosterops lateralis, have been used to support this idea. A large amount of background information on recent colonization history is available for one Zosterops subspecies, Z. lateralis lateralis, providing the opportunity to reconstruct the population dynamics of its colonization sequence. We used a Bayesian approach to combine historical and demographic information available on Z. l. lateralis with genotypic data from six microsatellite loci, and a rejection algorithm to make simultaneous inferences on the demographic parameters describing the recent colonization history of this subspecies in four southwest Pacific islands. Demographic models assuming mutation-drift equilibrium or a large number of founders were better supported than models assuming founder events for three of four recently colonized island populations. Posterior distributions of demographic parameters supported (i) a large stable effective population size of several thousands individuals with point estimates around 4000-5000; (ii) a founder event of very low intensity with a large effective number of founders around 150-200 individuals for each island in three of four islands, suggesting the colonization of those islands by one flock of large size or several flocks of average size; and (iii) a founder event of higher intensity on Norfolk Island with an effective number of founders around 20 individuals, suggesting colonization by a single flock of moderate size. Our inferences on demographic parameters, especially those on the number of founders, were relatively insensitive to the precise choice of prior distributions for microsatellite mutation processes and demographic parameters, suggesting that our analysis provides a robust description of the recent colonization history of the subspecies.

Bayes Theorem↗
PubMedDate not supplied

[Philadelphia translocation and the human c-abl oncogene--relations in the light of molecular genetics].

Application of recombinant DNA techniques led to the characterization of a heterogenous group of evolutionary conserved genes with potential transforming activity, called oncogenes. Regularly they seem to be involved in normal cell proliferation and differentiation. Various mechanisms including an increased dosage of gene product as well as subtile point mutations activate these sequences to oncogenes sensu strictu. Molecular analysis of the Philadelphia translocation in leukemic cells of CML-patients revealed a consistent translocation of the human c-abl-oncogene from chromosome 9 to the Ph1-chromosome, regardless of the cytogenetic subtype. Moreover we could demonstrate individual breakpoints for every patient investigated so far. However, these breakpoints are clustered on chromosome 22 within sequences of the bcr-gene. In leukemic cells containing the rearranged-c-abl/bcr sequences a new transcript is detected which is possibly the mRNA for an altered c-abl-protein that unmasks associated tyrosine specific kinase activity. These gene rearrangements were not detected in Ph1-negative CML-patients. Another human oncogene, c-sis, is located on chromosome 22, but seems not to play a crucial role in the generation of CML. These results are discussed in the context of recent advances in oncogene-research.

Child↗
PubMed2003

Understanding missense mutations in the BRCA1 gene: an evolutionary approach.

The role of missense changes in BRCA1 in breast cancer susceptibility has been difficult to establish. We used comparative evolutionary methods to identify potential functionally important amino acid sites in exon 11 and missense changes likely to disrupt gene function, aligning sequences from 57 eutherian mammals and categorizing amino acid sites by degree of conservation. We used Bayesian phylogenetic analyses to determine relationships among orthologs and identify codons evolving under positive selection. Most conserved residues occur in a region with the highest concentration of protein-interacting domains. Rapidly evolving residues are concentrated in the RAD51-interacting domain, suggesting that selection is acting most strongly on the role of BRCA1 in DNA repair. Investigation of the functional role of missense changes in breast-cancer susceptibility should focus on 38 missense changes in conserved and 3 in rapidly evolving regions of exon 11.

Algorithms↗
PubMed2002

Evolution of supercolonies: the Argentine ants of southern Europe.

