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J M Quattro

Publications and source records attributed to J M Quattro.

At least 19 recordsLinked to original sources
PubMed2001

Differential survival of three mitochondrial lineages of a marine benthic copepod exposed to a pesticide mixture.

In South Carolina estuaries, the harpacticoid copepod Microarthridion littorale (Poppe 1881) consists of three distinct mitochondrial lineages (liI, liII, and liIII), whose distributions may be partially explained by the presence of toxic contaminants in the sampled habitats. The frequencies of liII and liIII are greatly diminished and sometimes absent in South Carolina contaminated tidal creeks where liI is omnipresent. In this study, representatives of these lineages or haplotype groups were collected from sediments of an estuarine creek containing low to undetectable levels of toxicants and then exposed to a toxic (approximately LC90) aqueous mixture containing an organophosphate (chlorpyrifos) and organochlorine pesticide (DDT, mixed isomers). A comparison was conducted for the frequency of each of the three haplotypes among the survivors of the exposed animals relative to that among the survivors of the control group. The haplotype group with the highest frequency in contaminated SC estuaries (liI) was statistically higher in frequency in survivors of the pesticide-exposed group than in the control group. The two rarer groups (liII and liIII) were less abundant among the survivors of the pesticide-exposed group than the control group. The frequencies of liI, liII, and liIII did not change significantly among the survivors of the control group. The differential survival of the three haplotype groups in the pesticide mixture may be one of the reasons that some haplotype groups are more likely to be found in clean or contaminated tidal creeks on the South Carolina coast.

Animals↗
PubMed2001

Gene-gene concordance and the phylogenetic relationships among rare and widespread pygmy sunfishes (genus Elassoma).

Pygmy sunfishes (Elassoma) are primarily lowland species with an interesting biogeographic dichotomy: three species have broad geographic distributions, and three are narrowly distributed (and have been recommended for threatened or endangered status). To test phylogenetic predictions derived from the geographic distributions of pygmy sunfishes and possible historical factors contributing to the threatened/endangered status of the rare species, we reconstructed trees for two mitochondrial genes and introns of three nuclear genes. The pattern and rate of nuclear and mitochondrial sequence evolution were heterogeneous within Elassoma, but relationships were generally concordant across gene trees. Elassoma is monophyletic and, as predicted by geographic distributions, E. evergladei, E. okefenokee, and E. zonatum consistently branch from deeper nodes. Phylogeographic structure in mitochondrial and nuclear genes also supports an early origin of E. zonatum. Phylogenetic analyses of the five loci support widely divergent positions for the rare species E. alabamae. Two rare species, E. boehlkei and E. okatie, are sister taxa and are related to a widespread species, E. evergladei.

Animals↗
PubMed2001

Ecotoxicology and population genetics: the emergence of "phylogeographic and evolutionary ecotoxicology".

Genetics of ecotoxicology has recently emerged as a priority research field. The advent of polymerase chain reaction and molecular population genetics has made it possible to examine the genetics in even the smallest individuals. Although a potentially powerful technique, current approaches oversimplify the relationship of change in gene frequency to contaminant exposure. Many of these approaches cannot control for random correlation or accessory abiotic factors that impinge on the system tested. Indeed, the gestalt approaches of laboratory exposure or natural field experiments may ignore significant genome-level interactions that are important within a given system. At the very least, these approaches would benefit by a biogeographic survey of genetic variation to understand geographic microevolutionary patterns, or phylogeography, within a species to reduce spurious correlations and erroneous conclusions. Other single locus approaches can be chosen to enhance this approach if genetic/environmental interactions have been characterized for laboratory populations or for other model systems.

Animals↗
PubMed2001

Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase.

A striking correlation between neural expression and high net negative charge in some teleost isozymes led to the interesting, yet untested, suggestion that negative charge represents an adaptation (via natural selection) to the neural environment. We examine the evolution of the triosephosphate isomerase (TPI) gene family in fishes for periods of positive selection. Teleost fish express two TPI proteins, including a generally expressed, neutrally charged isozyme and a neurally expressed, negatively charged isozyme; more primitive fish express only a single, generally expressed TPI isozyme. The TPI gene phylogeny constructed from sequences isolated from two teleosts, a single acipenseriform, and other TPI sequences from the databases, supports a single gene duplication event early in the evolution of bony fishes. Comparisons between inferred ancestral TPI sequences indicate that the neural TPI isozyme evolved through a period of positive selection resulting in the biased accumulation of negatively charged amino acids. Further, the number of nucleotide changes required for the observed amino acid substitutions suggests that selection acted on the overall charge of the protein and not on specific key amino acids.

