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PubMed2005

Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae).

Giant salamanders of the genus Dicamptodon are members of the mesic forest ecosystem that occurs in the Pacific Northwest of North America. We estimate the phylogeny of the genus to test several hypotheses concerning speciation and the origin of current species distributions. Specifically, we test competing a priori hypotheses of dispersal and vicariance to explain the disjunct inland distribution of the Idaho giant salamander (D. aterrimus) and to test the hypothesis of Pleistocene speciation of Cope's giant salamander (D. copei) using Bayesian hypothesis testing. We determined that available outgroups were too divergent to root the phylogeny effectively, and we calculated Bayesian posterior probabilities for each of the 15 possible root placements for this four-taxon group. This analysis placed the root on the branch leading to D. aterrimus, indicating that current distribution and speciation of D. aterrimus fit the ancient vicariance hypothesis and are attributable to the orogeny of the Cascade Mountains rather than recent inland dispersal. Furthermore, test results indicate that D. copei is distantly related to other coastal lineages and likely originated much earlier than the Pleistocene. These results suggest that speciation within the genus is attributable to ancient geologic events, while more recent Pleistocene glaciation has shaped genetic variation and distributions within the extant species.

Animals↗

PubMed2005

Molecular phylogenetics of Phyllanthaceae inferred from five genes (plastid atpB, matK, 3'ndhF, rbcL, and nuclear PHYC).

Phyllanthaceae are a pantropical family of c. 2000 species for which circumscription is believed to be coincident with subfamily Phyllanthoideae of Euphorbiaceae sensu lato (Malpighiales) excluding Putranjivaceae. A phylogenetic study of the family using DNA sequence data has delivered largely congruent results from the plastid atpB, matK, ndhF, rbcL, and the nuclear PHYC. Our analyses include sampling from 54 of 59 genera, representing all tribes and subtribes of Phyllanthoideae. The family falls into two major clades characterized by inflorescence and leaf anatomical features. Several traditional taxonomic groupings were retrieved with minor modifications, but most clades recovered are considerably different from previous non-molecular based ideas of relationships. The enigmatic genus Dicoelia and the geographically disjunct genus Lingelsheimia are shown to be embedded in Phyllanthaceae. The taxonomic status of Leptopus diplospermus (=Chorisandrachne) and the debated placement of Andrachne ovalis have been clarified, and Protomegabaria and Richeriella are newly placed. Paraphyly of Cleistanthus and Phyllanthus is confirmed, having three and four other genera embedded, respectively. Petalodiscus is also paraphyletic, including all other Malagassian Wielandieae.

Base Sequence↗

PubMed2005

Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South American Hypochaeris (Asteraceae, Cichorieae).

Hypochaeris has a disjunct distribution, with more than 15 species in the Mediterranean region, the Canary Islands, Europe, and Asia, and more than 40 species in South America. Previous studies have suggested that the New World taxa have evolved from ancestors similar to the central European H. maculata. Based on internal transcribed spacer (ITS) sequences and fluorescence in situ hybridization (FISH) with 5S and 18S-25S rDNA of the previously overlooked Hypochaeris angustifolia from Moyen Atlas, Morocco, we show that it is sister to the entire South American group. A biogeographic analysis supports the hypothesis of long-distance dispersal from NW Africa across the Atlantic Ocean for the origin of the South American taxa rather than migration from North America, through the Panamian land bridge, followed by subsequent extinction in North America. With the assumption of a molecular clock, the trans-Atlantic dispersal from NW Africa to South America is roughly estimated to have taken place during Pliocene or Pleistocene.

Asteraceae↗

PubMed2005

Lusitania revisited: a phylogeographic analysis of the natterjack toad Bufo calamita across its entire biogeographical range.

Attempts to understand the current distributions of plants and animals require both historical and ecological information. Phylogeography has proved highly effective in elucidating historical events such as postglacial colonisations in north temperate zones. However, interesting questions still await resolution. Lusitanian distributions of fauna and flora in western Europe, for example, have puzzled biogeographers for more than 150 years. Lusitanian species have highly disjunct distributions in Ireland and in Iberia, often with few or no other populations inbetween. Despite much debate, no agreed explanation for Lusitanian distributions has yet emerged. We investigated the phylogeographic structure of one Lusitanian species, the natterjack toad Bufo calamita, using mitochondrial DNA control region sequences and allelic variation at eight microsatellite loci. Our results show that this amphibian must have survived in north European refugia, as well as in Iberia, during and since the last (Weichselian) glacial maximum around 20,000 years before present (BP). Subsequent local recolonisation after the Younger Dryas cooling around 11,000 years BP best explains the Lusitanian aspect of natterjack toad distribution.