Some ants have an extraordinary social organization, called unicoloniality, whereby individuals mix freely among physically separated nests. This type of social organization is not only a key attribute responsible for the ecological domination of these ants, but also an evolutionary paradox and a potential problem for kin selection theory because relatedness between nest mates is effectively zero. The introduction of the Argentine ant in Europe was apparently accompanied by a dramatic loss of inter-nest aggression and the formation of two immense supercolonies (which effectively are two unicolonial populations). Introduced populations experienced only limited loss of genetic diversity at neutral markers, indicating that the breakdown of recognition ability is unlikely to be merely due to a genetic bottleneck. Rather, we suggest that a "genetic cleansing" of recognition cues occurred after introduction. Indeed workers of the same supercolony are never aggressive to each other despite the large geographical distance and considerable genetic differentiation between sampling sites. By contrast, aggression is invariably extremely high between the two supercolonies, indicating that they have become fixed for different recognition alleles. The main supercolony, which ranges over 6,000 km from Italy to the Spanish Atlantic coast, effectively forms the largest cooperative unit ever recorded.

Aggression↗
PubMed1985

Prediction of homology and divergence in the secondary structure of polypeptides.

A quantitative procedure is described for the comparison of secondary structure of homologous proteins. Standard predictive methods are used to generate probability profiles from pairs of homologous amino acid sequences; correlation coefficients (R) are then computed between each pair of amino acids for alpha-helix (R alpha), extended structure (R beta), turn (R(t)), and coil (R(c)). R values are >0.2 for correctly aligned homologous sequences. Unrelated or incorrectly aligned sequences give R values near zero. Lack of correlation for a segment of otherwise well-correlated sequences is used to identify structural divergence, which is then evaluated graphically by using difference profiles. A combination of these techniques correctly predicts secondary structural differences between melittin or beta-endorphin and their respective synthetic analogs. The method is potentially useful to describe evolutionary changes in protein secondary structure as well as in the design of peptide analogs.

Amino Acid Sequence↗
PubMed2006

Pereskia and the origin of the cactus life-form.

The cactus life-form is cited as an example of a tight relationship between organism form and function: a succulent, long-lived, photosynthetic stem allows cacti to survive long periods of drought while maintaining a positive tissue water status. Pereskia (Cactaceae) comprises 17 species of leafy shrubs and trees that are thought to represent the original cactus condition. Recent phylogenetic work has shown that there are two separate clades of Pereskia species, which are basal and paraphyletic with respect to the rest of the cacti. We selected seven Pereskia species, representing both clades, and characterized their water relations by measuring a suite of physiological traits in wild populations. Additionally, we estimated basic climate parameters from collection localities for all 17 Pereskia species. Extant Pereskia species exhibit ecological water use patterns that are very similar to those of the leafless, stem-succulent cacti. Ancestral trait reconstruction for the physiological and environmental data provides a preliminary assessment of the ecology and water relations of the earliest cacti and suggests that several key elements of the cactus ecological niche were established before the evolution of the cactus life-form. We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti.

Biological Evolution↗
PubMed1996

Characterization of the human ABC superfamily: isolation and mapping of 21 new genes using the expressed sequence tags database.

As an approach to characterizing all human ATP-binding cassette (ABC) superfamily genes, a search of the human expressed sequence tag (EST) database was performed using sequences from known ABC genes. A total of 105 clones, containing sequences of potential ABC genes, were identified, representing 21 distinct genes. This brings the total number of characterized human ABC genes from 12 to 33. The new ABC genes were mapped by PCR on somatic cell and radiation hybrid panels and yeast artificial chromosomes (YACs). The genes are located on human chromosomes 1, 2, 3, 4, 6, 7, 10, 12, 13, 14, 16, 17 and X; at locations distinct from previously mapped members of the superfamily. The characterized genes display extensive diversity in sequence and expression pattern and this information was utilized to determine potential structural, functional and evolutionary relationships to previously characterized members of the ABC superfamily.

ATP-Binding Cassette Transporters↗
PubMed2025

A Million Years of Mammoth Mitogenome Evolution.

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Animals↗
PubMed1991

Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element.

