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PubMed1996

Species-specific segregation of gender-associated mitochondrial DNA types in an area where two mussel species (Mytilus edulis and M. trossulus) hybridize.

In each of the mussel species Mytilus edulis and M. trossulus there exist two types of mtDNA, the F type transmitted through females and the M type transmitted through males. Because the two species produce fertile hybrids in nature, F and M types of one may introgress into the other. We present the results from a survey of a population in which extensive hybridization occurs between these two species. Among specimens classified as "pure" M. edulis or "pure" M. trossulus on the basis of allozyme analysis, we observed no animal that carried the F or the M mitotype of the other species. In most animals of mixed nuclear background, an individual's mtDNA came from the species that contributed the majority of the individual's nuclear genes. Most importantly, the two mtDNA types in post-F1 male hybrids were of the same species origin. We interpret this to mean that there are intrinsic barriers to the exchange of mtDNA between these two species. Because such barriers were not noted in other hybridizing species pairs (many being even less interfertile than M. edulis and M. trossulus), their presence in Mytilus could be another feature of the unusual mtDNA system in this genus.

Animals↗
PubMed2002

Photosynthetic responses to water deficit in six Mediterranean sclerophyll species: possible factors explaining the declining distribution of Rhamnus ludovici-salvatoris, an endemic Balearic species.

We sought to explain the declining distribution in the Balearic Islands of the endemic shrub Rhamnus ludovici-salvatoris R. Chodat, by comparing its photosynthetic response to drought with that of several widely distributed, competing Mediterranean species (R. alaternus L., Quercus ilex L., Pistacia lentiscus L., Q. humilis Mill. and P. terebinthus L.). All of the study species, except for the two Rhamnus species, avoided desiccation by rapidly adjusting their stomatal conductance at the onset of drought, and maintaining constant leaf relative water content. The two Rhamnus species showed desiccation-tolerant behavior; i.e., as drought progressed, their predawn leaf relative water content decreased simultaneously with stomatal closure. All four desiccation-avoiding species showed a significant positive correlation between leaf thermal dissipation (estimated by the fluorescence parameter NPQ (non-photochemical quenching)) and the de-epoxidation state of the xanthophyll cycle (DPS). The two Rhamnus species exhibited maximum DPS regardless of treatment, but only R. alaternus increased NPQ in response to drought. Rhamnus ludovici-salvatoris had a high ratio of photorespiration to photosynthesis and a low intrinsic water-use efficiency; traits that are likely to be unfavorable for plant productivity under arid conditions. It also had the lowest DPS and thermal dissipation among the six species. We conclude that the photosynthetic traits of R. ludovici-salvatoris account for its limited ability to compete with other species in the Mediterranean region.

Carbon Dioxide↗
PubMed2005

Molecular phylogeny of the Pseudallescheria boydii species complex: proposal of two new species.

Pseudallescheria boydii (anamorph Scedosporium apiospermum) is the species responsible for human scedosporiosis, a fungal infection with a high mortality rate and which is difficult to treat. Recently, it has been demonstrated that high genetic variation exists within this species. We have performed a morphological and molecular study involving numerous strains of clinical or environmental origins and from different countries. The analysis of partial sequences of the beta-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rRNA gene has demonstrated that P. boydii is a species complex. The combined analysis of the sequences of the four loci of 60 strains has showed the presence of 44 haplotypes in the in group. Three species morphologically related to P. boydii sensu stricto, i.e., Pseudallescheria angusta, Pseudallescheria ellipsoidea, and Pseudallescheria fusoidea, which had previously been considered synonyms, could be differentiated genetically from P. boydii in our study. It is relevant that two of the three strains now included in P. ellipsoidea have caused invasive infections. The species Pseudallescheria minutispora and Scedosporium aurantiacum are clearly phylogenetically separated from the other species studied and are here proposed as new. Morphological features support this proposal. All the strains included in S. aurantiacum species have a clinical origin, while those included in P. minutispora are environmental. Further studies are needed to demonstrate whether all the species included in the P. boydii complex have different clinical spectra and antifungal susceptibility.

