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PubMed2004

Phylogenetic utility of the ribosomal internal transcribed spacer 2 in Strumigenys spp. (Hymenoptera: Formicidae).

Sequence variations and phylogenetic relationships of Strumigenys from different localities in Taiwan were inferred from sequences of the internal transcribed spacer 2 (ITS2) of nuclear ribosomal RNA genes. The ITS2 sequences of different species of Strumigenys vary in length from 659 to 953 bp, because there are many large repeated insertion-deletion fragments, and these short tandem repeat units form microsatellites. The average GC content of the ITS2 is 60.8%. Secondary structures from ITS2 sequences are similar and present several conserved structural motifs. Eleven species and three unnamed species were analyzed using both the maximum parsimony and maximum likelihood methods. Although diversity of the ITS2 sequence is high, these data can still be a potential tool for primary analysis of molecular phylogeny and biogeography of Strumigenys at the species level on islands around Taiwan.

Amino Acid Motifs↗

PubMed2001

Haplotype variation in a mitochondrial tandem repeat of Norway spruce (Picea abies) populations suggests a serious founder effect during postglacial re-colonization of the western Alps.

Populations from 13 elevational transects of Norway spruce [Picea abies (L.) Karst] across the Alpine range were sampled to elucidate the geographical pattern of genetic variation in relation to postglacial re-colonization and to study elevational effects on haplotypic diversity. We assessed fragment length variation in a tandem repeat region of the mitochondrial (mt) nad1 intron 2. This maternally inherited genetic marker is suited to infer migration as it is dispersed by seed only. A total of 10 haplotypes was found, most of which were due to repeat copy number variation. An analysis of molecular variance (amova) showed that overall population differentiation was high (F(ST)=0.41), and it revealed a significant differentiation between monomorphic western and moderately to highly variable eastern Alpine populations. This phylogeographic pattern may be explained by a founder effect during postglacial re-colonization. An early arriving haplotype, assumed to originate from a western Carpathian refugium, could expand into suitable habitats, reducing the chances for establishment of subsequently arriving haplotypes. On the other hand, the high variation in populations within an Italian transect of the south-eastern Alps may be the consequence of merging migration pathways from and close distance to putative glacial refugia, most likely those assumed in the Carpathian mountains and on the Balkan peninsula or possibly in the central plains of Italy. An effect of elevation on haplotypic diversity was not evident, though a low, but significant, partition of total genetic variation was attributed to among-population variation in one Italian transect. Various factors, such as vertical seed dispersal and forest management, may account for blurring an otherwise established pattern of genetic variation on a small geographical scale.

Analysis of Variance↗

PubMed2005

Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion.

Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.

Africa South of the Sahara↗

PubMed1999

Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana.

Molecular variation in genes that regulate development provides insights into the evolutionary processes that shape the diversification of morphogenetic pathways. Intraspecific sequence variation at the APETALA3 and PISTILLATA floral homeotic genes of Arabidopsis thaliana was analyzed to infer the extent and nature of diversity at these regulatory loci. Comparison of AP3 and PI diversity with three previously studied genes revealed several features in the patterning of nucleotide polymorphisms common between Arabidopsis nuclear loci, including an excess of low-frequency nucleotide polymorphisms and significantly elevated levels of intraspecific replacement variation. This pattern suggests that A. thaliana has undergone recent, rapid population expansion and now exists in small, inbred subpopulations. The elevated intraspecific replacement levels may thus represent slightly deleterious polymorphisms that differentiate distinct ecotypes. The distribution of replacement and synonymous changes in AP3 and PI core and noncore functional domains also indicates differences in the patterns of molecular evolution between these interacting floral regulatory genes.

Alleles↗

PubMed1997

Junk ain't what junk does: neutral alleles in a selected context.

A simulation study of the effects of linked selection on a neutral locus is described. Of six models of selection examined, four could be called variation-reducing as they lower the level of molecular variation at the neutral locus. Unfortunately, all four distort the neutral frequency spectrum in similar ways, making the problem of inferring the appropriate model quite difficult. Similarly, an examination of the effects of linked selection on the non-random association of mutations at two linked neutral loci did not suggest that this property would be useful for inferring the nature of linked selection either. Linked selection may have a profound effect on the 'effective population size' of the neutral locus. For two of the variation-reducing models, the effective size at the neutral locus is almost independent of the actual population size.

