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PubMed2005

Interaction of Klebsiella oxytoca and Burkholderia cepacia in dual-species batch cultures and biofilms as a function of growth rate and substrate concentration.

Dual-species microbial interactions have been extensively reported for batch and continuous culture environments. However, little research has been performed on dual-species interaction in a biofilm. This research examined the effects of growth rate and substrate concentration on dual-species population densities in batch and biofilm reactors. In addition, the feasibility of using batch reactor kinetics to describe dual-species biofilm interactions was explored. The scope of the research was directed toward creating a dual-species biofilm for the biodegradation of trichloroethylene, but the findings are a significant contribution to the study of dual-species interactions in general. The two bacterial species used were Burkholderia cepacia PR1-pTOM(31c), an aerobic organism capable of constitutively mineralizing trichloroethylene (TCE), and Klebsiella oxytoca, a highly mucoid, facultative anaerobic organism. The substrate concentrations used were different dilutions of a nutrient-rich medium resulting in dissolved organic carbon (DOC) concentrations on the order of 30, 70, and 700 mg/L. Presented herein are single- and dual-species population densities and growth rates for these two organisms grown in batch and continuous-flow biofilm reactors. In batch reactors, planktonic growth rates predicted dual-species planktonic species dominance, with the faster-growing organism (K. oxytoca) outcompeting the slower-growing organism (B. cepacia). In a dual-species biofilm, however, dual-species planktonic growth rates did not predict which organism would have the higher dual-species biofilm population density. The relative fraction of each organism in a dual-species biofilm did correlate with substrate concentration, with B. cepacia having a greater proportional density in the dual-species culture with K. oxytoca at low (30 and 70 mg/L DOC) substrate concentrations and K. oxytoca having a greater dual-species population density at a high (700 mg/L DOC) substrate concentration. Results from this research demonstrate the effectiveness of using substrate concentration to control population density in this dual-species biofilm.

Biodegradation, Environmental↗
PubMed2006

The use of macroalgal species richness and composition on intertidal rocky seashores in the assessment of ecological quality under the European Water Framework Directive.

The EC Water Framework Directive (WFD) suggests using abundance and species composition of intertidal seaweed communities for ecological quality classification of rocky seashores. There are two difficulties with this. According to WFD all sensitive species should be present on a shore. There is no accepted list of sensitive seaweed species and those which may be sensitive in one location may not be so in another. Second, natural successions can result in very large abundance changes of common species, e.g. from almost completely fucoid-dominated shores to almost totally barnacle-dominated shores, without any change in ecological quality. Studies have shown that numerical species richness, not the list of actual species present, is broadly constant in the absence of disturbance. The ephemeral species, possibly the sensitive members of the community, change regularly in such a way as to conserve species richness. It is proposed that species richness on a defined length of shore be used as a criterion of ecological quality. A database of species found on over 300 shores in the British Isles, under strictly controlled sampling conditions, has given ranges of values of species richness to be expected and has allowed for variations in these values due to sub-habitat variability, wave exposure and turbidity to be factored in. A major problem in applying such a tool is the lack of expertise of many workers in critical identification of seaweed species. A reduced species list has been extracted from the database using species commonly present and identifiable with reasonable certainty. A numerical index of ecological quality is proposed based on scores for various aspects of the physical nature of the habitat combined with a score for species richness which may be based on the reduced species list. The scoring system also uses further aspects of community structure, such as ecological status groups and the proportions of rhodophyta, chlorophyta and opportunist species. For this system to be effective there has to be close control of the way in which sampling is carried out to ensure a uniform level of thoroughness.

Databases, Factual↗
PubMed2026

Challenges for reproducibility in species delimitation.

