Sequence variation of the ribosomal DNA second internal transcribed spacer region in two spatially-distinct populations of Amblyomma americanum (L.) (Acari: Ixodidae).

Sequence analysis of the ribosomal DNA second internal transcribed spacer (ITS 2) region in 2 spatially distinct populations of Amblyomma americanum (L.) revealed intraspecific variation. Nucleotide sequences from multiple DNA extractions and several polymerase chain reaction amplifications of eggs from mixed-parentage samples from both populations of ticks revealed that 12 of 1,145 (1.0%) sites varied. Three of the 12 sites of variation were distinct between the 2 A. americanum populations, which corresponded to a rate of 0.26%. Phylogenetic analysis based on ITS 2 sequences provided strong support (i.e., bootstrap value of 80%) that wild A. americanum clustered into a distinguishable group separate from those derived from colony ticks.

Genetic diversity of the major histocompatibility complex of cotton rats (Sigmodon hispidus) inhabiting an oil refinery complex.

We examined genetic diversity of an immune-response gene within the major histocompatibility complex in cotton rats (Sigmodon hispidus) inhabiting an oil refinery complex. Genetic diversity of MHC-DQA exon-2 was examined within and among contaminated and noncontaminated reference grids. The level of gene diversity within contaminated grids (0.748) was lower than within reference grids (0.818), but the difference was not statistically significant (p > 0.5). Analysis of molecular variance, pairwise FST values, and hierarchical clustering failed to reveal population genetic structure related to contamination. Results of this study indicate either that the level of contaminant-induced selection is insignificant at this major histocompatibility complex (MHC) locus or that gene flow from surrounding areas has obliterated the effects of selection.

Population genetics of the hispid cotton rat (Sigmodon hispidus): patterns of genetic diversity at the major histocompatibility complex.

The hispid cotton rat, Sigmodon hispidus, is a common rodent widely distributed across the southern USA and south into South America. To characterize major histocompatibility complex (MHC) diversity in this species and to elucidate large-scale patterns of genetic partitioning, we examined MHC genetic variability within and among 13 localities, including a disjunct population in Arizona and a population from Costa Rica that may represent an undescribed species. We also tested the hypothesis that populations within the USA are at equilibrium with regard to gene flow and genetic drift, resulting in isolation-by-distance. Using single-strand conformation polymorphism (SSCP) analysis we identified 25 alleles from 246 individuals. Gene diversity within populations ranged from 0.000 to 0.908. Analysis of molecular variance (AMOVA) revealed that 83.7% of observed variation was accounted for by within-population diversity and 16.3% was accounted for by among-population divergence. The disjunct population in Arizona was fixed for a single allele. The Costa Rican population was quite divergent based on allelic composition and was the only population with unique alleles. Within the main portion of the geographical distribution of S. hispidus in the USA there was considerable divergence among some populations; however, there was no significant pattern of isolation-by-distance overall (P = 0.090). Based on the significant divergence of the only sampled population to its east, the Mississippi River appears to represent a substantial barrier to gene flow.

Molecular phylogeny and biogeography of North American isolates of Anaplasma marginale (Rickettsiaceae: Ehrlichieae).

Anaplasma marginale (A. marginale) is a tick-borne ehrlichial pathogen of cattle that causes the disease anaplasmosis. Six major surface proteins (MSPs) have been identified on A. marginale from cattle and ticks of which three, MSP1a, MSP4 and MSP5, are from single genes and do not vary within isolates. The other three, MSP1b, MSP2 and MSP3, are from multigene families and may vary antigenically in persistently infected cattle. Several geographic isolates have been identified in the United States which differ in morphology, protein sequence and antigenic properties. An identifying characteristic of A. marginale isolates is the molecular weight of MSP1a which varies in size among isolates due to different numbers of tandemly repeated 28-29 amino acid peptides. For these studies, genes coding for A. marginale MSP1a and MSP4, msp1alpha and msp4, respectively, from nine North American isolates were sequenced for phylogenetic analysis. The phylogenetic analysis strongly supports the existence of a south-eastern clade of A. marginale comprised of Virginia and Florida isolates. Analysis of 16S rDNA fragment sequences from the A. marginale tick vector, Dermacentor variabilis, from various areas of the United States was used to evaluate possible vector-parasite co-evolution. Our phylogenetic analysis supports identity between the most parsimonious tree from the A. marginale MSP gene data and the tree that reflected the western and eastern clades of D. variabilis. These phylogenetic analyses provide information that may be important to consider when developing control strategies for anaplasmosis in the United States.