Alleles↗

PubMed2000

Molecular evidence for repetitive parallel evolution of shell structure in Clausiliidae (Gastropoda, pulmonata).

The division of clausiliid genera, using the type of clausilial apparatus (CA) as the decisive criterion, is ambiguous. Two types of CA can be distinguished: the normal (N) type and the Graciliaria (G) type. Morphological resemblance between species with different types of CA led to the hypothesis that the CA type is homoplasious. Therefore sequence variation, phylogenetic relationships, and the evolution of the CA were studied in the genera Albinaria, Isabellaria, and Sericata. Phylogenetic relations were inferred from parsimony and neighbor-joining analyses of the nucleotide sequences of both internal transcribed spacers (ITS1 and ITS2) of the rDNA of 36 species. The variation among the sequences was great: 21.8% of the sequences were ambiguously aligned and excluded from the analysis. A high GC content in the unambiguously aligned portions and a substitutional bias toward a higher GC content are indicators of substitutional constraints in the spacers. We analyzed the data in several ways: using both spacers together and separately, weighting all mutations equally, correcting for transition/transversion bias by weighting, and using transversions only. In all resulting trees, Isabellaria is not a monophyletic group. Its division into two clades is supported by over 40 mutations and one large indel. Clade 1 consists of Isabellaria and Sericata and clade 2 consists of Isabellaria and Albinaria species. The present distribution of the CA type was plotted on the tree and its most parsimonious evolution was reconstructed. The CA type was shown to be highly homoplasious. In clade 1 and clade 2 both types of CA were found; depending on the ancestral state, either the G or the N type evolved several times in parallel. These results contribute decisively to the current debate on the morphological diagnoses of Albinaria, Sericata, and Isabellaria as monophyletic taxa.

Animals↗

PubMed2003

Differential expression in SAGE: accounting for normal between-library variation.

MOTIVATION: In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger 'pseudolibraries'. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation. RESULTS: We introduce a beta-binomial sampling model that correctly incorporates both sources of variation. We show how to fit the parameters of this model, and introduce a test statistic for differential expression similar to a two-sample t-test.

Algorithms↗

PubMed2003

Cortical index and size of hand bones: segregation analysis and linkage with the 11q12-13 segment.

BACKGROUND: Bone geometry (BG) and size (BS) are important factors in determining bone fragility. Previous studies have suggested that more than half of BG and BS variation is genetically determined. The possible chromosomal locations of genes involved in BS and BG determination have not been explored. We evaluated the extent and mode of inheritance of the radiographic hand BS index (BSI) and the metacarpal cortical index (MCI), and tested the hypothesis of linkage between these traits and the 11q 12-13 chromosomal region. MATERIAL/METHODS: Hand radiographs and blood samples were collected from 1190 individuals belonging to 349 Chuvasha nuclear families (Russian Federation). Segregation analysis was conducted on a total sample. Transmission disequilibrium testing (TDT) and model-based linkage analyses (MBLA) were performed on a sub-sample of 163 families. RESULTS: The hypothesis of a major gene effect was confirmed for both studied traits. The best-fitting models were Mendelian, with an additive type of inheritance. The inferred major gene explained 50% of the CI and 40% of the BSI variation. The TDT and MBLA results did not permit confirmation of hypotheses about linkage between hand BSI and the 11q 12-13 chromosomal region, but a possible linkage between CI and that region cannot be ruled out. CONCLUSIONS: We support the hypothesis of a major gene effect in the heritability of BSI and MCI. We provide suggestive evidence for possible linkage disequilibrium between MCI and the 11q12-13 chromosomal segment (marker D11S1983), but not for a linkage between BSI and this

Adolescent↗

PubMed1995

Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific.