Species richness is a foundational metric for comparing biodiversity among clades and regions in ecology, evolution, and conservation. As the biodiversity crisis accelerates, taxonomists face increasing pressure to delimit and name species rapidly, often relying on automated or semi-automated methods that prioritize speed over thoroughness. Yet the reproducibility of species delimitation (the degree to which independent experts reach consistent conclusions given the same evidence) remains largely unquantified, and its consequences for estimates of species richness have never been assessed at the scale of an entire fauna. This gap is consequential: if species delimitation is highly variable among practitioners, then published species counts may reflect the idiosyncrasies of individual taxonomists as much as the true biological structure of diversity within and among clades. Here we evaluate the precision, or reproducibility, of species delimitation in Neotropical freshwater fishes, the most species-rich continental vertebrate assemblage. We provided identical morphological and molecular datasets for species representing four genera to 40 taxonomic experts (10 per genus), who were asked to delimit species using (1) their preferred analytical approaches and (2) standardized analytical outputs. Total variance in species delimitation was partitioned into variance attributable to data analysis and interpretation of results. Total discordance was high (35.0%), and although standardization of analytical methods reduced discordance, substantial variance remained (23.5%) due to interpretative differences. Deviations from modal species estimates were not explained by any of seven expert attributes assessed, including taxonomic experience, publication record, geographic location, taxonomic concepts, or analytical methods. These results demonstrate that species delimitation can be subject to considerable subjectivity, even among experienced taxonomists working with identical data. Improving the precision of species delimitation will require coordinated advances across the full taxonomic workflow, including greater standardization of data acquisition and analysis, and clearer interpretative frameworks that explicitly define the evidentiary thresholds required to recognize species boundaries. Community-wide adoption of transparent reporting standards, analogous to those developed in genomics and clinical research, would help expose the sources of interpretative disagreement and facilitate more consistent application of species concepts across taxa and research groups. Developing benchmark datasets and shared reference taxonomies, against which new delimitation hypotheses can be evaluated, represents a tractable near-term goal for the systematic community. Ultimately, however, reproducible taxonomy cannot be achieved through procedural standardization alone. High-quality revisionary taxonomy must be grounded in experienced character evaluation and homology assessment, concept delimitation, and contingent analytical judgment, skills that are developed over years of immersive engagement with natural history collections, primary literature, and fieldwork. The decline of training opportunities in classical systematics therefore poses a direct threat not only to taxonomic productivity but to taxonomic consistency. Continued investment in a well-trained community of systematists, supported by institutions, collections, and funding agencies, remains the most reliable foundation for consistent and accurate species delimitation. Our results underscore that biodiversity metrics widely used in ecology, conservation planning, and macroevolutionary research are sensitive to practitioner variation in ways that have not previously been quantified, and that addressing this variation requires both methodological reform and sustained commitment to systematic expertise.

biodiversity↗
PubMedDate not supplied

[The species pool hypothesis: the necessity to shift emphasis].

The species pool of a biological community is determined as a group of species that inhabit some area and potentially can be included in a given community. The species pool hypothesis, i.e. the assumption that the size of species pool strongly influences species richness of local community can be confirmed if there is positive linear relationship between these two variables. The results of hypothesis testing however are not obvious. For example, correlation between local richness and species pool size can be caused by their dependence on the third variable--capacity of environment. It seems that in case of decreasing area occupied by local community the environmental conditions become more important than species pool size. If that is true, the influence of species pool on local species richness is not significant. However one can estimate the degree of unsaturation of species pool on the basis of relationships between the number of species in small locations occupied by similar local communities and their species pool. We think, that study of local and regional species richness should shift the emphasis--from the analysis of species pool influence on local community richness to the estimation of historical, ecological and anthropogenic factors in variation of species pool size. The local species richness should be considered rather as a tool (allowing to compare the species capacity of biological communities), than as an object of such study.

Animals↗
PubMed1997

Formation of reactive oxygen species by spermatozoa from asthenospermic patients: response to treatment with pentoxifylline.

