Observed trends of soil fauna in the Antarctic Dry Valleys: early signs of shifts predicted under climate change.

Long-term observations of ecological communities are necessary for generating and testing predictions of ecosystem responses to climate change. We investigated temporal trends and spatial patterns of soil fauna along similar environmental gradients in three sites of the McMurdo Dry Valleys, Antarctica, spanning two distinct climatic phases: a decadal cooling trend from the early 1990s through the austral summer of February 2001, followed by a shift to the current trend of warming summers and more frequent discrete warming events. After February 2001, we observed a decline in the dominant species (the nematode Scottnema lindsayae) and increased abundance and expanded distribution of less common taxa (rotifers, tardigrades, and other nematode species). Such diverging responses have resulted in slightly greater evenness and spatial homogeneity of taxa. However, total abundance of soil fauna appears to be declining, as positive trends of the less common species so far have not compensated for the declining numbers of the dominant species. Interannual variation in the proportion of juveniles in the dominant species was consistent across sites, whereas trends in abundance varied more. Structural equation modeling supports the hypothesis that the observed biological trends arose from dissimilar responses by dominant and less common species to pulses of water availability resulting from enhanced ice melt. No direct effects of mean summer temperature were found, but there is evidence of indirect effects via its weak but significant positive relationship with soil moisture. Our findings show that combining an understanding of species responses to environmental change with long-term observations in the field can provide a context for validating and refining predictions of ecological trends in the abundance and diversity of soil fauna.

The Soil Geochemistry in the Beardmore Glacier Region, Antarctica: Implications for Terrestrial Ecosystem History.

Although most models suggest continental Antarctica was covered by ice during the Last Glacial Maximum (LGM) it has been speculated that endemic species of soil invertebrates could have survived the Pleistocene at high elevation habitats protruding above the ice sheets. We analyzed a series of soil samples from different elevations at three locations along the Beardmore Glacier in the Transantarctic Mountains (in order of increasing elevation): Ebony Ridge (ER), Cloudmaker (CM), and Meyer Desert (MD). Geochemical analyses show the MD soils, which were exposed during the LGM, were the least weathered compared to lower elevations, and also had the highest total dissolved solids (TDS). MD soils are dominated by nitrate salts (NO3/Cl ratios >10) that can be observed in SEM images. High δ(17)O and δ(18)O values of the nitrate indicate that its source is solely of atmospheric origin. It is suggested that nitrate concentrations in the soil may be utilized to determine a relative "wetting age" to better assess invertebrate habitat suitability. The highest elevation sites at MD have been exposed and accumulating salts for the longest times, and because of the salt accumulations, they were not suitable as invertebrate refugia during the LGM.

Evolution of plant parasitism among nematodes.

Despite extraordinary diversity of free-living species, a comparatively small fraction of nematodes are parasites of plants. These parasites represent at least three disparate clades in the nematode tree of life, as inferred from rRNA sequences. Plant parasites share functional similarities regarding feeding, but many similarities in feeding structures result from convergent evolution and have fundamentally different developmental origins. Although Tylenchida rRNA phylogenies are not fully resolved, they strongly support convergent evolution of sedentary endoparasitism and plant nurse cells in cyst and root-knot nematodes. This result has critical implications for using model systems and genomics to identify and characterize parasitism genes for representatives of this clade. Phylogenetic studies reveal that plant parasites have rich and complex evolutionary histories that involve multiple transitions to plant parasitism and the possible use of genes obtained by horizontal transfer from prokaryotes. Developing a fuller understanding of plant parasitism will require integrating more comprehensive and resolved phylogenies with appropriate choices of model organisms and comparative evolutionary methods.

Mitochondrial DNA and RAPD polymorphisms in the haploid mite Brevipalpus phoenicis (Acari: Tenuipalpidae).

Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is recognized as the vector of citrus leprosis virus that is a significant problem in several South American countries. Citrus leprosis has been reported from Florida in the past but no longer occurs on citrus in North America. The disease was recently reported in Central America, suggesting that B. phoenicis constitutes a potential threat to the citrus industries of North America and the Caribbean. Besides B. phoenicis, B. obovatus Donnadieu, and B. californicus (Banks) have been incriminated as vectors of citrus leprosis virus and each species has hundreds of host plants. In this study, Brevipalpus mite specimens were collected from different plants, especially citrus, in the States of Florida (USA) and São Paulo (Brazil), and reared on citrus fruit under standard laboratory conditions. Mites were taken from these colonies for DNA extraction and for morphological species identification. One hundred and two Random Amplified Polymorphic DNA (RAPD) markers were scored along with amplification and sequencing of a mitochondrial cytochrome oxidase subunit I gene fragment (374 bp). Variability among the colonies was detected with consistent congruence between both molecular data sets. The mites from the Florida and Brazilian colonies were morphologically identified as belonging to B. phoenicis, and comprise a monophyletic group. These colonies could be further diagnosed and subdivided geographically by mitochondrial DNA analysis.

Parasitism of molluscs by nematodes: types of associations and evolutionary trends.

Although there are no confirmed fossil records of mollusc parasitic nematodes, diverse associations of more than 108 described nematode species with slugs and snails provide a fertile ground for speculation of how mollusc parasitism evolved in nematodes. Current phylogenic resolution suggests that molluscs have been independently acquired as hosts on a number of occasions. However, molluscs are significant as hosts for only two major groups of nematodes: as intermediate hosts for metastrongyloids and as definitive hosts for a number of rhabditids. Of the 61 species of nematodes known to use molluscs as intermediate hosts, 49 belong to Metastrongyloidea (Order Strongylida); of the 47 species of nematodes that use molluscs as definitive hosts, 33 belong to the Order Rhabditida. Recent phylogenetic hypotheses have been unable to resolve whether metastrongyloids are sister taxa to those rhabditids that use molluscs as definitive hosts. Although most rhabditid nematodes have been reported not to kill their mollusc hosts prior to their reproduction, some species are pathogenic. In fact, infective juveniles of Phasmarhabditis hermaphrodita vector a lethal bacterium into the slug host in which they reproduce. This life cycle is remarkably similar to the entomopathogenic nematodes in the families Steinernematidae and Heterorhabditidae. Also, the discoveries of Alloionema and Pellioditis in slugs are interesting, as these species have been speculated to represent the ancestral forms of the entomopathogenic nematodes. Development of the infective stage appears to be an important step toward the acquisition of molluscs as definitive hosts, and the association with specific bacteria may have arisen in conjunction with the evolution of necromeny.

The species delimitation uncertainty principle.

If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present.

Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

The ITS regions of 10 species of Steinernema were PCR amplified and directly sequenced. Restriction mapping of these sequences revealed diagnostic variation such that the number of cuts and the length of the resulting fragments can be used to diagnose Steinernema species. Nevertheless, identical fragment sizes produced by non-homologous restriction sites also were identified. Pronounced variation in sequence length and nucleotide composition resulted in optimized alignments containing extensive regions of dubious homology. Significant shifts in nucleotide base composition exist among taxa and appear to mirror evolutionary history. These shifts do not have an observable influence on phylogenetic reconstruction and are probably due to descent as opposed to convergence. Alignment instability and the presence of alignment-ambiguous regions had the greatest effect on phylogeny reconstruction. Our results support the taxonomic utility of the ITS region to diagnose nematode species of the genus Steinernema, and all sampled taxa show evidence (in the form of numerous autapomorphic characters) of lineage independence. However, the ITS region appears to be phylogenetically informative only for closely related sister species. High variability among more distantly related taxa preclude its use for confidently resolving relationships among all members of the genus.

Molecular and morphometric evidence for separate species of Uncinaria (Nematoda: Ancylostomatidae) in California sea lions and northern fur seals: hypothesis testing supplants verification.