Amino Acid Substitution↗
PubMed2000

Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora.

N(2) fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, Spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified nifH sequence segments was used in previous studies to examine the stability and dynamics of the Spartina rhizosphere diazotroph assemblages in the North Inlet salt marsh, near Georgetown, S.C. In this study, plugs were taken from gel bands from representative DGGE gels, the nifH amplimers were recovered and cloned, and their sequences were determined. A total of 59 sequences were recovered, and the amino acid sequences predicted from them were aligned with sequences from known and unknown diazotrophs in order to determine the types of organisms present in the Spartina rhizosphere. We recovered numerous sequences from diazotrophs in the gamma subdivision of the division Proteobacteria (gamma-Proteobacteria) and from various anaerobic diazotrophs. Diazotrophs in the alpha-Proteobacteria were poorly represented. None of the Spartina rhizosphere DGGE band sequences were identical to any known or previously recovered environmental nifH sequences. The Spartina rhizosphere diazotroph assemblage is very diverse and apparently consists mainly of unknown organisms.

Bacteria, Anaerobic↗
PubMed1999

Discordant patterns of morphological and molecular change in broadtail madtoms (genus Noturus).

Two morphologically distinct forms of an undescribed madtom catfish (Noturus sp.) occur in the rivers and lakes of southeastern USA. 'Lake' broadtail madtoms are endemic to Lake Waccamaw and are probably related to nearby 'river' broadtail populations. To investigate phylogenetic relationships, we surveyed mitochondrial DNA (mtDNA) sequence variation in 'lake' and 'river' broadtails and other members of the genus Noturus. Mitochondrial rDNA data suggest a sister group relationship between broadtail madtoms and N. insignis, not N. leptacanthus as posited previously. Population-level analyses using additional mtDNA characters (NADH dehydrogenase subunit 2 (ND2) and cytochrome b (Cytb)) identified two highly divergent genetic lineages within broadtail madtoms that do not correspond to the morphological designations 'river' and 'lake'.

Animals↗
PubMed1998

Patterns of gene duplication in lepidopteran pheromone binding proteins.

We have isolated and characterized cDNAs representing two distinct pheromone binding proteins (PBPs) from the gypsy moth, Lymantria dispar. We use the L. dispar protein sequences, along with other published lepidopteran PBPs, to investigate the evolutionary relationships among genes within the PBP multigene family. Our analyses suggest that the presence of two distinct PBPs in genera representing separate moth superfamilies is the result of relatively recent, independent, gene duplication events rather than a single, ancient, duplication. We discuss this result with respect to the biochemical diversification of moth PBPs.

Amino Acid Sequence↗
PubMed1998

Universal cytochrome b primers facilitate intraspecific studies in molluscan taxa.

We describe the construction of amplification primers designed to target a portion of the mitochondrial cytochrome b locus in a variety of molluscan taxa. Combinations of two sets of primers successfully amplified cytochrome b from several species of gastropods, bivalves, and cephalopods. Sequence analysis of these amplified products revealed nucleotide diversity in small samples within several of these taxa. We discuss the utility of these primer sets for studies of intraspecific phylogeny in mollusks and potentially other invertebrates.

Amino Acid Sequence↗
PubMed1997

Genetic diversity in black howler monkeys (Alouatta pigra) from Belize.

To assess the level of genetic variation in a threatened black howler monkey (Alouatta pigra) population, we examined 36 allozyme loci and restriction fragment profiles of mitochondrial DNA (mtDNA). Mean heterozygosity at allozyme loci was only 0.021 and 5.6 percent of the loci were polymorphic. Analyses of mtDNA also revealed low genetic diversity compared with other primates. F-statistics revealed no significant genetic heterogeneity among troops within the Bermudian Landing preserve, but did indicate a deficiency of heterozygotes at one of the two loci. We explore several explanations for this result, which is unexpected in a socially structured primate. Low genetic diversity in this population may reflect its history of demographic bottlenecks.