PURPOSE: We determined the incidence of reactive oxygen species formation by spermatozoa from asthenospermic patients, and the relationship between reactive oxygen species formation and sperm motion parameters. We also assessed the efficacy of in vitro and in vivo pentoxifylline treatment of asthenospermic patients whose spermatozoa generated high reactive oxygen species levels. MATERIALS AND METHODS: Reactive oxygen species formation by spermatozoa from asthenospermic patients and fertile volunteers was measured by chemoluminescence. Reactive oxygen species formation by the sperm preparations was investigated without stimulation (steady state), or after stimulation with N-formyl-methionyl-leucyl-phenylalanine (f-MLP) or phorbol-12-myristate-13-acetate. Spermatozoa from 15 asthenospermic patients whose spermatozoa produced high levels of reactive oxygen species at steady state were treated in vitro with pentoxifylline to determine its effect on reactive oxygen species generation and sperm motion parameters. These same 15 patients and 18 with asthenospermia whose spermatozoa did not produce reactive oxygen species at steady state were treated with pentoxifylline at 2 different dosages (300 and 1,200 mg. daily) to determine its effect on reactive oxygen species generation, sperm motion parameters and sperm fertilizing ability in vivo. RESULTS: When reactive oxygen species formation was detected in the steady state that was not stimulated by f-MLP, the source of reactive oxygen species could be attributed to the spermatozoa themselves. Spermatozoa from 15 of 71 asthenospermic patients generated reactive oxygen species at steady state. Pentoxifylline decreased reactive oxygen species generation by spermatozoa in these patients, and preserved the decrease of curvilinear velocity and beat cross frequency for 6 hours in vitro. For these patients orally administered pentoxifylline failed to decrease reactive oxygen species generation by spermatozoa, and had no effect on sperm motility, sperm motion parameters and sperm fertilizing ability at low dosage (300 mg. daily). However, it increased motility and beat cross frequency at high dosage (1,200 mg. daily) but it had no effect on sperm fertilizing ability. CONCLUSIONS: Stimulation of sperm preparations with f-MLP can identify the source of reactive oxygen species generated at steady state. Among asthenospermic patients there were some whose spermatozoa produced detectable steady state levels of reactive oxygen species. In this group pentoxifylline appeared to be effective for decreasing reactive oxygen species formation and preserving sperm motion parameters in vitro. Orally administered pentoxifylline had no effect at low dosage but it increased sperm motility and some sperm motion parameters without altering sperm fertilizing ability at high dosage.

Fertilization↗
PubMed2000

Cryo-scanning electron microscopic study on freezing behavior of xylem ray parenchyma cells in hardwood species

Differential thermal analysis (DTA) has indicated that xylem ray parenchyma cells (XRPCs) of hardwood species adapt to freezing of apoplastic water either by deep supercooling or by extracellular freezing, depending upon the species. DTA studies indicated that moderately cold hardy hardwood species exhibiting deep supercooling in the XRPCs were limited in latitudinal distribution within the -40 degrees C isotherm, while very hardy hardwood species exhibiting extracellular freezing could distribute in colder areas beyond the -40 degrees C isotherm. Predictions based on the results of DTA, however, indicate that XRPCs exhibiting extracellular freezing may appear not only in very hardy woody species native to cold areas beyond the -40 degrees C isotherm but also in less hardy hardwood species native to tropical and subtropical zones as well as in a small number of moderately hardy hardwood species native to warm temperate zones. Cryo-scanning electron microscopic (cryo-SEM) studies on the freezing behavior of XRPCs have revealed some errors in DTA. These errors are originated mainly due to the overlap between exotherms produced by freezing of water in apoplastic spaces (high temperature exotherms, HTEs) and exotherms produced by freezing of intracellular water of XRPCs by breakdown of deep supercooling (low temperature exotherms, LTEs), as well as to the shortage of LTEs produced by intracellular freezing of XRPCs. In addition, DTA results are significantly affected by cooling rates employed. Further, cryo-SEM observations, which revealed the true freezing behavior of XRPCs, changed the previous knowledge of freezing behavior of XRPCs that had been obtained by freeze-substitution and transmission electron microscopic studies. Cryo-SEM results, in association with results obtained from DTA that were reconfirmed or changed by observation using a cryo-SEM, revealed a clear tendency of the freezing behavior of XRPCs in hardwood species to change with changes in the temperature in the growing conditions, including both latitudinal and seasonal temperature changes. In latitudinal temperature changes, XRPCs in less hardy hardwood species native to tropical and subtropical zones exhibited deep supercooling to -10 degrees C, XRPCs in moderately hardy hardwood species native to temperate zones exhibited a gradual increase in the supercooling ability to -40 degrees C from warm toward cool temperate zones, and XRPCs in very hardy hardwood species native to boreal forests exhibited extracellular freezing via an intermediate form of freezing behavior between deep supercooling and extracellular freezing. In seasonal temperature changes, XRPCs in hardwood species native to temperate zones changed their supercooling ability from a relatively low degree in summer to a high degree in winter. XRPCs in hardwood species native to boreal forests changed their freezing behavior from deep supercooling to -10 degrees C in summer to extracellular freezing in winter. These results indicate that the freezing behavior of XRPCs in hardwood species tends to shift gradually from supercooling of -10 degrees C, to a gradual increase in the deep supercooling ability to -40 degrees C or less, and finally to extracellular freezing as a result of cold acclimation in response to both latitudinal and seasonal temperature changes. It is thought that these temperature-dependent changes in the freezing behavior of XRPCs in hardwood species are mainly controlled by changes in cell wall properties, although no distinct changes were detected by electron microscopic observations in cell wall organization between hardwood species or between seasons. Evidence of temperature-dependent changes in the freezing behavior of XRPCs in hardwood species provided by the results of studies using a cryo-SEM has indicated the need for further investigation to clarify cold acclimation-induced cell wall changes at the sub-electron microscopic level in order to understand the mechanisms of freezing adaptation.