Major-histocompatibility-complex-associated variation in secondary sexual traits of white-tailed deer (Odocoileus virginianus): evidence for good-genes advertisement.

Good-genes hypotheses predict that development of secondary sexual characters can be an honest advertisement of heritable male quality. We explored this hypothesis using a cervid model (adult, male white-tailed deer, Odocoileus virginianus) to determine whether antler development could provide an honest signal of a male's genetic quality and condition to adversaries. We compared antler, morphometric, hormonal, and parasitic data collected from hunter-harvested deer to characteristics of the Mhc-DRB (Odvi), the most widely studied gene of the major histocompatibility complex (MHC) in Artiodactyla. We detected associations between genetic characteristics at Odvi-DRB and antler development and body mass, suggesting that antler development and body mass may be associated with pathogen resistance in deer and thus may be an honest signal of genetic quality. We also detected associations between Odvi-DRB characteristics and serum testosterone during the breeding season, suggesting that certain MHC characteristics may help deer cope with stresses related to breeding activity. In addition, we observed a negative relationship between degree of antler development and overall abundance of abomasal helminths. Our observations provide support for the hypothesis that antler development in white-tailed deer is an honest signal of quality.

Phylogenetic relationships of Hepatozoon (Apicomplexa: Adeleorina) based on molecular, morphologic, and life-cycle characters.

To evaluate higher-level affinities of Hepatozoon species within Apicomplexa, we sequenced the 18S rRNA gene from 2 parasites (Hepatozoon americanum and Hepatozoon canis) of dogs and 1 (Hepatozoon catesbianae) of bullfrogs. Sequences from other apicomplexans among the Sarcocystiidae, Eimeriidae, Theileriidae, Plasmodiidae, Cryptosporiidae, and Babesiidae, a Perkinsus species and 2 dinoflagellates were obtained from GenBank. Phylogenetic analysis indicated that Plasmodium, Cryptosporidium, and Hepatozoon form a monophyletic group distinct from representatives of other apicomplexan families. Although equivocal, our analysis indicated that Plasmodium and Cryptosporidium are sister taxa and that Hepatozoon is basal to them. To evaluate phylogenetic affinities among H. americanum, H. canis, and other species of Hepatozoon, we examined 18 morphologic and life-cycle features of 13 species currently assigned to Hepatozoon. This analysis indicates paraphyly of Hepatozoon (as currently arranged) because Hepatozoon lygosomarum was found most closely related to Hemolivia mauritanicum. These results, combined with results of previous studies, support elevating Hepatozoon to familial level (Hepatozoidae) as originally suggested by Wenyon in 1926. Both DNA sequence data and morphologic and life-cycle characters support a sister-group relationship between H. americanum and H. canis.

Characterization of histone H3/H4 gene region and phylogenetic affinity of Ichthyophthirius multifiliis based on H4 DNA sequence variation.

