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C R Marshall

Publications and source records attributed to C R Marshall.

At least 19 recordsLinked to original sources
PubMed2001

Effects of sampling standardization on estimates of Phanerozoic marine diversification.

Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cretaceous and early Tertiary diversity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine biodiversity. These limitations will be addressed as the database and methods are refined.

Animals↗
PubMed2001

Temperature dependence of cloned mammalian and salmonid cardiac Na(+)/Ca(2+) exchanger isoforms.

The cardiac Na(+)/Ca(2+) exchanger (NCX), an important regulator of cytosolic Ca(2+) concentration in contraction and relaxation, has been shown in trout heart sarcolemmal vesicles to have high activity at 7 degrees C relative to its mammalian isoform. This unique property is likely due to differences in protein structure. In this study, outward NCX currents (I(NCX)) of the wild-type trout (NCX-TR1.0) and canine (NCX 1.1) exchangers expressed in oocytes were measured to explore the potential contributions of regulatory vs. transport mechanisms to this observation. cRNA was transcribed in vitro from both wild-type cDNA and was injected into Xenopus oocytes. I(NCX) of NCX-TR1.0 and NCX1.1 were measured after 3-4 days over a temperature range of 7-30 degrees C using the giant excised patch technique. The I(NCX) for both isoforms exhibited Na(+)-dependent inactivation and Ca(2+)-dependent positive regulation. The I(NCX) of NCX1.1 exhibited typical mammalian temperature sensitivities with Q(10) values of 2.4 and 2.6 for peak and steady-state currents, respectively. However, the I(NCX) of NCX-TR1.0 was relatively temperature insensitive with Q(10) values of 1.2 and 1.1 for peak and steady-state currents, respectively. I(NCX) current decay was fit with a single exponential, and the resultant rate constant of inactivation (lambda) was determined as a function of temperature. As expected, lambda decreased monotonically with temperature for both isoforms. Although lambda was significantly greater in NCX1.1 compared with NCX-TR1.0 at all temperatures, the effect of temperature on lambda was not different between the two isoforms. These data suggest that the disparities in I(NCX) temperature dependence between these two exchanger isoforms are unlikely due to differences in their inactivation kinetics. In addition, similar differences in temperature dependence were observed in both isoforms after alpha-chymotrypsin treatment that renders the exchanger in a deregulated state. These data suggest that the differences in I(NCX) temperature dependence between the two isoforms are not due to potential disparities in either the I(NCX) regulatory mechanisms or structural differences in the cytoplasmic loop but are likely predicated on differences within the transmembrane segments.

Animals↗
PubMed2000

Ca(2+) binding to cardiac troponin C: effects of temperature and pH on mammalian and salmonid isoforms.

A reduction in temperature lowers the Ca(2+) sensitivity of skinned cardiac myofilaments but this effect is attenuated when native cardiac troponin C (cTnC) is replaced with skeletal TnC. This suggests that conformational differences between the two isoforms mediate the influence of temperature on contractility. To investigate this phenomenon, the functional characteristics of bovine cTnC (BcTnC) and that from rainbow trout, Oncorhynchus mykiss, a cold water salmonid (ScTnC), have been compared. Rainbow trout maintain cardiac function at temperatures cardioplegic to mammals. To determine whether ScTnC is more sensitive to Ca(2+) than BcTnC, F27W mutants were used to measure changes in fluorescence with in vitro Ca(2+) titrations of site II, the activation site. When measured under identical conditions, ScTnC was more sensitive to Ca(2+) than BcTnC. At 21 degrees C, pH 7.0, as indicated by K(1/2) (-log[Ca] at half-maximal fluorescence, where [Ca] is calcium concentration), ScTnC was 2.29-fold more sensitive to Ca(2+) than BcTnC. When pH was kept constant (7.0) and temperature was lowered from 37.0 to 21.0 degrees C and then to 7.0 degrees C, the K(1/2) of BcTnC decreased by 0.13 and 0.32, respectively, whereas the K(1/2) of ScTnC decreased by 0.76 and 0.42, respectively. Increasing pH from 7.0 to 7.3 at 21.0 degrees C increased the K(1/2) of both BcTnC and ScTnC by 0.14, whereas the K(1/2) of both isoforms was increased by 1.35 when pH was raised from 7.0 to 7.6 at 7.0 degrees C.