Journal Article↗
PubMedDate not supplied

A cost-benefit analysis of leaves of four Australian savanna species.

We conducted a cost-benefit analysis of the contrasting phenologies of two evergreen and two deciduous species of the savannas of north Australia. Stomatal conductance, rates of light-saturated assimilation (A(max)) and dark respiration were measured for six leaves from each of five or six trees. These leaves were then analyzed for total nitrogen, ether-soluble lipids, ash content, and heat of combustion. Construction and maintenance costs, nitrogen-use efficiencies and instantaneous transpiration efficiencies were then calculated from these data. Evergreen species had significantly lower specific leaf area, leaf nitrogen and leaf ash content than deciduous species. Evergreen species also had significantly higher heat of combustion and lipid content of crude extracts than deciduous species. Light-saturated assimilation rates were higher in evergreen species on a leaf area basis, but were higher in deciduous species on a leaf dry weight basis. In both evergreen and deciduous species, A(max) and total Kjeldahl nitrogen were linearly related. Similarly, nitrogen-use efficiency did not differ among species. Leaf construction costs were significantly higher for evergreen species than for deciduous species, but maintenance costs did not differ among species. Evergreen species had a higher cost:benefit ratio than deciduous species but because of their longer-lived leaves, the payback interval was longer in evergreen species than in deciduous species. These results support the hypotheses that: (1) longer-lived leaves are more expensive to construct than shorter-lived leaves, and (2) there is a higher investment of nitrogen into short-lived leaves to support a higher A(max) over a shorter payback interval. We conclude that deciduous and evergreen species partition resources both temporally and spatially, thereby reducing interspecies competition.

Journal Article↗
PubMed2006

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

BACKGROUND: Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never been adequately addressed, particularly with respect to producing a consistent method to achieve high throughput. Using 1,147 mammalian cross-species primer pairs (1089 not previously reported), we tested several factors to determine their influence on the probability that a given target will amplify in a given species under a single amplification condition. These factors included: number of mismatches between the two species (the index species) used to identify conserved regions to which the primers were designed, GC-content of the gene and amplified region, CpG dinucleotides in the primer region, degree of encoded protein conservation, length of the primers, and the degree of evolutionary distance between the target species and the two index species. RESULTS: The amplification success rate for the cross-species primers was significantly influenced by the number of mismatches between the two index species (6-8% decrease per mismatch in a primer pair), the GC-content within the amplified region (for the dog, GC > or = 50%, 56.9% amplified; GC<50%, 74.2% amplified), the degree of protein conservation (R2 = 0.14) and the relatedness of the target species to the index species. For the dog, 598 products of 930 primer pairs (64.3%) (excluding primers in which dog was an index species) were sequenced and shown to be the expected product, with an additional three percent producing the incorrect sequence. When hamster DNA was used with the single amplification condition in a microtiter plate-based format, 510 of 1087 primer pairs (46.9%) produced amplified products. The primer pairs are spaced at an average distance of 2.3 Mb in the human genome and may be used to produce up to several hundred thousand bp of species-specific sequence. CONCLUSION: The most important factors influencing the proportion of successful amplifications are the number of index species mismatches, GC-richness of the target amplimer, and the relatedness of the target species to the index species, at least under the single PCR condition used. The 1147 cross-species primer pairs can be used in a high throughput manner to generate data for studies on the genetics and genomics of non-sequenced mammalian genomes.