We sequenced the amino-terminal third of the histone H3 and H4 genes and the intergenic region from Ichthyophthirius multifiliis. Fourteen recombinant clones of 646 bp were sequenced and the level of sequence variation detected among these clones was similar to that reported among closely related species of Tetrahymena and to levels of sequence variation detected within other ciliates. The intergenic region is 417 bp and approximately 92% AT rich, making it the longest and most AT-rich ciliate H3/H4 intergenic region yet identified. Similar to Tetrahymena, the intergenic region of Ichthyophthirius contains two CCAAT regions arranged in a complementary orientation. A neighbor-joining tree was constructed based on nucleotide sequence variation among H4 genes to evaluate evolutionary relationships within and among six classes of Ciliophora. The single shortest neighbor-joining tree depicted a sister-group relationship of Ichthyophthirius with taxa of Tetrahymenina, thereby supporting monophyly of Oligohymenophorea.

Allelic diversity at the Mhc-DQA locus in cotton rats (Sigmodon hispidus) and a comparison of DQA sequences within the family muridae (Mammalia: Rodentia).

The cotton rat (Sigmodon hispidus) is a common murid rodent of the southern United States, Mexico, and Central America. Using single-stranded conformation polymorphism analysis and DNA sequencing techniques, 11 DQA exon 2 alleles were detected among 180 S. hispidus from Caddo County, Oklahoma, USA. The alleles represent a single locus exhibiting a high level of polymorphism. Nucleotide and amino acid distance values among DQA alleles of S. hispidus were higher than those within Mus musculus and species of Rattus. Although the distribution of polymorphic amino acid residues among alleles of S. hispidus was similiar to that of Mus and Rattus, some residues of the alpha-helix region were more variable in S. hispidus. Comparisons of nonsynonymous and synonymous substitutions indicated a trend toward higher numbers of nonsynonymous substitutions; however, this difference was not significant statistically among S. hispidus alleles. To examine evolution of DQA alleles within Muridae, we performed a phylogenetic analysis that included DQA alleles from S. hispidus, Peromyscus leucopus, M. musculus, R. norvegicus, and six Australian species of Rattus. Results depicted monophyly for each genus, and this concordance between species and gene trees represents a lack of evidence for trans-species persistence of alleles among these genera.

Characterization of Mhc-DRB allelic diversity in white-tailed deer (Odocoileus virginianus) provides insight into Mhc-DRB allelic evolution within Cervidae.

Although white-tailed deer (Odocoileus virginianus) are one of North America's best studied mammals, no information is available concerning allelic diversity at any locus of the major histocompatibility complex in this taxon. Using the polymerase chain reaction, single-stranded conformation polymorphism analysis, and DNA sequencing techniques, 15 DRB exon 2 alleles were identified among 150 white-tailed deer from a single population in southeastern Oklahoma. These alleles represent a single locus and exhibit a high degree of nucleotide and amino acid polymorphism, with most amino acid variation occurring at positions forming the peptide binding sites. Furthermore, twenty-seven amino acid residues unique to white-tailed deer DRB alleles were detected, with 19 of these occurring at residues forming contact points of the peptide binding region. Significantly higher rates of nonsynonymous than synonymous substitutions were detected among these DRB alleles. In contrast to other studies of Artiodactyla DRB sequences, interallelic recombination does not appear to be playing a significant role in the generation of allelic diversity at this locus in white-tailed deer. To examine evolution of white-tailed deer (Odvi-DRB) alleles within Cervidae, we performed a phylogenetic analysis of all published red deer (Ceel-DRB), roe deer (Caca-DRB), and moose (Alal-DRB) DRB alleles. The phylogenetic tree clearly shows a trans-species persistence of DRB lineages among these taxa. Moreover, this phylogenetic tree provides insight into evolution of DRB allelic lineages within Cervidae and may aid in assignment of red deer DRB alleles to specific loci.

Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis.

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994, Curr. Biol. 4:277-280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's "flying DNA" hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the "flying DNA" hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.

DNA synapomorphies for a variety of taxonomic levels from a cosmid library from the New World bat Macrotus waterhousii.