Animals↗

PubMed2006

Phylogeny of the túngara frog genus Engystomops (= Physalaemus pustulosus species group; Anura: Leptodactylidae).

We present a phylogeny of the Neotropical genus Engystomops (= Physalaemus pustulosus species group) based on sequences of approximately 2.4 kb of mtDNA, (12S rRNA, valine-tRNA, and 16S rRNA) and propose a phylogenetic nomenclature. The phylogeny includes all described taxa and two unnamed species. All analyses indicate that Engystomops is monophyletic and contains two basal allopatric clades. Clade I (Edentulus) includes E. pustulosus and the Amazonian E. petersi + E. cf. freibergi. Clade II (Duovox) includes all species distributed in W Ecuador and NW Peru. Brevivox, a clade of small-sized species is strongly supported within Duovox. Populations of Engystomops pustulosus fall into two well-supported clades, each of which occupies two disjunct portions of the species range. Overall, our phylogeny is congruent with most previous hypotheses. This study is among the few published species-level phylogenies of Neotropical amphibians derived from molecular datasets. A review of the proportion of new species detected by similar studies suggests that the increasing use of molecular techniques will lead to the discovery of a vast number of species of Neotropical amphibians.

Animals↗

PubMed2006

Molecular phylogeny and intra- and intercontinental biogeography of Calycanthaceae.

Based on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions and intra-continental diversification in eastern Asia. Fossil-calibrated penalized likelihood and Bayesian divergence time estimates indicate that the Northern Hemisphere Calycanthus and Chimonanthus diverged from each other in the mid-Miocene, while the Australian Idiospermum had already diverged by the Upper Cretaceous and likely represents a remnant of a former Gondwanan distribution of Calycanthaceae that included South America, as indicated by the occurrence of Cretaceous Calycanthaceae fossils in Brazil. Relationships within Calycanthus were difficult to resolve, but a shared 155-bp deletion in the trnL-F intergenic spacer unites the two North American species, which were also sisters in a cpDNA restriction site study. Their ancestor apparently crossed the Bering land bridge in the Miocene. The six species of Chimonanthus, by contrast, diverged from each other as recently as 1-2my ago, and a DIVA analysis with four areas of endemism recognized within China suggests three vicariance and two dispersal events within Chimonanthus, with initial vicariance having occurred between eastern and southwestern or central China. Further divergence then appears to have involved eastern and south-central China, and southwestern and central China.

Cell Nucleus↗

PubMed2006

Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree.

We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of picid phylogeny. We tested the monophyly of sub-families within the Picidae, and sampled from widely distributed and diverse genera (Celeus, Colaptes, Dryocopus, Melanerpes, Picoides, Picumnus, Sasia, Piculus, and Picus). Relationships of three poorly known Southeast Asian genera (Dinopium, Reinwardtipicus, and Blythipicus) were also examined, revealing unexpected sister relationships. All phylogenetic approaches recovered largely congruent topologies, supporting a monophyletic Picinae and paraphyletic Picumninae, with the monotypic piculet, Nesoctites micromegas, as sister to the Picinae. We report paraphyly for Celeus and Piculus, whereas the broadly distributed genera Picumnus and Dryocopus were supported as monophyletic. Our phylogenetic results indicate a complex geographic history for the Picidae, with multiple disjunct sister lineages distributed between the New World and Asia. The relationships and geographic distribution of basal picid lineages indicates an Old World origin of the Picidae; however, the geographic origin of the Picinae remains equivocal, as the sister relationship between the Caribbean N. micromegas and the true woodpeckers presents the possibility of a New World origin for the Picinae.

Animals↗

PubMed2006

Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus).

The mygalomorph spider genera Antrodiaetus and Atypoides (Antrodiaetidae) belong to an ancient lineage that has persisted since at least the Cretaceous. These spiders display a classic disjunct Holarctic distribution with species in the eastern Palaearctic plus the western and eastern Nearctic. Prior phylogenetic analyses of this group have been proposed on the basis of morphology, but lack strong support and independent corroboration. Here we present the first phylogenetic analysis of species-level relationships based on molecular data obtained from the mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S and 28S rRNA) genomes. Analyses corroborate earlier findings that Atypoides forms a paraphyletic grade with respect to Antrodiaetus, and consequently, that genus is formally synonymized under Antrodiaetus. In addition, our results support the relatively early divergence of Antrodiaetus roretzi. Antrodiaetus pacificus is "paraphyletic" with respect to the A. lincolnianus group and is likely an assemblage of numerous species. The final topology based on a combined molecular dataset, in conjunction with two different molecular dating techniques (penalized likelihood plus a Bayesian approach) and ancestral distribution reconstructions, was used to infer the historical biogeography of these spiders. Trans-Beringian and trans-Atlantic routes appear to account for the present-day distribution of Antrodiaetus in Japan and North America. Future studies on Antrodiaetus phylogeny will be used to address questions regarding morphological stasis and the evolution of quantitative morphological characters.