Animals↗
PubMed2004

Five new species of Pedibothrium (Tetraphyllidea: Onchobothriidae) from the tawny nurse shark, Nebrius ferrugineus, in the Pacific Ocean.

The spiral intestines of 7 Tawny nurse sharks (Nebrius ferrugineus; Rhincodontidae) from Australia and French Polynesia were examined for tapeworms. These sharks hosted 5 new species of Pedibothrium. The 5 species were prepared for light and scanning electron microscopy. Whereas 3 of the species exhibit the bipronged hooks typical of members of Pedibothrium, 1 species was found to possess tiny unipronged hooks or to lack some, or all, hooks, and all individuals of the fifth species appeared to lack bothridial hooks entirely. Nonetheless, the otherwise remarkable similarities between these species and the species of Pedibothrium bearing bipronged hooks were considered to be sufficient to justify the placement of these 2 species in this genus. All 5 species possess proglottid features typical of Pedibothrium, including a uterus that extends anteriorly only to the level of the cirrus sac and a cirrus sac that is bent anteriorly and is crossed by the vagina. All 5 species also exhibit uniloculated bothridia. Of particular note was the fact that all 5 species exhibit bladelike spinitrichs with elongated distal tips, a form of microthrix currently known only from species of Pedibothrium. As a consequence, these species were treated as possessing modified hooks or as having lost hooks. The diagnoses of Pedibothrium and Onchobothriidae were emended to include these species. Each of the 5 new species bears a strong resemblance to 1 or more species of Pedibothrium hosted by a species of rhincodontid shark other than N. ferrugineus. Much of Southwell's type and voucher material of Pedibothrium was located and used to verify the identity of Pedibothrium kerkhami and many of the hosts from which Southwell's material of Pedibothrium was collected. This material suggests that P. kerkhami parasitizes Stegostoma fasciatum and not N. ferrugineus.

Animals↗
PubMed2005

A revision of Phoreiobothrium (Tetraphyllidea: Onchobothriidae) with descriptions of five new species.

Five new species of Phoreiobothrium (Cestoda: Tetraphyllidea) are described from carcharhiniform sharks collected from a diversity of localities throughout the world. These are Phoreiobothrium perilocrocodilus n. sp. from Negaprion acutidens, Phoreiobothrium anticaporum n. sp. from Negaprion brevirostris, Phoreiobothrium lewinense n. sp. from Sphyrna lewini, Phoreiobothrium robertsoni n. sp. from Carcharhinus brachyurus, and Phoreiobothrium blissorum n. sp. from C. plumbeus, This brings the number of described species of Phoreiobothrium to 17. The new species from the lemon sharks, P. perilocrocodilus n. sp. and P. anticaporum n. sp., both possess more bothridial subloculi than do all species from hammerhead sharks, and fewer subloculi than do all species from sharks of Carcharhinus spp. Phoreiobothrium anticaporum n. sp. is unique among Phoreiobothrium species in that its genital pore is located in the extreme anterior portion of the proglottid. Phoreiobothrium lewinense n. sp. is unique in its possession of a combination of 8-11 subloculi and basal hook prongs that lack internal channels. Phoreiobothrium robertsoni n. sp. possesses 25-29 subloculi, triangular bothridia that flare posteriorly, and hooks that extend well beyond the middle of the bothridia. Phoreiobothrium blissorum n. sp. is most similar to Phoreiobothrium lasium in that it possesses rectangular bothridia with greater than 22 subloculi and long filitriches on its scolex. However, it differs from the latter species in that rather than articulating with one another, the bases of the medial and lateral hooks are widely separated; it also possesses 5-6 (vs.) 7-8 columns of testes. Phoreiobothrium lasium and Phoreiobothrium tiburonis are redescribed. The host associations of P. lasium are reevaluated and a neotype is designated for this species. The mature proglottid of P. tiburonis is described for the first time from voucher material collected from the type host and locality. These data suggest that the proglottid information provided in the original description, which was obtained from detached gravid proglottids, may have come from a tapeworm species other than P. tiburonis. All 7 species treated here in detail were examined with scanning electron microscopy; most were found to exhibit a microthrix pattern similar to that described previously for other members of the genus, e.g., Phoreiobothrium manirei. Bladelike spinitriches were present on the strobila, cephalic peduncle, and proximal bothridial surfaces, but were lacking from the distal bothridial surfaces. These spinitriches varied in length and density among species. Filitriches were present on all of these surfaces, but varied somewhat in length among species. Phoreiobothrium lewinense n. sp. is exceptional in that spinitriches were not seen on the proximal bothridial surfaces. A key to Phoreiobothrium species is provided. This work brings the number of carcharhinid shark species known to host this onchobothriid genus to 6, and the number of sphyrnid species to 5. Like many other onchobothriid tapeworms, species of Phoreiobothrium appear to exhibit oioxenous specificity for their hosts. Given this, and the fact that a total of 9 genera and 46 species of carcharhinid and sphyrnid sharks have yet to be examined for Phoreiobothrium, the diversity of the genus globally is likely to greatly exceed that described to date.