California sea lions (Zalophus californianus) and northern fur seals (Callorhinus ursinus) are each believed to host distinct hookworm species (Uncinaria spp.). However, a recent morphometric analysis suggested that a single species parasitizes multiple pinniped hosts, and that the observed differences are host-induced. To explore the systematics of these hookworms and test these competing hypotheses, we obtained nucleotide sequences of nuclear ribosomal DNA (D2/D3 28S, D18/D19 28S, and internal transcribed spacer [ITS] regions) from 20 individual hookworms parasitizing California sea lion and northern fur seal pups where their breeding grounds are sympatric. Five individuals from an allopatric population of California sea lions were also sampled for ITS-1 and D18/D19 28S sequences. The 28S D2/D3 sequences showed no diagnostic differences among hookworms sampled from individual sea lions and fur seals, whereas the 28S D18/D19 sequences had one derived (apomorphic) character demarcating hookworms from northern fur seals. ITS sequences were variable for 7 characters, with 4 derived (apomorphic) states in ITS-1 demarcating hookworms from California sea lions. Multivariate analysis of morphometric data also revealed significant differences between nematodes representing these 2 host-associated lineages. These results indicate that these hookworms represent 2 species that are not distributed indiscriminately between these host species, but instead exhibit host fidelity, evolving independently with each respective host species. This evolutionary approach to analyzing sequence data for species delimitation is contrasted with similarity-based methods that have been applied to numerous diagnostic studies of nematode parasites.

Characterization of a beta-1,3-glucanase encoded by chlorella virus PBCV-1.

Sequence analysis of the 330-kb chlorella virus PBCV-1 genome revealed an open-reading frame, A94L, that encodes a protein with significant amino acid identity to Glycoside Hydrolase Family 16 beta-1,3-glucanases. The a94l gene was cloned and the protein was expressed as a GST-A94L fusion protein in Escherichia coli. The recombinant A94L protein hydrolyzed the beta-1,3-glucose polymer laminarin and had slightly less hydrolytic activity on beta-1,3-1, 4-glucose polymers, lichenan and barley beta-glucan. The recombinant enzyme had the highest activity at 65 degrees C and pH 8. We predicted that the a94l-encoded beta-1,3-glucanase is involved in degrading the host cell wall either during virus release and/or is packaged in the virion particle and involved in virus entry. Therefore, we expected a94l to be expressed late in virus infection. However, contrary to expectations, both the a94l mRNA and the A94L protein appeared 15 min after PBCV-1 infection and disappeared 60- and 120-min p.i. postinfection, respectively, indicating that a94l is an early gene. Twenty-seven of 42 chlorella viruses contained the a94l gene. To our knowledge, this is the first report of a virus-encoded beta-1,3-glucanase.

Utility of the mitochondrial cytochrome oxidase II gene for resolving relationships among black flies (Diptera: simuliidae).

The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. Phylogenetic trees based on weighted parsimony (a priori and a posteriori), maximum likelihood, and neighbor-joining (log-determinant distances) differed topologically, with deeper nodes being the least well-supported. All analyses supported current classification into species groups but relationships among those groups were poorly resolved. The majority of phylogenetic signal came from closely related sister taxa. The CO-II gene may be useful for exploring relationships at or below the subgeneric level, but is of questionable value at higher taxonomic levels. The weighting method employed gave phylogenetic results similar to those reported by other authors for other insect CO-II data sets. A best estimate of phylogenetic relationships based on the CO-II gene is presented and discussed in relation to current black fly classification.

Species concepts and the evolutionary paradigm in modem nematology.

Given the task of recovering and representing evolutionary history, nematode taxonomists can choose from among several species concepts. All species concepts have theoretical and (or) operational inconsistencies that can result in failure to accurately recover and represent species. This failure not only obfuscates nematode taxonomy but hinders other research programs in hematology that are dependent upon a phylogenetically correct taxonomy, such as biodiversity, biogeography, cospeciation, coevolution, and adaptation. Three types of systematic errors inherent in different species concepts and their potential effects on these research programs are presented. These errors include overestimating and underestimating the number of species (type I and II error, respectively) and misrepresenting their phylogenetic relationships (type III error). For research programs in hematology that utilize recovered evolutionary history, type II and III errors are the most serious. Linnean, biological, evolutionary, and phylogenefic species concepts are evaluated based on their sensitivity to systematic error. Linnean and biological species concepts are more prone to serious systematic error than evolutionary or phylogenetic concepts. As an alternative to the current paradigm, an amalgamation of evolutionary and phylogenetic species concepts is advocated, along with a set of discovery operations designed to minimize the risk of making systematic errors. Examples of these operations are applied to species and isolates of Heterorhabditis.

