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Molecular species identification methods are an important component of CITES monitoring programs for trade in sturgeon and caviar. To date, obtaining molecular evidence for distinguishing caviar from four closely related Eurasian sturgeon species Acipenser baerii(Siberian sturgeon), A. gueldenstaedtii(osetra), A. persicus(Persian sturgeon), A. naccarii(Italian sturgeon) remains problematic. Using approximately 2.3 kb of mtDNA sequence data (cytochrome b, NADH5, control region), we find this to be attributable to the polyphyletic nature of these mitochondrial DNA markers in the Russian sturgeon, A. gueldenstaedtii. Two mitochondrial lineages are present within this species: one is phylogenetically affiliated with A. persicusand A. naccarii, while the other clusters with A. baerii. These findings have a direct impact on molecular testing of commercial caviar and demonstrate the necessity of using large sample sizes when constructing forensic databases. Furthermore, the results affect current taxonomic designations for these species as well as hypotheses concerning their evolutionary origins.

The evolutionary history of cnidarian life cycles has been debated since the 1880s, with different hypotheses favored even by current textbooks. Contributing to the disagreement is the fact that the systematic relationships of the four cnidarian classes have received relatively little examination using modern systematic methods. Here we present analyses of class-level relationships based on 18S ribosomal DNA (rDNA) sequence, mitochondrial 16S rDNA sequence, mitochondrial genome structure, and morphological characters. DNA sequences were aligned using a repeatable parsimony-based approach incorporating a range of alignment parameters. Analyses of individual data sets and of all data combined are unanimous in grouping the classes possessing a medusa stage, leaving the holobenthic Anthozoa basal within the phylum.

Sequence divergence in the internal transcribed spacer region 1 (ITS-1) of the ribosomal DNA locus was assessed in subspecies of the coastal North American tiger beetle, Cicindela dorsalis. The spacer region was amplified using the polymerase chain reaction and cloned for sequencing. Of a total of 50 clones obtained from 12 specimens, 42 clones were different in at least one nucleotide position. In a parsimony analysis of these sequences, the main phylogenetic distinction was found to separate sequences from the Gulf of Mexico and the Atlantic Ocean. Within these two assemblages phylogenetic resolution was low, and the variation within individuals was almost as high as the variation within the entire lineage. The pattern of sequence variation suggests the existence of two forms of the ITS-1 that are maintained on different chromosomes. Polymorphisms of limited geographical distribution could be detected, and 41 additional clones were partly sequenced, to assess the geographic distribution of these polymorphisms in more detail. In a population aggregation analysis, the geographic pattern of ITS-1 distribution was basically congruent with that obtained in earlier studies from mitochondrial DNA in the same C. dorsalis populations.

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.

The origins and times of divergence of the speciose Hawaiian Drosophilidae are examined using mtDNA sequences. The Hawaiian Drosophilidae are resolved as the sister group to the subgenus Drosophila. No one member of the subgenus Drosophila could be determined to be more closely related to the Hawaiian Drosophilidae than could any other. This result suggests that the Hawaiian Drosophilidae arose before the diversification of the subgenus Drosophila and after the divergence of the subgenus Sophophora. In light of fossil evidence, this phylogenetic scenario suggests that the Hawaiian Drosophilidae lineages are no younger than 30 Myr.

We report nuclear small-subunit rDNA sequences for two species of the benthic foraminifer Ammonia. Because of their abundance in present and past seas, the foraminifera are a very important group of organisms used in a wide range of geologic studies; however, the ancestry of this group was, until now, unknown. Difficulties in purifying foraminiferal DNA and avoiding PCR contamination led us to develop DNA.DNA in situ hybridization techniques to verify our sequence data. Phylogenetic analysis of verified foraminiferal DNA sequence indicates these taxa are a divergent, "alveolate" lineage, within the major eukaryotic radiation. Our findings cast doubt upon the assumption that all foraminifera are derived from an amoebalike ancestor. Cytological features and the DNA sequences presented herein suggest that the foraminifera were derived from a heterokaryotic flagellated marine protist, probably sometime in the later Proterozoic.