Animals↗
PubMed2005

Ernst Mayr and the modern concept of species.

Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayr's definition, as necessary properties of species. On the other hand, the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayr's popular species definition are commonly confused under the name "the biological species concept," they are more or less clearly distinguished in Mayr's early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr. Definitions of the species category that identify a particular contingent property of metapopulation lineages (including intrinsic reproductive isolation) as a necessary property of species reduce the number of metapopulation lineages that are to be recognized taxonomically as species, but they cause conflicts among alternative species definitions and compromise the status of the species as a basic category of biological organization.

Animals↗
PubMed2003

Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote.

We critically examined methods for recognizing species in the model filamentous fungal genus Neurospora by comparing traditional biological species recognition (BSR) with more comprehensive applications of both BSR and phylogenetic species recognition (PSR). Comprehensive BSR was applied to a set of 73 individuals by performing extensive crossing experiments and delineating biological species based on patterns of reproductive success. Within what were originally considered two species, N. crassa and N. intermedia, we recognized four reproductively isolated biological species. In a concurrent study (Dettman et al. 2003), we used genealogical concordance of four independent nuclear loci to recognize phylogenetic species in Neurospora. Overall, the groups of individuals identified as species were similar whether recognized by reproductive success or by phylogenetic criteria, and increased genetic distance between parents was associated with decreased reproductive success of crosses, suggesting that PSR using genealogical concordance can be used to reliably recognize species in organisms that are not candidates for BSR. In one case, two phylogenetic species were recognized as a single biological species, indicating that significant phylogenetic divergence preceded the development of reproductive isolation. However, multiple biological species were never recognized as a single phylogenetic species. Each of the putative N. crassa x N. intermedia hybrids included in this study was confidently assigned to a single species, using both PSR and BSR. As such, no evidence for a history of hybridization in nature among Neurospora species was observed. By performing reciprocal mating tests, we found that mating type, parental role, and species identity of parental individuals could all influence the reproductive success of matings. We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms.

Cluster Analysis↗
PubMed1996

A wide-range survey of cross-species microsatellite amplification in birds.

The possibility to perform cross-species microsatellite amplification in birds was surveyed by analysing sets of primers developed from the swallow and the pied flycatcher genomes on a panel of 48 different bird species. In total, 162 cases (species/marker combinations) of heterologous amplification were recorded. Ten amplification products were sequenced and all were found to be true homologues of the original loci. There was a significant and negative relationship between microsatellite performance and evolutionary distance between the original species and the tested species. As a rough indicator of expected cross-species microsatellite performance we estimate that 50% of markers will reveal polymorphism in a species with a DNA-DNA hybridization delta T(m)H value of 5 separating it from the original species. This corresponds to a divergence time of = 11 million years before present for passerine birds. The established relationship between performance and evolutionary distance agrees very well with data obtained from some mammalian species. The proportion of polymorphic loci among those markers that amplified decreased with increasing genetic distance, suggesting that few long repeats are preserved during evolution. One of the swallow markers, HrU2, amplified a specific product in all species analyzed and will thus allow access of nuclear sequence data over a broad range of species. The only predictor of cross-species performance was the amount of non-specific amplification seen in the original species. An analysis of 10 species from within the family Hirundinidae with the swallow primers consistently revealed extensive polymorphism with average probabilities of identical genotypes ranging from 6 x 10(-4) to 6 x 10(-7). There were distinct allele frequency differences between the Hirundinidae species and we envisage that microsatellite cross-species amplification will be a useful tool in phylogeny construction and in species identification.