Animals↗

PubMed2001

Electronic publishing of science: better late than never.

The time required for medical publication in the print literature has changed little in 200 years, whereas scientific discovery now proceeds at a dizzying pace. There is a growing disjunction between the efficiency of science and the inefficiency of scientific reporting. Electronic publication as proposed for PubMedCentral is a logical solution to this problem.

Humans↗

PubMedDate not supplied

Formation of uniparental disomy 7 delineated from new cases and a UPD7 case after trisomy 7 rescue. Presentation of own results and review of the literature.

Maternal uniparental disomy for the entire chromosome 7 (matUPD7) has been reported several times in Silver-Russell syndrome (SRS) and growth-restricted patients. Here we present our results from the analysis of an abortion with confined placental mosaicism (CPM) for trisomy 7 which showed a maternal meiotic origin of the trisomy in the placenta and rescue to maternal UPD7 in foetal membrane. Furthermore, two newly detected SRS cases with maternal UPD7 revealed isodisomy and partial heterodisomy, respectively. Summarising these results with those published previously on the origin of UPD7, similar numbers of isodisomy (n=11) and cases with complete or partial heterodisomy (n=12) have been reported. In respect to the different formation mechanisms of UPD, complete isodisomy should be the result of a post-zygotic mitotic segregation error, whereas heterodisomic UPDs should be caused by trisomic rescue after meiotic non-disjunction events. In maternal UPD7, 50% of cases seem to be caused by post-zygotic mitotic segregation errors, which is similar to the situation in trisomy 7. This result corresponds to the situation in trisomy 8 but is in contrast to observations in the frequent aneuploidies. Thus, the different findings in these aberrations reflect the presence of multiple factors that act to ensure normal segregation, varying in importance for each chromosome.

Abnormalities, Multiple↗

PubMed2003

Identification of Ncd tail domain-binding sites on the tubulin dimer.

The Drosophila non-claret disjunctional (Ncd) kinesin-like protein is required for spindle assembly in oocytes and spindle maintenance in early embryos. Through the action of ATP-dependent microtubule (MT)-binding sites in the head and ATP-independent MT-binding sites in the tail, Ncd may bundle and, perhaps, slide MTs relative to each other. Our previous work on the MT-binding site of the Ncd tail domain demonstrated that this site, like the MT-binding sites of tau, contains basic residues flanked by proline residues and can promote MT assembly and stability. Here, we characterize the interactions of a monomeric Ncd tail protein with subtilisin-digested MTs in order to identify sites on the tubulin dimer that interact with the Ncd tail. The results provide evidence for four such binding sites per tubulin dimer and support the hypothesis that each binding site consists of a cluster of acidic residues in the C-terminal regions of alpha- and beta-tubulin.

Animals↗

PubMed1998

Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing.

The structure of an ATP-bound kinesin motor domain is predicted and conformational differences relative to the known ADP-bound form of the protein are identified. The differences should be attributed to force-producing ATP hydrolysis. Candidate ATP-kinesin structures were obtained by simulated annealing, by placement of the ATP gamma-phosphate in the crystal structure of ADP-kinesin, and by interatomic distance constraints. The choice of such constraints was based on mutagenesis experiments, which identified Gly-234 as one of the gamma-phosphate sensing residues, as well as on structural comparison of kinesin with the homologous nonclaret disjunctional (ncd) motor and with G-proteins. The prediction of nucleotide-dependent conformational differences reveals an allosteric coupling between the nucleotide pocket and the microtubule binding site of kinesin. Interactions of ATP with Gly-234 and Ser-202 trigger structural changes in the motor domain, the nucleotide acting as an allosteric modifier of kinesin's microtubule-binding state. We suggest that in the presence of ATP kinesin's putative microtubule binding regions L8, L12, L11, alpha4, alpha5, and alpha6 form a face complementary in shape to the microtubule surface; in the presence of ADP, the microtubule binding face adopts a more convex shape relative to the ATP-bound form, reducing kinesin's affinity to the microtubule.

