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J E Neigel

Publications and source records attributed to J E Neigel.

8 recordsLinked to original sources
PubMed2002

Genetic, ecological, and behavioural divergence between two sibling snapping shrimp species (Crustacea: Decapoda: Alpheus).

Examination of genetic and ecological relationships within sibling species complexes can provide insights into species diversity and speciation processes. Alpheus angulatus and A. armillatus, two snapping shrimp species with overlapping ranges in the north-western Atlantic, are similar in morphology, exploit similar ecological niches and appear to represent recently diverged sibling species. We examined phylogenetic and ecological relationships between these two species with: (i) sequence data from two mitochondrial genes (16S rRNA and COI); (ii) data on potential differences in microhabitat distribution for A. armillatus and A. angulatus; and (iii) data from laboratory experiments on the level of reproductive isolation between the two species. DNA sequence data suggest A. armillatus and A. angulatus are sister species that diverged subsequent to the close of the Isthmus of Panama, and that haplotype diversity is lower in A. armillatus than in A. angulatus. Both species are distantly related to A. heterochaelis and A. estuariensis, two species with which A. angulatus shares some similarities in coloration. Ecological data on the distribution of A. angulatus and A. armillatus from two locations revealed differences in distribution of the two species between habitat patches, with each patch dominated by one or the other species. However, there was no apparent difference in distribution of the two species within habitat patches with respect to microhabitat location. Ecological data also revealed that heterospecific individuals often occur in close proximity (i.e. within metres or centimetres) where sympatric. Behavioural data indicated that these species are reproductively isolated, which is consistent with speciation in transient allopatry followed by post-divergence secondary contact. Our data further resolve taxonomic confusion between the sibling species, A. armillatus and A. angulatus, and suggest that sympatry in areas of range overlap and exploitation of similar ecological niches by these two recently diverged species have selected for high levels of behavioural incompatibility.

Animals↗
PubMed2000

Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks.

Evolutionary and conservation biologists often use molecular markers to evaluate whether populations have experienced demographic bottlenecks that resulted in a loss of genetic variation. We evaluated the utility of microsatellites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experimental mesocosms, we established replicate populations by releasing 1, 2, 4 or 8 pairs of the western mosquitofish, Gambusia affinis (Poeciliidae). Using eight polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demographic bottlenecks on populations. We compared indices for the experimentally bottlenecked populations to those for the source population and examined differences between populations established with different numbers of founders. Direct count heterozygosity and the proportion of polymorphic loci were not very sensitive to genetic changes that resulted from the experimental bottlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and temporal variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was slightly more correlated with bottleneck size than was allelic diversity. Based on comparisons to a previous study with allozymes, heterozygosity, temporal variance in allele frequencies and allelic diversity, but not proportion of polymorphic loci, appear to be more sensitive to demographic bottlenecks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottleneck and to obtain an estimate of the magnitude of bottleneck severity.

Animals↗
PubMed1997

A large-subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genome of two stone crabs (Menippe).

Two DNA sequences that appear to be homologous to large-subunit mitochondrial ribosomal RNA genes have been identified in the stone crabs Menippe mercenaria and M. adina. Amplification from whole genomic DNA by polymerase chain reaction (PCR) with oligonucleotide primers based on conserved portions of large-subunit mitochondrial rRNA genes consistently amplified two products of similar length (565 and 567 bp). These products differed at 3% of their nucleotide bases, and could be distinguished by a HindIII site. Only one of these sequences (designated the A sequence) was detected by PCR in purified mitochondrial DNA. The other (designated the B sequence) hybridized to total genomic DNA at a level consistent with a nuclear genome location. It is unlikely that the type B product would have been recognized as a nuclear copy by examination of its sequence alone. This is the first report of a mitochondrial gene sequence translocated into the nuclear genome of a crustacean.

Animals↗
PubMed1993

Application of a random walk model to geographic distributions of animal mitochondrial DNA variation.