To understand the role of U2 RNA structure in pre-mRNA splicing we have characterized several cold-sensitive mutations in an essential stem-loop of yeast U2. Although mutant U2 is stable in vivo after a shift to restrictive temperature, splicing is rapidly inhibited, suggesting a direct effect on U2 function rather than U2 synthesis or snRNP assembly. Splicing complexes form at 23 degrees C in both mutant and wild-type extracts; however, stable association of mutant U2 snRNPs with pre-mRNA in vitro is inefficient at 15 degrees C, a temperature permissive for spliceosome assembly in wild-type extracts, indicating that the cold-sensitive defect is in U2 snRNP association with the assembling spliceosome. In vivo RNA structure probing reveals that the bulk of U2 RNA is misfolded in the mutants, even at permissive temperature. We propose that U2 stem-loop IIa is recognized by an assembly factor that assists U2 snRNP binding to pre-mRNA and that the cold sensitivity is due to a critical deficiency of correctly folded U2 for spliceosome assembly at low temperatures. Evolutionary conservation of the potential to form an interfering alternative RNA structure suggests the possibility that splicing could be regulated negatively at an early step by control of U2 snRNA conformation.

Base Sequence↗
PubMed2004

Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human.

Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been known as a typical example of convergent evolution. To study the molecular basis of convergent evolution of camera eyes, we conducted a comparative analysis of gene expression in octopus and human camera eyes. We sequenced 16,432 ESTs of the octopus eye, leading to 1052 nonredundant genes that have matches in the protein database. Comparing these 1052 genes with 13,303 already-known ESTs of the human eye, 729 (69.3%) genes were commonly expressed between the human and octopus eyes. On the contrary, when we compared octopus eye ESTs with human connective tissue ESTs, the expression similarity was quite low. To trace the evolutionary changes that are potentially responsible for camera eye formation, we also compared octopus-eye ESTs with the completed genome sequences of other organisms. We found that 1019 out of the 1052 genes had already existed at the common ancestor of bilateria, and 875 genes were conserved between humans and octopuses. It suggests that a larger number of conserved genes and their similar gene expression may be responsible for the convergent evolution of the camera eye.

Animals↗
PubMed1992

A maize protein associated with the G-box binding complex has homology to brain regulatory proteins.

The G-box element is a moderately conserved component of the promoter of many inducible genes, including the alcohol dehydrogenase genes of Arabidopsis and maize. We used monoclonal antibodies generated against partially purified G-box binding factor (GBF) activity to characterize maize proteins that are part of the DNA binding complex. Antibodies interacted with partially purified maize GBF complexes to produce a slower migrating complex in the gel retardation assay. Immunoprecipitation experiments suggested that the protein recognized by the antibody is not a DNA binding protein in and of itself, but rather is associated with the DNA binding complex. These monoclonal antibodies were used to isolate cDNA clones encoding a protein that we have designated GF14. Maize GF14 contains a region resembling a leucine zipper and acidic carboxy and amino termini, of which the latter can form an amphipathic alpha-helix similar to known transcriptional activators such as VP16 and GAL4. Protein gel blot analysis of cell culture extract showed that a single, major protein of approximately 30 kD is recognized by anti-GF14; the protein is also present predominantly in the kernel and root. The deduced amino acid sequence of maize GF14 is more than 80% identical to Arabidopsis GF14 and Oenothera PHP-O, and is more than 60% identical to a class of mammalian brain proteins described as both protein kinase C inhibitors and activators of tyrosine and tryptophan hydroxylases. GF14 is found in a variety of monocotyledons and dicotyledons, gymnosperms, and yeast. This suggests a deep evolutionary conservation of a potential regulatory protein associated with a core sequence found in the promoter region of many genes.

14-3-3 Proteins↗
PubMed2001

An unusual sex-determination system in South American field mice (Genus Akodon): the role of mutation, selection, and meiotic drive in maintaining XY females.

The mechanism of sex determination in mammals appears highly conserved: the presence of a Y chromosome triggers the male developmental pathway, whereas the absence of a Y chromosome results in a default female phenotype. However, if the Y chromosome fails to initiate the male pathway (referred to as Y*), XY* females can result, as is the case in several species of South American field mice (genus Akodon). The breeding genetics in this system inherently select against the Y* chromosome such that the frequency of XY* females should decrease rapidly to very low frequencies. However, in natural populations of Akodon, XY* females persist at substantial frequencies; for example, 10% of females are XY* in A. azarae and 30% in A. boliviensis. We develop a mathematical model that considers the potential roles of three evolutionary forces in maintaining XY* females: Y-to-Y* chromosome transitions (mutation), chromosome segregation distortion (meiotic drive), and differential fecundity (selection). We then test the predictions of our model using data from breeding colonies of A. azarae. We conclude that any single force is inadequate to maintain XY* females. However, a combination of segregation bias of the male and female Y chromosomes during spermatogenesis/oogenesis and increased fecundity in XY* females could account for the observed frequencies of XY* females.