Alleles↗
PubMed2006

Oligonucleotide array for identification and detection of pythium species.

A DNA array containing 172 oligonucleotides complementary to specific diagnostic regions of internal transcribed spacers (ITS) of more than 100 species was developed for identification and detection of Pythium species. All of the species studied, with the exception of Pythium ostracodes, exhibited a positive hybridization reaction with at least one corresponding species-specific oligonucleotide. Hybridization patterns were distinct for each species. The array hybridization patterns included cluster-specific oligonucleotides that facilitated the recognition of species, including new ones, belonging to groups such as those producing filamentous or globose sporangia. BLAST analyses against 500 publicly available Pythium sequences in GenBank confirmed that species-specific oligonucleotides were unique to all of the available strains of each species, of which there were numerous economically important ones. GenBank entries of newly described species that are not putative synonyms showed no homology to sequences of the spotted species-specific oligonucleotides, but most new species did match some of the cluster-specific oligonucleotides. Further verification of the specificity of the DNA array was done with 50 additional Pythium isolates obtained by soil dilution plating. The hybridization patterns obtained were consistent with the identification of these isolates based on morphology and ITS sequence analyses. In another blind test, total DNA of the same soil samples was amplified and hybridized on the array, and the results were compared to those of 130 Pythium isolates obtained by soil dilution plating and root baiting. The 13 species detected by the DNA array corresponded to the isolates obtained by a combination of soil dilution plating and baiting, except for one new species that was not represented on the array. We conclude that the reported DNA array is a reliable tool for identification and detection of the majority of Pythium species in environmental samples. Simultaneous detection and identification of multiple species of soilborne pathogens such as Pythium species could be a major step forward for epidemiological and ecological studies.

Oligonucleotide Array Sequence Analysis↗
PubMed2000

Individual odour similarities across species parallel phylogenetic relationships in the S. ehrenbergi superspecies of mole-rats.

Research using habituation techniques has shown that rodents from the same kin group, population, or species share similarities in their individual odours that covary with shared genetic similarities between them, that is, the closer their genetic relatedness, the more similar their odours. We assessed similarities in individual odours across four sibling species of subterranean mole-rats from the Spalax ehrenbergi superspecies in Israel. Mole-rats were habituated to the urine odour of a same-sex individual from one species then tested with urine odours of individuals from two different species of the superspecies. Subjects treated urine odours of individuals from more closely genetically related species as similar compared with the odours of individuals from a less closely related species, showing that the covariance between odours and genes extends across species. These similarities in odour also paralleled genetic similarities determined by molecular analysis: odours of descendent species were perceived as similar to those of their closest ancestral species, suggesting that some qualities of the odour of the ancestral species persist in the descendent species. It is generally assumed that during speciation incipient species develop species-specific markers, including, for example, odour markers, to facilitate discrimination of conspecifics from close ancestral heterospecifics. Our findings indicate that similarities in odours across species are more salient than species-specific odour markers. Such findings may also have important implications for mechanisms of species recognition. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1995

A genetical theory of species selection.

Species selection, differential rates of speciation or extinction resulting from species level characters, is often invoked as the main mechanism of macroevolution that is not simply an extension of microevolutionary processes. So long as we are careful in defining "species", the logic of species selection is sound. This does not mean, however, that this process can influence evolutionary dynamics under realistic conditions. The principal challenge to the efficacy of species selection as an evolutionary mechanism is the idea that selection between individuals within species will be so much more efficient as to swamp out any effects of selection between species. To assess this, a genetic model is constructed that includes simultaneous selection within and between species, and this is used to ask: under what conditions could species selection influence evolutionary dynamics, even in the face of opposing selection between individuals? The model shows that the efficacy of species selection is strongly determined by the time between speciation events (measured in individual generations), the mutation rate of the character under consideration, and the initial size of a newly formed reproductively isolated population. Data indicate that a few studied lineages have shown sufficiently high speciation rates to make species selection an important mechanism in the evolution of characters with mutation rates on the order of 10(-6) per generation. Quantitative characters, such as body size, generally change too readily for species selection to be relevant to their evolution. Complex characters, however, may be good candidates to be influenced by species selection. The interaction of selection within and between species can be subtle, with individual selection looking, from the standpoint of a species, very much like development of an individual. Furthermore, selection between individuals may be the main process assembling complex adaptations, while species selection allows them to persist over long periods of time.