Length changes in human mitochondrial DNA (mtDNA) are potentially useful markers for inferring the evolutionary history of populations. One such length change is a nine base pair (9-bp) deletion that is located in the intergenic region between the COII gene and the Lysine tRNA gene (COII/tRNALys intergenic region). This deletion has been used as a genetic marker to trace descent from peoples of East Asian origin. A geographic cline of the deletion frequency across modern Pacific Islander populations suggests that the deletion may be useful for tracing prehistoric Polynesian origins and affinities. Mitochondrial DNA sequence variation within two variable segments of the control region (CR) permits a number of inferences regarding the evolutionary history of the 9-bp deletion that cannot be determined from frequency data alone. We obtained CR sequences from 74 mtDNAs with the 9-bp deletion from Indonesia, coastal Papua New Guinea (PNG), and American Samoa. Phylogenetic and pairwise distribution analysis of these CR sequences pooled with previously published CR sequences reveals that the deletion arose independently in Africa and Asia and suggests possible multiple origins of the deletion in Asia. A clinal increase of the frequency of the 9-bp deletion across the three Pacific populations is associated with a decrease in CR sequence diversity, consistent with founder events. Furthermore, analysis of pairwise difference distributions indicates an expansion time of proto-Polynesians that began 5,500 yr ago from Southeast Asia. These results are consistent with the express train model of Polynesian origins.

Base Sequence↗

PubMed1995

Evolutionary relationships and sequence variation of alpha-amylase variants encoded by duplicated genes in the Amy locus of Drosophila melanogaster.

To infer the genealogical relationships of alpha-amylase electromorphs of Drosophila melanogaster, we determined the nucleotide sequences of a collection of electromorphs sampled throughout the world. On average there were 1.0 amino acid substitutions between identical electromorphs and 3.9 between different electromorphs, respectively. We found that the evolution of AMY1 through AMY6 electromorphs occurred by sequential accumulation of single amino acid substitutions each causing one charge difference. The nucleotide diversities at synonymous sites within Amy1,Amy2,Amy3,Amy4 and Amy6 were 0.0321, 0.0000, 0.0355, 0.0059 and 0.0030, respectively. We also obtained evidence of genetic exchanges, such as intrachromosomal recombination, interchromosomal recombination or gene conversion, between the two duplicated Amy genes as well as among the alleles.

Amino Acid Sequence↗

PubMed1997

Natural variability in the number of dendritic segments: model-based inferences about branching during neurite outgrowth.

A study was made of the possible basis for naturally occurring variations in the number of segments in individual dendritic trees. Distributions of the number of terminal segments have been studied in dendrites from rat, cat, and frog motoneurons, basal dendrites from rat visual cortex pyramidal and non-pyramidal neurons, in rat cerebellar Purkinje cell dendritic trees, and in human hippocampal dentate granule cells. By means of a mathematical model for dendritic branching, it was shown that the variation in the number of dendritic segments can be accounted for by assuming that new branches during neurite outgrowth are formed randomly at terminal segments. The observed terminal segment number distributions could be closely approximated by additionally assuming that branching probabilities decline with increasing number of terminal segments in growing dendrites. The pyramidal neuron group differed significantly from the other neuron groups in such a way as to suggest that this decline is stronger than in the dendrites of other types of neurons. By using literature data on the mean number of terminal segments in rat cerebellar Purkinje cells, measured at different times during early development, an estimate could be obtained of the time-course of the branching probabilities. The branching probability of a terminal segment was found to be in the order of 0.002 per hour in the first 4 weeks postnatal with a 5-fold transient increase in the second week.

Animals↗

PubMed2000

Variational learning for switching state-space models.

We introduce a new statistical model for time series that iteratively segments data into regimes with approximately linear dynamics and learnsthe parameters of each of these linear regimes. This model combines and generalizes two of the most widely used stochastic time-series models -- hidden Markov models and linear dynamical systems -- and is closely related to models that are widely used in the control and econometrics literatures. It can also be derived by extending the mixture of experts neural network (Jacobs, Jordan, Nowlan, & Hinton, 1991) to its fully dynamical version, in which both expert and gating networks are recurrent. Inferring the posterior probabilities of the hidden states of this model is computationally intractable, and therefore the exact expectation maximization (EM) algorithm cannot be applied. However, we present a variational approximation that maximizes a lower bound on the log-likelihood and makes use of both the forward and backward recursions for hidden Markov models and the Kalman filter recursions for linear dynamical systems. We tested the algorithm on artificial data sets and a natural data set of respiration force from a patient with sleep apnea. The results suggest that variational approximations are a viable method for inference and learning in switching state-space models.

Algorithms↗

PubMed1983

Principal glycopeptide of the tetrodotoxin/saxitoxin binding protein from Electrophorus electricus: isolation and partial chemical and physical characterization.