Adenosine Diphosphate↗

PubMed1999

A chemically reversible Brownian motor: application to kinesin and Ncd.

Kinesin and nonclaret disjunctional protein (ncd) are two microtubule-based molecular motors that use energy from ATP hydrolysis to drive motion in opposite directions. They are structurally very similar and bind with similar orientations on microtubule. What is the origin of the different directionality? Is it some subtle feature of the structure of the motor domains, not apparent in x-ray diffraction studies, or possibly some difference near the neck regions far from the microtubule binding site? Perhaps because the motors function as dimers, the explanation involves differences in the strength of the interaction between the two motor monomers themselves. Here we present another possibility, based on a Brownian ratchet, in which the direction of motion of the motor is controlled by the chemical mechanism of ATP hydrolysis and is an inherent property of a single head. In contrast to conventional power stroke models, dissociation of the individual heads is not obligatory in the chemomechanical cycle, and the steps during which motion and force generation occurs are best described as one-dimensional thermally activated transitions that take place while both heads are attached to the microtubule. We show that our model is consistent with experiments on kinesin in which the velocity is measured as a function of external force and with the observed stiochiometry of one ATP/8-nm step at low load. Further, the model provides a way of understanding recent experiments on the ATP dependence of the variance (randomness) of the distance moved in a given time.

Adenosine Triphosphate↗

PubMed1999

Kinetics processivity and the direction of motion of Ncd.

The kinetic mechanism of the nonclaret disjunctional protein (Ncd) motor was investigated using the dimer termed MC1 (residues 209-700), which has been shown to exhibit negative-end directed motility (Chandra et al., 1993). The kinetic properties are similar to those of the monomeric Ncd motor domain (Pechatnikova and Taylor, 1997). The maximum steady-state ATPase activity of 1.5 s(-1) is half as large as for the monomeric motor. Dissociation constants in the presence of nucleotides showed the same trend but with approximately a two-fold decrease in the values: K(d) values are 1.0 microM for ADP-AlF(4), 1.1 microM for ATPgammaS, 1.5 microM for ATP, 3 microM for ADP, and 10 microM for ADP-vanadate (in 25 mM NaCl, 22 degrees C). The apparent second-order rate constants for the binding of ATP and ADP to the microtubule-motor complex (MtMC1) are 2 microM(-1) s(-1). Based on measurements at high microtubule concentrations the kinetic steps were fitted to the scheme,[see text] where N refers to one head of the dimer and T, D, and P stand for ATP, ADP, and inorganic phosphate. k(1) and k(-4) are the first-order rate constants of the transition induced by the binding of mant ATP and mant ADP respectively. ADP release is the main rate-limiting step in the MtMC1 mechanism. The binding of the MC1-mant ADP complex to microtubules released less than half of the mant ADP (alternating site reactivity). The second mant ADP is only released by the binding of nucleotides that dissociate the MtMC1 complex (ATP and ADP but not AMPPNP). The apparent rate constant for dissociation of the second mant ADP is four times smaller than the first and much smaller than the rate of dissociation of MtMC1 by ATP or ADP. These results are explained by a model in which MC1.ADP is first dissociated from the microtubule by ATP, followed by rebinding to the microtubule by the ADP-containing head. Ncd may follow a different reaction pathway than does kinesin, but the differences in rate constants do not explain the opposite direction of motion. The kinetic evidence and the high ratio of motile velocity to ATPase support a nonprocessive, low duty cycle mechanism for the Ncd motor.

Adenine Nucleotides↗

PubMed2003

Scalar implicatures: experiments at the semantics-pragmatics interface.