A phylogenetic analysis of heterorhabditis (nemata: rhabditidae) based on internal transcribed spacer 1 DNA sequence data.

Internal transcribed spacer 1 sequences were used to infer phylogenetic relationships among 8 of the 9 described species and one putative species of the entomopathogenic nematode genus Heterorhabditis. Sequences were aligned and optimized based on pairwise genetic distance and parsimony criteria and subjected to a variety of sequence alignment parameters. Phylogenetic trees were constructed with maximum parsimony, cladistic, distance, and maximum likelihood algorithms. Our results gave strong support for four pairs of sister species, while relationships between these pairs also were resolved but less well supported. The ITS1 region of the nuclear ribosomal repeat was a reliable source of homologous characters for resolving relationships between closely related taxa but provided more tenuous resolution among more divergent lineages. A high degree of sequence identity and lack of autapomorphic characters suggest that sister species pairs within three distinct lineages may be mutually conspecific. Application of these molecular data and current morphological knowledge to the delimitation of species is hindered by an incomplete understanding of their variability in natural populations.

Predicting the extension of equivalence classes from primary generalization gradients: the merger of equivalence classes and perceptual classes.

In Experiment 1, 6 college students were given generalization tests using 25 line lengths as samples with a long line, a short line, and a "neither" option as comparisons. The neither option was to be used if a sample did not go with the other comparisons. Then, four-member equivalence classes were formed. Class 1 included three nonsense words and the short line. Class 2 included three other nonsense words and the long line. After repeating the generalization test for line length, additional tests were conducted using members of the equivalence classes (i.e., nonsense words and lines) as comparisons and intermediate-length lines as samples. All Class 2 comparisons were selected in the presence of the test lines that also evoked the selection of the long line in the generalization test that had been given before equivalence class formation. Class 1 yielded complementary findings. Thus, the preclass primary generalization gradient predicted which test lines acted as members of each equivalence class. Regardless of using comparisons that were nonsense words or lines, the post-class-formation gradients overlapped, showing the substitutability of class members. Experiment 2 assessed the discriminability of the intermediate-length test lines from the Class 1 (shortest) and Class 2 (longest) lines. The test lines that functioned as members of an equivalence class were discriminable from the line that was a member of the same class by training. Thus, these test lines also acted as members of a dimensionally defined class of "long" or "short" lines. Extension of an equivalence class, then, involved its merger with a dimensionally defined class, which converted a close-ended class to an open-ended class. These data suggest a means of predicting class membership in naturally occurring categories.

Expansion of the 16S and 23S ribosomal RNA mutation databases (16SMDB and 23SMDB).

The Ribosomal RNA Mutation Databases (16SMDB and 23SMDB) provide lists of mutated positions in 16S and 23S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods; and (iii) relevant literature citations. The databases are available via ftp and on the World Wide Web. Expansion of the databases to include information about mutations isolated in organisms other than E.coli is currently in progress.

Maintained nodal-distance effects in equivalence classes.

Twelve subjects were trained to select one of two stimuli from a pair (the B pair) when presented with one of two stimuli from another pair (the A pair), thus establishing two AB relations, A1-B1 and A2-B2. In a similar fashion, additional stimuli were used to establish BC, CD, and DE relations. Trials used to train all relations occurred in each session. Once performances were established, probe trials were introduced that tested for the emergence of untrained relations (e.g., B1-D1 or A1-E1). These emergent relations were categorized according to nodal distance (i.e., the number of stimuli across which transitivity would have to hold in order for the relation to emerge). For example, a test for A2-C2 crosses one node (B2), whereas a test for A1-E1 crosses three nodes (B1, C1, and D1). Only 2 of the subjects formed equivalence classes. The evocation of class-appropriate responding by each emergent-relation probe was an inverse function of nodal distance for all 12 subjects. In addition, performance on the originally trained relations was disrupted by the introduction of probes. The 2 subjects who exhibited equivalence classes were then trained to make different numbers of key presses in the presence of each of the four A and E stimuli. In a response-transfer test, the B, C, and D stimuli evoked the responses trained to the A and E stimuli in the same equivalence class. Likelihood of class-appropriate responses was an inverse function of nodal distance, and this pattern persisted across testing. Reaction times in the transfer test were an inverted U-shaped function of nodal distance. Because training of the baseline relations occurred concurrently and the B, C, and D stimuli were presented an equal number of times before the transfer test, the test performances illustrate effects of nodal distance that were not confounded by order or amount of experience with the stimuli. The results imply that ordered, sequential exposure to individual stimulus relations may facilitate the development of equivalence classes and that the relatedness of stimuli within an equivalence class is a relatively permanent inverse function of nodal distance.