Calmodulin↗
PubMed2003

Species identification within the Anopheles funestus group of malaria vectors in Cameroon and evidence for a new species.

Anopheles funestus is a major vector of malaria in Africa. It belongs to a group of sibling species that can be identified morphologically only at certain stages of their development. A diagnostic polymerase chain reaction (PCR)-based tool made it possible to differentiate five species of the group. The assay seems to be applicable over all their distribution area for four of these species: An. funestus, An. leesoni, An. parensis, and An. vaneedenip. The fifth species, An. rivulorum, is the second most abundant species of the group and can be mistaken at its adult stage for the major vector of malaria An. funestus. Molecular and morphologic observations of specimens identified as An. rivulorum from Cameroon and South Africa showed that they belong to two different taxa. The species identified in Cameroon, and named here An. rivulorum-like, might extend to western Africa and central Africa. The species-specific PCR assay is supplemented by a primer specific to An. rivulorum-like and thus makes it possible to differentiate the five species of the An. funestus group and the newly defined taxon.

Animals↗
PubMed2024

DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings.

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 23 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. Model, codes, and data is publicly available at https://github.com/MAGlCS-LAB/DNABERT_S.

Journal Article↗
PubMed2005

Species and sex differences in brain distribution of corticotropin-releasing factor receptor subtypes 1 and 2 in monogamous and promiscuous vole species.

Corticotropin-releasing factor (CRF) receptor subtypes 1 and 2 have been implicated in rodent models of anxiety, but much less is known about the CRF system and social behavior. Both corticosterone and central CRF receptors modulate pair bonding in the monogamous prairie vole. Using receptor autoradiography, we mapped CRFR(1) and CRFR(2) in the brains of two monogamous vole species, the prairie vole and pine vole, and two promiscuous vole species, the meadow vole and montane vole. We found markedly different patterns of brain CRFR(1) and CRFR(2) binding among the four species, including species differences in the olfactory bulb, nucleus accumbens, lateral septum, hippocampus, laterodorsal thalamus, cingulate cortex, superior colliculus, and dorsal raphe. Interestingly, we also observed striking sex differences in voles: CRFR(2) binding was higher in the encapsulated bed nucleus of the stria terminalis in males than females for all four vole species. These results suggest possible sites of action for CRF-induced facilitation of pair bond formation in prairie voles, as well as potential sex differences in the CRF modulation of pair bonding. Further examination of CRF receptors in vole species may reveal a novel role for CRF in social behavior. Ultimately, our results identify several brain regions with conserved CRF receptor patterns across rodent and primate species, in contrast to several brain regions with phylogenetically plastic CRF receptor patterns, and have interesting implications for the evolution of CRF receptor patterns and behavior.

Analysis of Variance↗
PubMed2005

Simultaneous multi-species determination of trimethyllead, monomethylmercury and three butyltin compounds by species-specific isotope dilution GC-ICP-MS in biological samples.