Abstract The proliferation of molecular data in systematics has opened a Pandora's box of alternate approaches to inferring hierarchical patterns of relationship among taxa. In this review, we examine practical and theoretical reasons for employing some methods and avoiding others. We offer a philosophical overview of the relationship between systematics patterns and evolutionary processes, and we discuss the differential emphasis given to each of these areas by opposing methodological camps. We review the sources and types of incongruence between data partitions from different sources and recommend a specific procedure for contending with incongruence. We then focus on inference of relationships among closely related taxa, with particular emphasis on mtDNA as a source of characters, its advantages and potential pitfalls. We conclude with a review of several widely cited empirical studies and suggest that the gene tree-species tree problem may be less severe than its prevalence in the literature would suggest.

Genetic, morphological, and behavioral analyses have been used to examine the evolutionary dynamics and phylogeny of the rare Hawaiian Drosophila species, D. silvestris. Critical to understanding the evolution of this species is the examination of the distribution of populations of D. silvestris on the Big Island of Hawaii. Behavioral analysis using mating asymmetries and the Kaneshiro hypothesis as an indicator of ancestral behavioral state has suggested that flies from the northern part of the island are ancestral to those on the southern part of the island. Consequently, a sequential pattern of colonization going from north to south is predicted for these flies on the east side of the Island of Hawaii. We have examined this prediction using mitochondrial DNA (mtDNA) restriction site analysis with four-base cutters and DNA sequencing. The resulting mtDNA phylogeny based on 23 phylogenetically informative restriction sites and two phylogenetically informative DNA sequence characters agrees in part with the phylogeny predicted from the behavioral data.

Drosophila differens, endemic to Molokai, Drosophila planitibia of Maui, and Drosophila silvestris and Drosophila heteroneura from the island of Hawaii are chromosomally homosequential species that presumably have colonized the newer islands of the Hawaiian archipelago by sequential founder events. We have examined the phylogenetic relationships of these four species by using mitochondrial DNA restriction site data for 23 enzymes. Both distance and character-state analyses indicate that a sequential or monotonic branching relationship exists for mtDNA restriction site data from the four species. The mtDNA data suggest that the maternal lineage that gave rise to D. differens is ancestral to the D. planitibia maternal lineage, which in turn shares the most recent common ancestor with the D. silvestris and D. heteroneura maternal lineages [with Drosophila hemipeza (Oahu) and Drosophila neopicta (Molokai and Maui) as outside references]. We also discuss the phylogenetic implications of the mtDNA data in comparison with other sources of phylogenetic data. We conclude that hybridization of the species in this group has been an important factor in the evolution of the nuclear genomes. Because of small population sizes and mating asymmetries, it is possible that the nuclear genetic distance of species that are physically capable of hybridizing (e.g., on the same island or island complex) is depressed. Consequently the mtDNA genetic distance appears to be more sensitive in establishing the sequence of evolutionary events responsible for the present distribution and population structure of these species.

We used the polymerase chain reaction (PCR) to amplify, clone, and sequence 10 engrailedhomeodomains from 8 species in the five major molluscan classes, including the serially organized chiton (Polyplacophora) lineage. The Drosophila melanogastergene engrailed(en) is one of several genes involved in embyonic segment polarity determination. Studies of engrailedsequence and expression in molluscs are of interest due to questions regarding the evolution and homology of segmentation in these taxa. Nucleotide and deduced amino acid sequence comparisons reflect evolutionary conservation within helices of the enhomeodomain and ancient divergences in the region 3′ to the homeodomain.