In this article we present two sets of experiments designed to investigate the acquisition of scalar implicatures. Scalar implicatures arise in examples like Some professors are famous where the speaker's use of some typically indicates that s/he had reasons not to use a more informative term, e.g. all. Some professors are famous therefore gives rise to the implicature that not all professors are famous. Recent studies on the development of pragmatics suggest that preschool children are often insensitive to such implicatures when they interpret scalar terms (Cognition 78 (2001) 165; Chierchia, G., Crain, S., Guasti, M.T., Gualmini, A., & Meroni, L. (2001). The acquisition of disjunction: evidence for a grammatical view of scalar implicatures. In A.H.-J. Do, L. Dominguez, & A. Johansen (Eds.), Proceedings of the 25th Boston University Conference on Language Development (pp. 157-168). Somerville, MA: Cascadilla Press; Musolino, J., & Lidz, J. (2002). Preschool logic: truth and felicity in the acquisition of quantification. In B. Skarabela, S. Fish, & A.H.-J. Do, Proceedings of the 26th Boston University Conference on Language Development (pp. 406-416). Somerville, MA: Cascadilla Press). This conclusion raises two important questions: (a) are all scalar terms treated in the same way by young children?, and (b) does the child's difficulty reflect a genuine inability to derive scalar implicatures or is it due to demands imposed by the experimental task on an otherwise pragmatically savvy child? Experiment 1 addresses the first question by testing a group of 30 5-year-olds and 30 adults (all native speakers of Greek) on three different scales, ( ), ( ) and ( ). In each case, subjects were presented with contexts which satisfied the semantic content of the stronger (i.e. more informative) terms on each scale (i.e. all, three and finish) but were described using the weaker terms of the scales (i.e. some, two, start). We found that, while adults overwhelmingly rejected these infelicitous descriptions, children almost never did so. Children also differed from adults in that their rejection rate on the numerical scale was reliably higher than on the two other scales. In order to address question (b), we trained a group of 30 5-year-olds to detect infelicitous statements. We then presented them with modified versions of the stories of Experiment 1, which now more readily invited scalar inferences. These manipulations gave rise to significantly higher rejection rates than those observed in Experiment 1. Overall, these findings indicate that children do not treat all scalar terms alike and, more importantly, that children's ability to derive scalar implicatures is affected by their awareness of the goal of the task. Developmental and methodological implications as well as theoretical implications for the semantics of numeral terms are discussed.

Child, Preschool↗

PubMedDate not supplied

Plato versus Aristotle: categorical and dimensional models for common mental disorders.

There are two quite different ways of conceptualizing common mental disorders: as categorically distributed or as dimensions. In the former case, individuals with "subthreshold" disorders may contain a small proportion of "true cases"; while in the latter, they are seen as having the same basic disorder, but in insufficient degree to warrant a diagnostic label. The categorical school postulates the phenomenon of "comorbidity" to account for those who are both depressed and anxious. The dimensional school regards them as cases of "anxious depression," and observes that the 2 dimensions are highly correlated with one another. This article considers 3 levels of severity of cases satisfying research diagnostic criteria for depression: mild, moderate, and severe. At ascending levels of initial severity, there is increasing disability, and a worse outcome at 12 months. The only positive treatment effect is that favoring antidepressants over sedatives at 3 months, and this effect is related to initial severity-being much greater for the "severe" group of depressions. Initial severity is linearly related to disability, and there is no disjunction at the usual division between "non-cases" and "cases" of depression. Clinicians are obliged to use categorical concepts, as they must decide who is sufficiently ill to justify treatment. But in our efforts to understand the relationships between social and biological variables, dimensional models are far more appropriate.

Anxiety Disorders↗

PubMed1997

Hydrolysis of AMPPNP by the motor domain of ncd, a kinesin-related protein.

AMPPNP was found to be hydrolyzed by the motor domain of ncd (the product of a Drosophila gene, non-claret disjunctional), a kinesin-related protein. This hydrolysis could be monitored by 31P NMR spectroscopy and by an assay of phosphate, one of the products of the hydrolysis. The rate was approximately 0.00004 s(-1), 1% of the ATP turnover rate. The AMPPNP turnover was not stimulated by microtubules. Kinesin motor domain also turned over AMPPNP but at a somewhat lower rate. Although the turnover was slow, the present finding may present an important caveat, since AMPPNP has been widely used for investigations of kinesin and kinesin-related proteins as a non-hydrolyzable ATP analogue.

Adenosine Triphosphate↗

PubMed1995

Functional interaction between the CSE2 gene product and centromeres in Saccharomyces cerevisiae.

The cse2-1 allele was identified through a genetic screen for mutations affecting chromosome segregation in Saccharomyces cerevisiae. This mutation confers cold and temperature sensitivity and causes increases in mitotic chromosome non-disjunction and loss. The CSE2 gene encodes a 17 kDa protein with a basic region-leucine zipper motif. Disruption of CSE2 is not lethal but results in the accumulation of large-budded cells. Here, we report that disruption of CSE2 results in a significant increase in chromosome missegregation, slower growth and defective meiosis. The combination of the CSE2 disruption and a mutant centromere results in a synergistic effect on both cell growth and cell viability. These data suggest a functional interaction between the CSE2 protein and the yeast centromere.

Centromere↗