An effective method yielding taxon-specific markers from the genome of a single individual would be valuable for many types of scientific investigations, including systematic, forensic, conservation, and evolutionary studies. We explored the use of cosmid libraries, with insert sizes averaging 35 kb, to streamline the process of locating sequences of DNA that can serve as taxonomic markers from the specific to the ordinal levels. By screening approximately 2.6% of the leaf-nosed bat (Macrotus waterhousii) genome, we identified several potential DNA fragments that appear to be synapomorphic for a variety of taxonomic levels. A more thorough analysis of the markers documented that 17 Macrotus-specific clones represent three distinct DNA generic markers, whereas 30 microchiropteran clones represent multiple copies of a single family of repetitive DNA. The Microchiroptera taxon markers hybridize with representatives of most of the Microchiroptera families; however, no hybridization was detected for members of the superfamily Rhinolophoidea. These results demonstrate that cosmid libraries can be a valuable source for isolating taxon-specific markers from mammals even when the insert size is as large as 35 kb.

High levels of genetic change in rodents of Chernobyl.

Base-pair substitution rates for the mitochondrial cytochrome beta gene of free-living, native populations of voles collected next to reactor 4 at Chernobyl, Ukraine, were estimated by two independent methods to be in excess of 10(-4) nucleotides per site per generation. These estimates are hundreds of times greater than those typically found in mitochondria of vertebrates, suggesting that the environment resulting from this nuclear power plant disaster is having a measurable genetic impact on the organisms of that region. Despite these DNA changes, vole populations thrive and reproduce in the radioactive regions around the Chernobyl reactor.

Retrotransposon Mys was active during evolution of the Peromyscus leucopus-maniculatus complex.

Mys is a retrovirus-like transposable element found throughout the genus Peromyscus. Several mys subfamilies identified on the basis of restriction site variation occur in more than one species. The distribution of these subfamilies is consistent with the accepted species phylogeny, suggesting that mys was present in the ancestor of Peromyscus and has been active through much of the evolution of this genus. Quantitative Southern blot analysis was used to examine the variability of subfamilies in P. leucopus and maniculatus. We found that subfamilies with phylogenetically narrow distributions were more variable in copy number both within and between species than subfamilies with a broader distribution. Taken together, our data suggest that mys has undergone multiple rounds of transposition since the peromyscine radiation, and that five subfamilies have been amplified during the evolution of the leucopus-maniculatus species complex.

How bats achieve a small C-value: frequency of repetitive DNA in Macrotus.

Bats possess a genome approximately 50-87% the size of other eutherian mammals. We document that the events that have achieved or maintained a small genome size in the Mexican leaf-nosed bat Macrotus waterhousii have resulted in a lower copy number of interspersed and tandemly repetitive elements. These conclusions are based on examination of 1726 randomly chosen recombinant cosmids, with an average insert size of 35.7 kb and representing 2.6% of the haploid genome of M. waterhousii. Probes representative of microsatellites [(GT)n, (CT)n, (AT)n, (GC)n] and a tandem repeat (rDNA) were used to estimate frequency of repetitive elements in the M. waterhousii genome. Of the four dinucleotides, (GT)n was present in 33.5% of the clones, (CT)n was present in 31.0% of the clones, and (AT)n and (GC)n were not represented in any of the clones examined. The 28S rDNA and a repetitive element from M. californicus were found in three and four clones, respectively. The dinucleotides (GT)n and (CT)n occurred together in the same clone more frequently than expected from chance. Although our data do not allow us to empirically test which mechanisms are maintaining copy number of repetitive DNA in the bat genome, the nonrandom association of these different families of repetitive DNA may provide insight into a mechanism that proportionately reduces diverse families of repetitive DNA that are known to be amplified by very different mechanisms.

Unusual pattern of bacterial ice nucleation gene evolution.