DNA from 30-million-year-old amber preserved termites (Mastotermes electrodominicus) was PCR amplified with nuclear ribosomal RNA small subunit primers and cloned into the TA vector (INVITROGEN). We obtained several classes of recombinant clones as a result. AuthenticMastotermes electrodominicus clones were identified. The source of other classes of clones was identified as contaminants of the ancient DNA template. Several of the clones appeared to be chimeric in structure with half of the clone identical to the termite sequence and the other half identical to contaminant sequences. The phenomenon of PCR jumping was identified as a possible source for the chimeric clones.

The utility of DNA sequence characters from fossil specimens is examined from a phylogenetic perspective. Four ways that fossil characters can alter phylogenetic hypotheses are discussed. Two empirical examples and a third hypothetical example concerning amber-preserved insects are presented to illustrate these phenomena. Fossil DNA sequences as characters will be affected by the problem of missing data and missing taxa. In general, cladogram accuracy will be more greatly affected by missing taxa and cladogram resolution will be affected more acutely by missing data. Due to these points, an examination of the importance of the phylogenetic question being addressed, the utility of the fossil DNA sequences and the rarity of the fossil should be considered before damage of a fossil is undertaken.

rDNA nontranscribed spacer (NTS) lengths of Drosophila mercatorum have been measured in individuals from several geographic regions. Individuals from the different geographic subpopulations share some length fragments but are in general distinct. The length differences, both within and between individuals, arise from different copy numbers of a 250-bp repeating unit that is localized to one part of the NTS. In addition to the length differences caused by the 250-bp repeat, there is a Y chromosome (male)-specific length variant elsewhere in the NTS that is approximately 70 bp shorter than the NTS fragment from the X chromosome. Sexual dimorphism seems to be present in all Drosophila. Also, D. mercatorum has fewer NTS length variants per individual than does D. melanogaster while possessing comparable levels of restriction-site polymorphism. The mechanisms that may cause this pattern of variation are selection, gene conversion, and unequal recombination.

The phylogenetic relationships of the Recent cnidarian classes remain one of the classic problems in invertebrate zoology. We survey the structure of the mitochondrial genome in representatives of the four extant cnidarian classes and in the phylum Ctenophora. We find that all anthozoan species tested possess mtDNA in the form of circular molecules, whereas all scyphozoan, cubozoan, and hydrozoan species tested display mtDNA in the form of linear molecules. Because ctenophore and all other known metazoan mtDNA is circular, the shared occurrence of linear mtDNA in three of the four cnidarian classes suggests a basal position for the Anthozoa within the phylum.

The subfamily Serrasalminae (Characidae, Teleostei) is an endemic Neotropical group of fishes distributed along the Amazon, Paraná-Paraguay and Orinoco Basins. The pacu (Piaractus mesopotamicus) is found in all major rivers that comprise the Pantanal of Mato Grosso. In order to investigate population genetic structure within the group, an enriched microsatellite library was constructed. Eight polymorphic were loci screened, with an average of 6.5 alleles per locus. Five loci exhibited greater than 60% heterozygosity. Additionally, a high level of cross-species amplification was obtained.

Microsatellite loci were isolated within the St Vincent parrot (Amazona guildingii), an endangered island endemic, from a GTnenriched genomic library. Nine polymorphic loci were characterized varying from two to nine alleles per locus. Seven loci exhibited levels of heterozygosity ranging from 39 to 100% within the 28 individuals genotyped. Furthermore, the primers were demonstrated to cross-amplify within four genera of Neotropical parrots, indicating the potential utility of these markers to further population-level studies and conservation efforts of New World Psittacines.

Two kinds of characters of reduncine antelopes were analyzed cladistically: (1) quantitative osteological characters treated allometrically to remove the effects of body weight and (2) discretely coded characters. Character congruence was tested by combined cladistic analysis of all the data. We analyzed reduncine ontogeny and addressed the general question of how cladistics can be used together with ontogenetic information to study heterochrony. We tested whether characters of waterbuck evolved by paedomorphosis within the genus Kobus or whether these characters are plesiomorphic retentions. The plesiomorphic hypothesis was falsified and the paedomorphosis hypothesis was supported.