An accurate and sensitive multi-species species-specific isotope dilution GC-ICP-MS method was developed for the simultaneous determination of trimethyllead (Me3Pb+), monomethylmercury (MeHg+) and the three butyltin species Bu3Sn+, Bu2Sn2+, and BuSn3+ in biological samples. The method was validated by three biological reference materials (CRM 477, mussel tissue certified for butyltins; CRM 463, tuna fish certified for MeHg+; DORM 2, dogfish muscle certified for MeHg+). Under certain conditions, and with minor modifications of the sample pretreatment procedure, this method could also be transferred to environmental samples such as sediments, as demonstrated by analyzing sediment reference material BCR 646 (freshwater sediment, certified for butyltins). The detection limits of the multi-species GC-ICP-IDMS method for biological samples were 1.4 ng g(-1) for MeHg+, 0.06 ng g(-1) for Me3Pb+, 0.3 ng g(-1) for BuSn3+ and Bu3Sn+, and 1.2 ng g(-1) for Bu2Sn2+. Because of the high relevance of these heavy metal alkyl species to the quality assurance of seafood, the method was also applied to corresponding samples purchased from a supermarket. The methylated lead fraction in these samples, correlated to total lead, varied over a broad range (from 0.01% to 7.6%). On the other hand, the MeHg+ fraction was much higher, normally in the range of 80-100%. Considering that we may expect tighter legislative limitations on MeHg+ levels in seafood in the future, we found the highest methylmercury contents (up to 10.6 microg g(-1)) in two shark samples, an animal which is at the end of the marine food chain, whereas MeHg+ contents of less than 0.2 microg g(-1) were found in most other seafood samples; these results correlate with the idea that MeHg+ is usually of biological origin in the marine environment. The concentration of butyltins and the fraction of the total tin content that is from butyltins strongly depend on possible contamination, due to the exclusively anthropogenic character of these compounds. A broad variation in the butylated tin fraction (in the range of <0.3-49%) was therefore observed in different seafood samples. Corresponding isotope-labeled spike compounds (except for trimethyllead) are commercially available for all of these compounds, and since these can be used in the multi-species species-specific GC-ICP-IDMS method developed here, this technique shows great potential for routine analysis in the future.

Animals↗
PubMed2006

Species-specific oligonucleotides and multiplex PCR for forensic discrimination of two species of scallops, Placopecten magellanicus and Chlamys islandica.

Characterization of DNA that remains in seafood products after skin, scales, and shells are removed is widely used in forensic species identification, however, ordinary methods may be prohibitively expensive or time-consuming if large sample series need to be discriminated. Forensic discrimination of two species of bivalves commercially harvested from the North Atlantic, sea scallops (Placopecten magellanicus) and Icelandic scallops (Chlamys islandica), was made by means of species-specific oligonucleotides (SSOs) in a multiplex polymerase chain reaction (PCR). The test is a simultaneous in vitro amplification of a portion of the mitochondrial Cytochrome Oxidase I locus with a PCR anchor primer for a sequence identical in both species, and two alternative SSOs that selectively amplify either a 619-bp in Placopecten or a 459-bp DNA fragment in Chlamys. Fragment size and thus species identity are determined directly by gel electrophoresis. In the forensic application, analysis of more than 900 scallops from a series of samples seized from two fishing vessels showed significantly variable proportions of the species from the closed and open fisheries (Placopecten versus Chlamys, respectively). The multiplex SSO test provides a direct means of forensic identification of large population sample series, without the necessity of secondary DNA sequencing, RFLP mapping, or fingerprinting, and can be adapted to other loci and species.

Animals↗
PubMed2026

Genome-wide SNP data support species boundaries in sympatric Polylepis Ruiz & Pav. (Rosaceae) species from Bolivia and Ecuador.

Species delimitation in the South American genus Polylepis is notoriously challenging due to high morphological similarity and phenotypic plasticity, likely driven by hybridization and gene flow. Previous phylogenetic studies suggested that genetic structure aligns more strongly with geography than with taxonomy, questioning existing species concepts and hampering conservation efforts. We used double-digest RAD sequencing (ddRADseq) to generate genome-wide SNP data for 11 Polylepis species sampled across multiple localities in Bolivia and Ecuador. Population genetic analyses, phylogenetic inference, and network approaches were combined to assess whether genetic structure aligns more closely with taxonomy or geography. Morphologically defined species formed largely cohesive genetic lineages across regions, with species identity explaining substantially more genetic variation than locality. While localized admixture and reticulation were detected among closely related taxa, widespread species showed strong genetic cohesion and clear separation from congeners. Our results indicate that the sampled Polylepis species from Bolivia and Ecuador maintain distinct genetic identities despite localized signals consistent with gene flow. This genome-wide support for current taxonomy highlights Polylepis as a valuable model for studying speciation under gene flow and indicates that multiple geographic sampling will be essential in reconstructing a robust phylogeny of the genus, with important implications for conservation planning in Andean montane forests.