In rapidly evolving molecules, such as animal mitochondrial DNA, mutations that delineate specific lineages may not be dispersed at sufficient rates to attain an equilibrium between genetic drift and gene flow. Here we predict conditions that lead to nonequilibrium geographic distributions of mtDNA lineages, test the robustness of these predictions and examine mtDNA data sets for consistency with our model. Under a simple isolation by distance model, the variance of an mtDNA lineage's geographic distribution is expected be proportional to its age. Simulation results indicated that this relationship is fairly robust. Analysis of mtDNA data from natural populations revealed three qualitative distributional patterns: (1) significant departure of lineage structure from equilibrium geographic distributions, a pattern exhibited in three rodent species with limited dispersal; (2) nonsignificant departure from equilibrium expectations, exhibited by two avian and two marine fish species with potentials for relatively long-distance dispersal; and (3) a progression from nonequilibrium distributions for younger lineages to equilibrium distributions for older lineages, a condition displayed by one surveyed avian species. These results demonstrate the advantages of considering mutation and genealogy in the interpretation of mtDNA geographic variation.

Animals↗
PubMed1993

Genomic and transcriptional linkage of the genes for calmodulin, EF-hand 5 protein, and ubiquitin extension protein 52 in Trypanosoma brucei.

We report genomic linkage of a pair of tandem, identical ubiquitin-extension protein 52 (EP52) genes, a novel EF-hand superfamily member gene (EFH5), and the calmodulin gene cluster in Trypanosoma brucei. The intergenic regions of these four genes are short: about 108 bp between the calmodulin gene C and the EFH5 gene, about 111 bp between the EFH5 gene and the ubiquitin-EP52/1 gene, and about 116 bp between the ubiquitin-EP52/1 and -EP52/2 genes. RNA molecules that span these three intergenic regions have been detected by polymerase chain reaction, which suggests that the genes are transcribed in a polycistronic manner. Transcription of the calmodulin, EFH5, and ubiquitin-EP52 genes in isolated nuclei is rapidly inactivated by UV irradiation, which further strengthens the hypothesis that this cluster of three different genes is transcribed in a polycistronic manner and suggests that they are under the control of a single distant upstream promoter. These results suggest that polycistronic transcription is common in trypanosomes and will probably be found for most, if not all, protein-encoding genes. The presence of at least three housekeeping genes with different known or potential regulatory functions within a polycistronic unit suggests that regulation of transcription initiation plays an important role in the coordinated expression of housekeeping genes in trypanosomes.

Amanitins↗
PubMed1984

Demographic influences on mitochondrial DNA lineage survivorship in animal populations.

Probability models of branching processes and computer simulations of these models are used to examine stochastic survivorship of female lineages under a variety of demographic scenarios. A parameter II, defined as the probability of survival of two or more independent lineages over G generations, is monitored as a function of founding size of a population, population size at carrying capacity, and the frequency distributions of surviving progeny. Stochastic lineage extinction can be very rapid under certain biologically plausible demographic conditions. For stable-sized populations initiated by n females and/or regulated about carrying capacity k = n, it is highly probable that within about 4n generations all descendants will trace their ancestries to a single founder female. For a given mean family size, increased variance decreases lineage survivorship. In expanding populations, however, lineage extinction is dramatically slowed, and the final k value is a far more important determinant of II than is the size of the population at founding. The results are discussed in the context of recent empirical observations of low mitochondrial DNA (mtDNA) sequence heterogeneity in humans and expected distributions of asexually transmitted traits among sexually reproducing species.

Animals↗
PubMedDate not supplied

A prototype object database for mitochondrial DNA variation.

Surveys of biochemical and molecular genetic variation in natural populations have generated a wealth of data, but this valuable resource has not been adequately preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype for animal mitochondrial DNA (mtDNA) surveys. This prototype includes the specification of a format for data files that are to be submitted to the database, an open-source object database that encapsulates data with methods to display and analyze data, and a website where data can be retrieved in either its original form or extensible markup language (XML). Data from more than 50 published surveys of mtDNA variation were retrieved from the literature and entered into the database. We hope that the population genetics community will support this project by contributing both data and expertise.

Animals↗