Bacterial ice nucleation activity (INA+ phenotype) can be traced to the product of a single gene, ina. A remarkably sparse distribution of this phenotype within three bacterial genera indicates that the ina gene may have followed an unusual evolutionary path. Southern blot analyses, coupled with assays for ice-nucleating ability, revealed that within four bacterial species an ina gene is present in some strains but absent from others. Results of hybridization experiments using DNA fragments that flank the ina gene suggested that the genotypic dimorphism of ina may be anomalous. A phylogenetic analysis of 16S ribosomal RNA gene sequences from a total of 14 ina+ and ina- bacterial strains indicated that the ina+ bacteria are not monophyletic but instead phylogenetically interspersed among ina- bacteria. The relationships of ina+ bacteria inferred from ina sequence did not coincide with those inferred from the 16S data. These results suggest the possibility of horizontal transfer in the evolution of bacterial ina genes.

Molecular evolution of the staphylococcal and streptococcal pyrogenic toxin gene family.

The pyrogenic toxin (PT) family is composed of the staphylococcal enterotoxins (SE), the toxic shock syndrome toxin, and the streptococcal pyrogenic exotoxins (SPE). Whereas considerable effort has focused on characterization of PTs due to their unique biological properties, our understanding of the evolution of this gene family is incomplete. Phylogenetic relationships for members of the PT family were estimated by examining the previously reported nucleotide sequences of the genes encoding SPEA, SPEC, SEA, SEB, SEC1, SEC2, SEC3, SED, and SEE. Additionally, we present and analyze sequence data on seven previously unreported sec genes. Within the PT family, sequence divergence was partitioned in a hierarchical fashion such that mean sequence divergence ranged from 1.179 among all 16 toxin genes, 0.443 among those restricted to Staphylococcus, and 0.028 among the genes encoding 10 variants of Type C SE. Results of this study are interpreted as suggesting that the PT family consists of two large clades. One clade consists of the staphylococcal toxins SEA, SEE, and SED, being closely related to the streptococcal toxin SPEC, whereas the other clade depicts close relationships of the staphylococcal toxins SEC and SEB with the streptococcal toxin SPEA.

Molecular phylogenetics of Stenodermatini bat genera: congruence of data from nuclear and mitochondrial DNA.

Within the tribe Stenodermatini the systematics of the complex of species allied with the genus Artibeus has generated several alternative phylogenetic hypotheses. The most recent treatment recognized four genera (Artibeus, Dermanura, Enchisthenes, and Koopmania) and suggested that the most recent common ancestor of these four genera would include the common ancestor of all other currently recognized Stenodermatini genera except Sturnira. To test this hypothesis, we examined an EcoRI-defined nuclear satellite DNA repeat and 402 bp of DNA sequence variation from the mitochondrial cytochrome b gene. Phylogenetic conclusions based on Southern blot analyses, in situ hybridization, and mitochondrial DNA sequence data indicate that Enchisthenes is not closely related to Dermanura, Artibeus, or Koopmania and that Dermanura, Artibeus, and Koopmania shared a common ancestor after diverging from the remainder of the Stenodermatini. If our conclusions are correct, then justification for recognizing Dermanura and Koopmania as generically distinct from Artibeus must be based on the magnitude of difference that distinguishes each rather than on the conclusion that to place them as congeneric with Artibeus creates a paraphyletic taxon.

In search of retrotransposons: exploring the potential of the PCR.

A rapid and universal procedure for isolating reverse transcriptase encoding elements from diverse mammalian genomes using PCR is described. We have designed short, degenerate primers to conserved amino acid domains of retroviral reverse transcriptase. These primers amplify a region, predicted to be 342-396 base pairs for most mammalian retroviruses, that spans several conserved domains of reverse transcriptase. The region encoded by the amplified PCR product contains a number of highly conserved amino acids that aid in identification of either degenerate reverse transcriptase or reverse transcriptase from new, undescribed elements. Additionally, these primers allow the amplification of a piece of DNA large enough to be used for phylogenetic analysis. The primers have been used successfully to isolate a region of three related reverse transcriptases from two mammalian taxa. The generality of this approach is discussed.