Preparations of the tetrodotoxin (TTX) and saxitoxin binding protein isolated from the electroplax of Electrophorus electricus are of high specific activity (greater than or equal to 2000 pmol of TTX binding sites/mg of protein) and appear to be homogeneous in that they contain only the large polypeptide previously identified to make up part of the voltage-sensitive sodium channel [Agnew, W. S., Moore, A. C., Levinson, S. R., & Raftery, M. S. (1980) Biochem. Biophys. Res. Commun. 92, 860-866]. This permits the inference that the TTX binding site, thought to be associated with the mouth of the ion channel, is located on this peptide. This peptide presumably corresponds to the large peptide, designated the alpha-peptide subunit, of the synaptosomal sodium channel [Hartshorne, R. P., & Catterall, W. A. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 4620-4624]. No convincing evidence for lower molecular weight peptides has yet been found for the electroplax protein. A rapid and convenient method is described for preparation of milligram quantities of the pure, sodium dodecyl sulfate (NaDodSO4) denatured form of the peptide, and its amino acid and carbohydrate compositions are reported. The peptide behaved anomalously on NaDodSO4-polyacrylamide gels. It was demonstrated that the molecular weight cannot be accurately quantified by this method but that the true value likely exceeds the value of 260 000 reported previously. The denatured peptide displayed an electrophoretic microheterogeneity which may be ascribed to variations in bulky carbohydrate substituents and an extremely high free mobility which is inferred to result from binding of unusually large amounts of NaDodSO4.

Amino Acids↗

PubMed2004

Olfactory fossa of Tremacebus harringtoni (platyrrhini, early Miocene, Sacanana, Argentina): implications for activity pattern.

CT imaging was undertaken on the skull of approximately 20-Myr-old Miocene Tremacebus harringtoni. Here we report our observations on the relative size of the olfactory fossa and its implications for the behavior of Tremacebus. The endocranial surface of Tremacebus is incomplete, making precise estimate of brain size and olfactory fossa size imprecise. However, olfactory fossa breadth and maximum endocranial breadth measured from CT images of one catarrhine species and eight platyrrhine species for which volumes of the olfactory bulb and brain are known show that the osteological proxies give a reasonably accurate indication of relative olfactory bulb size. Nocturnal Aotus has the largest relative olfactory fossa breadth and the largest olfactory bulb volume compared to brain volume among extant anthropoids. Tremacebus had a much smaller olfactory fossa breadth and, by inference, bulb volume--within the range of our sample of diurnal anthropoids. Variations in the relative size of the olfactory bulbs in platyrrhines appear to relate to the importance of olfaction in daily behaviors. Aotus has the largest olfactory bulbs among platyrrhines and relies more on olfactory cues when foraging than Cebus, Callicebus, or Saguinus. As in other examples of nocturnal versus diurnal primates, nocturnality may have been the environmental factor that selected for this difference in Aotus, although communication and other behaviors are also likely to select for olfactory variation in diurnal anthropoids. Considering the olfactory fossa size of Tremacebus, olfactory ability of this Miocene monkey was probably not as sensitive as in Aotus and counts against the hypothesis that Tremacebus was nocturnal. This finding accords well with previous observations that the orbits of Tremacebus are not as large as nocturnal Aotus.

Adaptation, Physiological↗

PubMedDate not supplied

Determination of the highest no-effect dose (HNED) and of the elimination pattern for cocaine in horses.

Cocaine is one of the most widespread illegal stimulants utilized by the human population throughout the world. The aim of this study was to establish the highest no-effect dose (HNED) of cocaine on the spontaneous locomotor activity (SLA) of horses in a behavior chamber, and thereby to determine the maximal acceptable threshold of the urinary drug concentration in horses. Twelve English thoroughbred mares received 0.02, 0.03, 0.04, 0.08 or 0.12 mg kg(-1) cocaine i.v. or saline solution (control). It was noted that doses above 0.04 mg kg(-1) induced a significant increase in SLA (P < 0.05, Tukey's test). No significant increase in SLA was seen in the mares that received 0.03 mg kg(-1), but the animals showed important behavioral changes that did not occur after the 0.02 mg kg(-1) dose. It was concluded that the HNED of cocaine for horses in a behavior chamber is 0.02 mg kg(-1). After injection of this dose in five horses, urine samples were collected at predetermined intervals through vesical catheterization. The concentrations of cocaine, norcocaine, benzoylecgonine and ecgonine methyl ester were quantified by liquid chromatography/electrospray ionization tandem mass spectrometry. Cocaine and norcocaine concentrations remained consistently below the level of detection. Benzoylecgonine reached a mean (+/- SEM) maximum concentration of 531.9 +/- 168.7 ng ml(-1) after 4 h, whereas ecgonine methyl ester peaked 2 h after injection at a concentration of 97.2 +/- 26.5 ng ml(-1). The maximum admissible concentration for cocaine and/or metabolites in the urine of horses is difficult to establish unequivocally because of the substantial individual variation in the drug elimination pattern observed in horses, which can be inferred by the large standard error of the means obtained.