Animals↗
PubMed1999

Morphological innovation and developmental genetics.

How do the actions of individual genes contribute to the complex morphologies of animals and plants? How widespread are these genes taxonomically? How many genes are involved in the morphological differences observed between species, and can we identify them? To what extent can empirical data and theory be reconciled? We provide an overview of some recent attempts to answer these questions, answers that have taken us to the threshold of understanding the mechanistic basis and evolutionary factors that underlie morphological innovation.

Animals↗
PubMed1999

Mutations of c-kit JM domain are found in a minority of human gastrointestinal stromal tumors.

The c-kit gene encodes a transmembrane receptor kinase (KIT) which is expressed in the majority of human gastrointestinal stromal tumors (GISTs), a subtype of gastrointestinal mesenchymal neoplasms. A previous study identified mutations in the juxtamembrane (JM) domain of c-kit in five of six GISTs (Science 279: 577, 1998). To better define the frequency and spectrum of c-kit gene mutations in mesenchymal neoplasms of the GI tract that had been characterized for KIT protein expression, we examined archived tissue samples for mutations in the JM domain by PCR amplification and DNA sequencing. c-kit JM domain mutations were found in nine of 56 mesenchymal tumors (46 GISTs, eight leiomyomas, two leiomyosarcomas) and occurred exclusively in GISTs (21%). Seven of the nine mutations consisted of intragenic deletions of one to 19 codons. There was one insertion mutation that added 12 codons and one missense mutation (Val560Asp). None of the mutations disrupted the downstream reading frame of the gene. The single missense mutation (Val560Asp) is very similar to the only other missense mutation reported in GISTs (Val599Asp). Of the 46 GISTs, 43 were strongly positive for KIT protein expression and negative for diffuse expression of desmin. Neither KIT expression nor gene mutations were found in gastrointestinal leiomyomas or leiomyosarcomas. We conclude that mutation of the c-kit JM domain does not occur in gastrointestinal mesenchymal neoplasms with well developed-smooth muscle differentiation, and is restricted to GISTs. However, since these mutations are only found in a minority of GISTs, further investigation into the mechanisms of c-kit gene activation in this group of neoplasms is warranted.

Amino Acid Sequence↗
PubMed1997

Molecular systematics of the Canidae.

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.

Animals↗
PubMed1996

Analysis of partial sequences of genes coding for 16S rRNA of actinomycetes isolated from Casuarina equisetifolia nodules in Mexico.

Filamentous bacteria isolated from surface-sterilized nodules of Casuarina equisetifolia trees in México were capable of reducing acetylene, a diagnostic test for nitrogenase, but were unable to nodulate their host. Analysis of partial 16S rRNA gene sequences suggests that the Mexican isolates are not Frankia strains but members of a novel clade.

Actinomycetales↗
PubMed1995

Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3.

The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial for nitrogen fixation. Previous phylogenetic analysis of the amino acid sequence of nifH suggested that this gene had been horizontally transferred from a proteobacterium to the gram-positive/cyanobacterial clade, although the confounding effects of paralogous comparisons made interpretation of the data difficult. An additional test of nif gene horizontal transfer using nifD was made, but the NifD phylogeny lacked resolution. Here nif gene phylogeny is addressed with a phylogenetic analysis of a third and longer nif gene, nifK. As part of the study, the nifK gene of the key taxon Frankia was sequenced. Parsimony and some distance analyses of the nifK amino acid sequences provide support for vertical descent of nifK, but other distance trees provide support for the lateral transfer of the gene. Bootstrap support was found for both hypotheses in all trees; the nifK data do not definitively favor one or the other hypothesis. A parsimony analysis of NifH provides support for horizontal transfer in accord with previous reports, although bootstrap analysis also shows some support for vertical descent of the orthologous nifH genes. A wider sampling of taxa and more sophisticated methods of phylogenetic inference are needed to understand the evolution of nif genes. The nif genes may also be powerful phylogenetic tools. If nifK evolved by vertical descent, it provides strong evidence that the cyanobacteria and proteobacteria are sister groups to the exclusion of the firmicutes, whereas 16S rRNA sequences are unable to resolve the relationships of these three major eubacterial lineages.