Animals↗
PubMed2002

Assessing vulnerability to invasion by nonnative plant species at multiple spatial scales.

Basic information on where nonnative plant species have successfully invaded is lacking. We assessed the vulnerability of 22 vegetation types (25 sets of four plots in nine study areas) to nonnative plant invasions in the north-central United States. In general, habitats with high native species richness were more heavily invaded than species-poor habitats, low-elevation areas were more invaded than high-elevation areas, and riparian zones were more invaded than nearby upland sites. For the 100 1000-m2 plots (across all vegetation types), 50% of the variation in nonnative species richness was explained by longitude, latitude, native plant species richness, soil total percentage nitrogen, and mean maximum July temperature (n = 100 plots; P < 0.001). At the vegetation-type scale (n = 25 sets of four 1000-m2 plots/type), 64% of the variation in nonnative species richness was explained by native plant species richness, elevation, and October to June precipitation (P < 0.001). The foliar cover of nonnative species (log) was strongly positively correlated with the nonnative species richness at the plot scale (r = 0.77, P < 0.001) and vegetation-type scale (r = 0.83, P < 0.001). We concluded that, at the vegetation-type and regional scales in the north-central United States, (1) vegetation types rich in native species are often highly vulnerable to invasion by nonnative plant species; (2) where several nonnative species become established, nonnative species cover can substantially increase; (3) the attributes that maintain high native plant species richness (high light, water, nitrogen, and temperatures) also help maintain nonnative plant species richness; and (4) more care must be taken to preserve native species diversity in highly vulnerable habitats.

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PubMed2003

Delta15N values of tropical savanna and monsoon forest species reflect root specialisations and soil nitrogen status.

A large number of herbaceous and woody plants from tropical woodland, savanna, and monsoon forest were analysed to determine the impact of environmental factors (nutrient and water availability, fire) and biological factors (microbial associations, systematics) on plant delta(15)N values. Foliar delta(15)N values of herbaceous and woody species were not related to growth form or phenology, but a strong relationship existed between mycorrhizal status and plant delta(15)N. In woodland and savanna, woody species with ectomycorrhizal (ECM) associations and putative N(2)-fixing species with ECM/arbuscular (AM) associations had lowest foliar delta(15)N values (1.0-0.6 per thousand ), AM species had mostly intermediate delta(15)N values (average +0.6 per thousand ), while non-mycorrhizal Proteaceae had highest delta(15)N values (+2.9 to +4.1 per thousand ). Similar differences in foliar delta(15)N were observed between AM (average 0.1 and 0.2 per thousand ) and non-mycorrhizal (average +0.8 and +0.3 per thousand ) herbaceous species in woodland and savanna. Leguminous savanna species had significantly higher leaf N contents (1.8-2.5% N) than non-fixing species (0.9-1.2% N) indicating substantial N acquisition via N(2) fixation. Monsoon forest species had similar leaf N contents (average 2.4% N) and positive delta(15)N values (+0.9 to +2.4 per thousand ). Soil nitrification and plant NO(3)(-) use was substantially higher in monsoon forest than in woodland or savanna. In the studied communities, higher soil N content and nitrification rates were associated with more positive soil delta(15)N and plant delta(15)N. In support of this notion, Ficus, a high NO(3)(-) using taxa associated with NO(3)(-) rich sites in the savanna, had the highest delta(15)N values of all AM species in the savanna. delta(15)N of xylem sap was examined as a tool for studying plant delta(15)N relations. delta(15)N of xylem sap varied seasonally and between differently aged Acacia and other savanna species. Plants from annually burnt savanna had significantly higher delta(15)N values compared to plants from less frequently burnt savanna, suggesting that foliar (15)N natural abundance could be used as marker for assessing historic fire regimes. Australian woodland and savanna species had low leaf delta(15)N and N content compared to species from equivalent African communities indicating that Australian biota are the more N depauperate. The largest differences in leaf delta(15)N occurred between the dominant ECM Australian and African savanna (miombo) species, which were depleted and enriched in (15)N, respectively. While the depleted delta(15)N of Australian ECM species are similar to those of previous reports on ECM species in natural plant communities, the (15)N-enriched delta(15)N of African ECM species represent an anomaly.

Environmental Monitoring↗