Alleles↗
PubMed1997

Lactate dehydrogenase (LDH) gene duplication during chordate evolution: the cDNA sequence of the LDH of the tunicate Styela plicata.

L-Lactate dehydrogenase (L-LDH, E.C. 1.1.1.27) is encoded by two or three loci in all vertebrates examined, with the exception of lampreys, which have a single LDH locus. Biochemical characterizations of LDH proteins have suggested that a gene duplication early in vertebrate evolution gave rise to Ldh-A and Ldh-B and that an additional locus, Ldh-C arose in a number of lineages more recently. Although some phylogenetic studies of LDH protein sequences have supported this pattern of gene duplication, others have contradicted it. In particular, a number of studies have suggested that Ldh-C represents the earliest divergence among vertebrate LDHs and that it may have diverged from the other loci well before the origin of vertebrates. Such hypotheses make explicit statements about the relationship of vertebrate and invertebrate LDHs, but to date, no closely related invertebrate LDH sequences have been available for comparison. We have attempted to provide further data on the timing of gene duplications leading to multiple vertebrate LDHs by determining the cDNA sequence of the LDH of the tunicate Styela plicata. Phylogenetic analyses of this and other LDH sequences provide strong support for the duplications giving rise to multiple vertebrate LDHs having occurred after vertebrates diverged from tunicates. The timing of these LDH duplications is consistent with data from a number of other gene families suggesting widespread gene duplication near the origin of vertebrates. With respect to the relationships among vertebrate LDHs, our data are not consistent with previous claims that Ldh-C represented the earliest divergence. However, the precise relationships among some of the main lineages of vertebrate LDHs were not resolved in our analyses.

Amino Acid Sequence↗
PubMed1997

Highly polymorphic microsatellite loci in the colonial ascidian Botryllus schlosseri.

Five mircosatellite loci are characterized for the colonial ascidian Botryllus schlosseri. Within one population from Monterey, California, these loci have 3 to 17 alleles, observed heterozygosities from 0.40 to 0.63, expected heterozygosities from 0.52 to 0.84, and an overall paternity exclusion rate (QT) of 0.78. Three of the five loci demonstrated Mendelian patterns of inheritance in laboratory crosses. The size distribution of alleles suggests that most allelic diversity within these loci is generated by single-step and less frequently multistep mutations. However, several alleles may also have been generated by single based insertions or deletions. Mutation rates for the five microsatellite loci are less than 1 x 10(-2) per generation. Because or their highly polymorphic nature, these loci should prove useful for exploring issues of identity, kinship, population structure, and phylogenetics.

Alleles↗
PubMed1997

An efficient DNA extraction method for small metazoans.

The isolation of total nucleic acids from small metazoan taxa is difficult and often leads to an unacceptably large percentage of unsuccessful polymerase chain reaction (PCR) amplifications. Our work with the evolutionary genetics of harpacticoid copepods was an incentive to refine techniques such that consistent amplifications from minute marine organisms were feasible. We describe these modifications and demonstrate their utility for the amplification of multiple loci from single harpacticoid copepods.

Animals↗
PubMed1996

Ontogeny of odorant receptor gene expression in zebrafish, Danio rerio.

We cloned three putative odorant receptor (OR) genes from the zebrafish to use as in situ hybridization probes to follow the temporal patterns of neurons expressing OR genes through a developmental progression from embryo (12 h postfertilization) to adult. The identification of these genes is supported by sequence homology to previously reported ORs and by the morphology and location of labeled cells in in situ hybridization experiments. Cells expressing OR mRNA were first observed in the olfactory placodes between 31 and 38 h after fertilization (fish reared at 26 degrees C). Initially, only single cells were observed to hybridize the probe; the number of labeled cells increased throughout the remainder of embryogenesis and through postembryonic growth and morphogenesis of the olfactory organ. At all ages, the positively hybridizing cells were scattered throughout the olfactory epithelium but not in the nonsensory epithelium of the olfactory organ.

Amino Acid Sequence↗
PubMed1995

Evolutionary relations among vertebrate muscle-type lactate dehydrogenases.