Amino Acid Sequence↗
PubMed1994

Dollo's law and the death and resurrection of genes.

Dollo's law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or "lost" developmental programs. Conversely, the reactivation of long (> 10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints; the classic example of the resurrection of "hen's teeth" is most likely an experimental artifact, and the experimental reactivation of the Archaeopteryx limb developmental program has been shown to be a misinterpretation. For groups undergoing adaptive radiations, lost features may "flicker" on and off, resulting in a distribution of character states that does not reflect the phylogeny of the group.

Ambystoma mexicanum↗
PubMed1992

DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values.

A DNA hybridization phylogeny of four sand dollars using a sea biscuit as an outgroup is presented. The study is unusual in that the normalized percent hybridization (NPH) values were all less than 50%, yet the same topology was obtained regardless of which distance metric was used, i.e., whether reciprocal distances were averaged or not, or whether or not a molecular clock was assumed. The tree also appears robust under jackknifing and bootstrapping. The extent of hybridization between homologous hybrids was measured with a five- to sevenfold higher precision than is typical, and by implication NPH was also measured with a higher than normal precision. The ability to measure highly reproducible NPH values offers the possibility of examining the phylogeny of more widely divergent species than typically studied using DNA hybridization techniques, using 1/NPH as a distance metric. The hypothesis of a molecular clock within the sand dollars was rejected, adding sand dollars to the growing list of groups where significant rate variation is known. A small fraction of the sand dollar genomes hybridized with the distantly related regular sea urchin Lytechinus. These slowly evolving sequences probably represent conserved exonic components of the genome.

Animals↗
PubMed1992

Character analysis and the integration of molecular and morphological data in an understanding of sand dollar phylogeny.

Reconciling discordant morphological and molecular phylogenies remains a problem in modern systematics. By examining conflicting DNA-hybridization and morphological phylogenies of sand dollars, I show that morphological criteria may be used to help evaluate the reliability of molecular phylogenies where they differ from morphological trees. All available criteria for assessing the reliability of DNA-hybridization phylogenies suggest that the sand dollar DNA-hybridization phylogeny is robust. Standard homology-recognition criteria are used to assess the a priori reliabilities of the morphological attributes associated with the node drawn into question by the DNA data, and it is shown that these attributes are among the least phylogenetically informative of all the morphological characters. Moreover, the questioned node has the smallest number of supporting characters, and most of these characters are associated with the food grooves, which suggests that they may be functionally correlated. Thus, on the basis of the analysis of the morphological data and given the robustness of the DNA tree, the DNA phylogeny is preferred. Further, paleobiogeographic data support the DNA tree rather than the morphological tree, and a plausible heterochronic mechanism has been proposed that may account for the homoplasious morphological evolution that must have occurred if the DNA tree is correct.

Animals↗
PubMed1990

The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies.

Bounded estimates on divergence times between lineages are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessity, constitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil record to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramatically affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or correlation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of species within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherian mammals, echinoids, and geese are used as examples.

Animals↗
PubMed1983

Vestibular stimulation for supranuclear gaze palsy: case report.

Gaze palsies following severe destruction or irritative lesions of the cerebral hemispheres are rare. This report describes a patient with supranuclear ophthalmoplegia secondary to stroke which was rapidly resolved by cold caloric vestibular stimulation. The patient had a severe infarction of the right cerebral hemisphere and had a fixed deviated gaze to the right 3 months after onset. Cold caloric vestibular stimulation was used in an attempt to evaluate brain stem integrity. Following three successive injections of cold water at OC-5C into the external auditory canal, the patient regained full voluntary extraocular eye movements. The improvement continued for more than 12 months after the last treatment. A literature review of the neuroanatomy and neurophysiology of voluntary and reflex ocular movements is presented. A possible explanation for the improvement in this case is that vestibular input inhibits the tonic phase of antagonistic extraocular muscles while facilitating agonistic extraocular muscles.

Caloric Tests↗