Animals↗
PubMed2004

Rates of evolution of hybrid inviability in birds and mammals.

Almost 30 years ago, A. C. Wilson and colleagues presented results indicating that hybrid inviability between species evolves 10 times faster in mammals than in birds and frogs. Here I revisit this question for birds and mammals using modern molecular data (mitochondrial cytochrome b DNA) and a more phylogenetically appropriate statistical approach. My analyses confirm that diverging mammals lose the ability to form viable hybrids faster than birds. To explain the difference in rates of evolutionary loss of hybridization potential, Wilson and coworkers proposed that mammals have higher rates of regulatory evolution, causing higher probabilities of developmental incompatibilities between mammal species. I briefly discuss this and other potential explanations.

Animals↗
PubMed2004

Phenotypic consequences of genetic variation in a gynogenetic complex of Phoxinus eos-neogaeus clonal fish (Pisces: Cyprinidae) inhabiting a heterogeneous environment.

We examined the genetic composition, habitat use, and morphological variation of a Phoxinus eos-neogaeus unisexual hybrid complex and its sexually reproducing progenitor species inhabiting beaver-modified drainages of Voyageurs National Park, Minnesota. In addition to the single diploid P. eos-neogaeus gynogenetic clone, triploid and diploid-triploid mosaic biotypes were present at our study sites. Both P. eos and P. neogaeus, and all three hybrid biotypes were ubiquitous throughout one intensively surveyed drainage, but abundances and relative frequencies of the parental species and hybrids varied considerably within and among successional environments. Data from a large number of additional sites indicated that the proportion of polyploid hybrids within an environment was negatively related to hybrid relative frequency, implying that the genomic constitution of hybrids is an important determinant of clonal fitness among successional environments. Statistical comparisons of variation along size-free multivariate body shape axes indicated that despite its genetic uniformity, the P. eos-neogaeus clone is no less variable than its sexual progenitors, suggesting that a single genotype may actually respond to environmental variation with as much phenotypic variation as a genetically variable sexual population. The incorporation and expression of a third genome in triploid and diploid-triploid mosaic biotypes derived from the gynogenetic clone significantly expanded phenotypic variation of the clone. This additional variation results in greater similarities in habitat use and morphological overlap with the parental species, primarily P. eos, the predominant sperm donor for gynogenetic hybrid females in this complex. Polyploid augmentation of a diploid gynogenetic clone appears to be typical in the P. eos-neogaeus complex, and the additional genetic and phenotypic variation that it generates has potentially significant ecological and evolutionary consequences for the success and persistence of a single genotype in highly variable environments.

Animals↗
PubMed2005

Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica.

The study of hybrid zones resulting from Pleistocene vicariance is central in examining the potential of genetically diverged evolutionary units either to introgress and merge or to proceed with further isolation. The hybrid zone between two mitochondrial lineages of Chioglossa lusitanica is located near the Mondego River in Central Portugal. We used mitochondrial and nuclear diagnostic markers to conduct a formal statistical analysis of the Chioglossa hybrid zone in the context of tension zone theory. Key results are: (i) cline centres are not coincident for all markers, with average widths of ca. 2-15 km; (ii) heterozygote deficit was not observed across loci near the transect centre; (iii) associations of parental allele combinations ('linkage disequilibrium'R) were not detected either across loci or across the transect. These observations suggest that the Chioglossa hybrid zone is not a tension zone with strong selection against hybrids but instead one shaped mostly by neutral mixing. The patterns uncovered suggest a complex history of populations over a small scale that may be common in southern Pleistocene refugia.

Animals↗