Differentiation of perimortem and postmortem trauma using taphonomic indicators.

Skeletal remains discovered at a construction site in Georgia display classic "butterfly" fractures on several long bones. Although this fracture pattern is usually associated with perimortem trauma, in this case taphonomic indicators demonstrate that they can also occur on dry defleshed bone. Variations in bone color at the fracture sites indicate recent postmortem trauma. Analysis of the directions of force and points of impact indicates that the bones were most likely disarticulated when the trauma occurred.

Interactions among emergent relations during equivalence class formation.

The interactions among symmetry, transitivity, and equivalence tests during the formation of 3-member equivalence classes were studied with 14 college students. After training AB and BC, a test with BA, CB, AC, and CA was conducted concurrently. Failure led to serial testing with probes for CA equivalence, BA symmetry, CA equivalence, CB symmetry, CA equivalence, AC transitivity, and CA equivalence. For five subjects, equivalence tests were passed immediately once BA and CB symmetry as well as AC transitivity had been induced. Thus, symmetry and transitivity were precursors for successful performance on equivalence tests. The conjoint function of symmetry and transitivity was assessed with the equivalence probes. As the equivalence probes were passed immediately, the presence of symmetry alone and transitivity alone were sufficient for their conjoint function without additional intervention. For different subjects, transitivity alone and symmetry were induced either directly with BA, CB, or AC probes or indirectly with equivalence probes. Equivalence probes can also induce various combinations of symmetry and transitivity. Thus, different subjects formed classes in various patterns at different rates.

Stimulus generalization and equivalence classes: a model for natural categories.

Two three-member classes were formed by training AB and BC using a conditional discrimination procedure. The A and B stimuli were nonsense syllables, and the C stimuli were sets of "short" or "long" lines. To test for equivalence, C1 or C2 was presented as a sample with A1 and A2 as comparisons. Once the class-related comparison was chosen consistently, different line lengths were substituted for the training lines in the CA tests. In general, the likelihood of choosing a given comparison was an inverse function of the difference in the length of the test line from the training line. Stimuli in an equivalence class became functionally related not only to each other but also to novel stimuli that resembled a member of the equivalence class. The combination of primary generalization and equivalence class formation, then, can serve as a model to account for the development of naturally occurring categories.

The effects of nodality on the formation of equivalence classes.

A four-member equivalence class (A----B----C----D) can be formed by training AB, BC, and CD. The nodal stimuli, B and C, mediate all of the derivative (transitive and equivalence) relations in the class. The derivative relations AC, CA, BD, and DB are separated by one node, whereas AD and DA are separated by two nodes. How do the number of nodes that separate the stimuli in a derivative relation influence the induction of stimulus control exerted by that relation? Seven college students learned two four-member classes made up of nonsense syllables. After training, all derivative relations were presented repeatedly without informative feedback. Stimulus control exerted by each derivative relation was assessed concurrently. For the 7 subjects, control exerted by the derivative relations increased gradually with repeated presentations. With 6 of the 7 subjects, the one-node relations exerted more control than the two-node relations during the process. However, the disparity between the one- and two-node relations decreased with repeated presentations. Eventually, all derivative relations exerted complete control. The control exerted by derivative relations during induction was inversely related to the number of nodes separating the terms in the derivative relations. These results demonstrate that nodal distance is a determinant of the relatedness of stimuli in equivalence classes. The findings are discussed in terms of remote association, semantic memory networks, and the study of transitive inference.