Animals↗

PubMed2002

The measurement of puberty: a review.

This paper has two main objectives. Firstly, to review the feasibility and validity of the various methods that have been used to measure puberty. With an appreciation of these measurement issues, the second objective is to summarize the evidence-base as to whether the age at menarche and the age at onset of puberty has decreased in recent years. In consideration of these methodologies, all of which report different levels of reliability and validity, it is only possible at present to draw inferences about possible changes in pubertal age and onset. Moreover, the wide variations in sample size, selection of participants (usually non-random), and study design reported in the reviewed studies have compounded this situation further. The paper closes by providing a summary of the findings which will be of relevance to those intending to critically review the current evidence surrounding age of puberty, as well as those set on carrying out future research into this area.

Adolescent↗

PubMed1990

A measure of semantic complexity among predications.

A scale for assessing the complexity or density of utterances was developed using 10 categories of semantic relations (e.g., temporal ordering, causality). The categories are inferable from the particular "meanings" of the words (e.g., connectives, particular tense variations) used in an utterance. The scale was applied to three samples of subjects to assess its interjudge reliability and to compare the utterances of fourth-, sixth-, and eighth-grade children from middle- and working-class neighborhoods. It was also used to compare the complexity of utterances for different types of visual stimuli (used to elicit language samples). Interjudge reliabilities were more than acceptable for each of the samples, and significant differences in semantic density were found across grade, between children from working-class and middle-class neighborhoods, and for the stimuli used to elicit the utterances. When two of the three types of eliciting visual stimuli were equated for content and exposure conditions, the differences in verbal density between eliciting conditions were not replicated. The usefulness of the scale for assessing utterance density and by implication, comprehension difficulty of utterances and of texts, is discussed.

Attention↗

PubMed2007

A phylogeographic split in Buxus balearica (Buxaceae) as evidenced by nuclear ribosomal markers: when ITS paralogues are welcome.

Sequences from the ribosomal nuclear internal transcribed spacers (ITS) have been widely used to infer evolutionary hypotheses across a broad range of living organisms. Intraspecific sequence variation is assumed to be absent or negliable in most species, but few detailed studies have been conducted to assess the apportionment of ITS sequence variation within and between plant populations. Buxus balearica was chosen as a model species to assess the levels of infraspecific and intragenomic ITS variation in rare and endangered species occurring in disjunct populations around the Mediterranean basin. Intragenomic polymorphic sites were detected for western and eastern accessions of B. balearica and in two accessions of the sister species B. sempervirens. Overall, 19 different ribotypes were found in B. balearica after sequencing 48 clones, whereas 15 ribotypes were detected in 19 clones of B. sempervirens. The integrity and secondary structure stability of the ribosomal sequences suggest that they are not pseudogenes. The high number of ribotypes recovered through cloning suggested that some sequences could be chimeric or generated in vivo by partial homogenization through gene conversion or unequal crossing-over. Average sequence divergence among B. balearica clones was 0.768%, and the most divergent sequences differed by 1.62%. Available evidence does not suggest that B. balearica paralogues have been obtained from other extant Buxus species through interspecific hybridization. The presence of several ribosomal sequences in box implies that the molecular forces driving the concerted evolution of this multigene family are not fully operational in this genus. Phylogenetic analyses of cloned ITS sequences from B. balearica displayed very poor resolution and only two clades received moderate bootstrap support. Despite the marked intragenomic sequence divergence found, ribosomal data suggest a clear phylogeographic split in B. balearica between western and eastern accessions. The distinct, nonchimeric sequences that are postulated as being present in each biogeographic group suggest that box populations from Anatolia (eastern Mediterranean) are relict.

Base Sequence↗