Gene duplication has produced two lactate dehydrogenase (LDH) isozymes, LDH-A and LDH-B, that are found in essentially all vertebrates. On the basis of the biochemical properties of the LDH-A and LDH-B isozymes, it has been suggested that each locus is orthologous among all vertebrates. However, phylogenetic studies have not supported a common evolutionary history among the LDH-A isozymes, particularly when those from lower vertebrates are examined. We present here the sequence of a muscle-type LDH from Fundulus heteroclitus, a teleost fish for which the LDH-B sequence has been determined and shown to be unrelated phylogenetically to tetrapod LDH-A isozymes. Although the sequence of the teleost muscle LDH shares certain features with the LDH-A of tetrapods, phylogenetic analyses do not support an orthologous relation among the LDH-A isozymes of teleost fish and tetrapod vertebrates.

Amino Acid Sequence↗
PubMed1993

Sequence analysis of teleost retina-specific lactate dehydrogenase C: evolutionary implications for the vertebrate lactate dehydrogenase gene family.

At least two gene duplication events have led to the three lactate dehydrogenase (LDH; EC 1.1.1.27) isozymes (LDH-A, LDH-B, and LDH-C) of chordates. The prevailing model for the evolution of the LDH loci involves duplication of a primordial LDH locus near the origin of vertebrates, giving rise to Ldh-A and Ldh-B. A third locus, designated Ldh-C, is expressed in the spermatocytes of mammals and a single family of birds and in the eye or liver tissues of teleost fishes. Ldh-C might have arisen independently in these taxa as duplications of either Ldh-A or Ldh-B. Several authors have challenged this traditional hypothesis on the basis of amino acid sequence and immunological similarity of the three LDH isozymes. They suggest that the primordial LDH gene was duplicated to form Ldh-C and a locus that later gave rise to Ldh-A and Ldh-B. We have differentiated between these hypotheses by determining the cDNA sequence of the retina-specific LDH-C from a teleost, Fundulus heteroclitus. On the basis of amino acid sequence similarity, we conclude that the LDH-C isozymes in fish and mammals are not orthologous but derive from independent gene duplications. Furthermore, our phylogenetic analyses support previous hypotheses that teleost Ldh-C is derived from a duplication of the Ldh-B locus.

Amino Acid Sequence↗
PubMed1992

An ancient clonal lineage in the fish genus Poeciliopsis (Atheriniformes: Poeciliidae).

Genetic diversity in mtDNA was assessed within the unisexual (all female) hybridogenetic fish Poeciliopsis monacha-occidentalis and the two sexual species from which it arose. Results confirm that P. monacha was the maternal ancestor and that paternal leakage of P. occidentalis mtDNA has not occurred. Of particular interest is the high level of de novo mutational divergence within one hybridogenetic lineage that on the basis of independent zoogeographic considerations, protein electrophoretic data, and tissue grafting analysis is of monophyletic (single hybridization) origin. Using a conventional mtDNA clock calibration, we estimate that this unisexual clade might be >100,000 generations old. Contrary to conventional belief, this result shows that some unisexual vertebrate lineages can achieve a substantial evolutionary age.

Journal Article↗
PubMed1992

Mode of origin and sources of genotypic diversity in triploid gynogenetic fish clones (Poeciliopsis: Poeciliidae).

Most tributaries of the Río Fuerte in northwestern Mexico contain one or more clones of allotriploid fish of the genus Poeciliopsis. We used multilocus allozyme genotypes and mitochondrial DNA (mtDNA) haplotypes to examine several potential modes of origin of these gynogenetic all-female fish. The allozyme studies corroborated earlier morphological work revealing the hybrid constitution of two triploid biotypes, Poeciliopsis 2 monacha-lucida and Poeciliopsis monacha-2 lucida. Each biotype carries one or two whole genomes from the each of the sexual species P. monacha and P. lucida. Restriction site analysis of mtDNA revealed that P. monacha was the maternal ancestor of five electrophoretically distinguishable triploid clones. Four of five clones were marked by closely related, composite, allozyme/mtDNA genotypes, suggesting they had common origins from an allodiploid clone of the P. monacha-lucida biotype. Genotypic analysis revealed that all five clones arose via the "genome addition" pathway. Fertilization of unreduced ova in P. monacha-lucida females by sperm from P. monacha and P. lucida males, respectively, gave rise to both biotypes.

Animals↗