Bolivia↗
PubMed2003

Explaining the excess of rare species in natural species abundance distributions.

The observation that a few species in ecological communities are exceptionally abundant, whereas most are rare, prompted the development of species abundance models. Nevertheless, despite the large literature on the commonness and rarity of species inspired by these pioneering studies, some widespread empirical patterns of species abundance resist easy explanation. Notable among these is the observation that in large assemblages there are more rare species than the log normal model predicts. Here we use a long-term (21-year) data set, from an estuarine fish community, to show how an ecological community can be separated into two components. Core species, which are persistent, abundant and biologically associated with estuarine habitats, are log normally distributed. Occasional species occur infrequently in the record, are typically low in abundance and have different habitat requirements; they follow a log series distribution. These distributions are overlaid, producing the negative skew that characterizes real data sets.

Animals↗
PubMed2025

One mother for two species via obligate cross-species cloning in ants.

Living organisms are assumed to produce same-species offspring1,2. Here, we report a shift from this norm in Messor ibericus, an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste. As a result, males from the same mother exhibit distinct genomes and morphologies, as they belong to species that diverged over 5&#x2009;million years ago. The evolutionary history of this system appears as sexual parasitism3 that evolved into a natural case of cross-species cloning4,5, resulting in the maintenance of a male-only lineage cloned through distinct species' ova. We term females exhibiting this reproductive mode as xenoparous, meaning they give birth to other species as part of their life cycle.

Animals↗
PubMed2002

PCR assay for identification of Anopheles quadriannulatus species B from Ethiopia and other sibling species of the Anopheles gambiae complex.

Sibling species A and B of Anopheles quadriannulatus (Theobald) are recognized as allopatric members of the Anopheles gambiae Giles complex of Afrotropical mosquitoes (Diptera: Culicidae). Species A represents An. quadriannulatus sensu stricto, widespread in southern Africa, whereas An. quadriannulatus species B occurs in Ethiopia. Because of difficulty of identification, distribution of An. quadriannulatus sensu lato remains poorly known. Cytotaxonomy and the standard DNA polymerase chain reaction (PCR) assay do not distinguish between species A and B of An. quadriannulatus. By optimizing the standard PCR assay (Scott et al., 1993) for identification of members of the An. gambiae complex, we identified two discriminant fragments of 153 bp and 900 bp from DNA of An. quadriannulatus species B, whereas only the 153 bp fragment was amplified for species A from South Africa. This modified PCR assay can therefore be used to distinguish between species A and B of An. quadriannulatus s.l. as well as other members of the An. gambiae complex.

Africa, Southern↗
PubMed1987

Demonstration of species-specific sensitization to major allergens of Dermatophagoides species by solid-phase absorption of human IgE antibodies.

Twenty-five mite-allergic patients in the Brussels area were tested with the skin-prick test (1, 5 and 10 histamine equivalents by prick test (HEP] and RAST with standardized extracts of Dermatophagoides pteronyssinus (Dp) and D. microceras (Dm). Highly significant correlations (0.69 less than rS less than 0.96) between the two species coincided with marginal, but highly significant (P less than 0.01), greater reactions to Dp in all comparisons. Species-specific IgE antibodies to antigen Dp-42 (= P1) and Dp-X were readily detected by solid-phase serum absorption with heterologous antigen and subsequent crossed radioimmunoelectrophoresis (CRIE). An absorption single radial immunodiffusion (SRID) technique, involving major allergens Dp-42, Dm-6 and Df-6 of Dp, Dm and D. farinae (Df), demonstrated the presence of IgE antibodies reacting with epitopes common to all species, epitopes common to two species, absent on the third, and epitopes strictly specific for Dp. The majority of patients with a strong IgE binding reacted to both common and strictly species-specific epitopes. The serological findings were in good agreement with the exposure situation in the area: by species-specific ELISA for dust allergen content, Dp occurred as the dominating species, 20 out of 24 homes having dust levels of Dp-42 above 30 ng/g. Five and four homes had detectable levels of Dm-6 and Df-6, respectively, in dust.

Adolescent↗
PubMedDate not supplied

Soil ciliate species richness and abundance associated with the rhizosphere of different subtropical plant species.

Soil protozoa, and ciliates in particular, represent a microbial group abundant in the rhizosphere with an influential role on nutrient cycling. Under laboratory conditions, ciliates regulate the size and the composition of bacterial communities, and appear to stimulate ammonification and nitrification. In spite of their important ecological role, our understanding about the factors that control their diversity and abundance in natural forest ecosystems is still rudimentary. Plant species-specific interactions have been demonstrated between plants and soil bacteria and mycorrhizal fungi, due in part to the release of phytohormones and C- and N-rich exudates. We tested the hypothesis that the rhizosphere environments of different plant species also influence the species richness and abundance of soil ciliates. Plant effect, soil pH, moisture content, microbial biomass C, and inorganic nitrogen were measured among five plant species to determine the best predictor variables for soil ciliate species richness and total abundance in a subtropical moist forest in Puerto Rico. Based on an analysis of variance, we rejected the hypothesis that there was a plant species-specific effect on soil ciliates, unlike other microbial groups mentioned above. Using multiple regression analysis, we demonstrated that the flush of total inorganic nitrogen was the best predictor variable for both species richness and abundance of ciliates.

Animals↗
PubMed1986

Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes.

DNA probes that are specific for each of five predominant species of human colonic Bacteroides (B. thetaiotaomicron, B. uniformis, B. distasonis, "Bacteroides group 3452-A", and B. ovatus) were used to detect and enumerate these species in fecal samples from two adult volunteers. These five species are capable of fermenting many of the complex polysaccharides that are thought to be sources of carbon and energy for bacteria in the colon. Estimates for the concentrations of some of these species in feces have not been previously available because of the difficulties in differentiating colonic Bacteroides spp. by conventional biochemical tests. Our results indicate that all the species except B. ovatus were present in high numbers (greater than 10(9)/g [dry weight]) in the feces of both volunteers. However, the concentrations of the more versatile polysaccharide-degrading species within this group of organisms (7.6 X 10(9) to 12.0 X 10(9)/g [dry weight] for B. thetaiotaomicron; 2.9 X 10(9) to 6.3 X 10(9)/g [dry weight] for "Bacteroides group 3452-A") did not differ significantly from the concentrations of less versatile polysaccharide-degrading species (1.2 X 10(10) to 2.0 X 10(10)/g [dry weight] for B. uniformis; 5.8 X 10(9) to 8.4 X 10(9)/g [dry weight] for B. distasonis). B. ovatus was not detectable by our method. Since our lower limit of detection is approximately 1 X 10(9) to 2 X 10(9)/g (dry weight) of feces, this is consistent with earlier estimates that indicated that the concentration of B. ovatus in feces is near or below this value.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteroides↗
PubMed1993

Analysis of mitochondrial DNA in two species of the bipectinata species complex of Drosophila.

Drosophila bipectinata and D. malerkotliana are members of the bipectinata species complex of the ananassae subgroup in the melanogaster species group of Drosophila. The mtDNA from 18 isofemale strains of these species was analyzed, using 13 restriction endonucleases. Altogether, eight mtDNA haplotypes were detected, of which the haplotype 1B was shared by the two species. Restriction cleavage map of mtDNA of these species was constructed. The net nucleotide substitutions per site calculated between these species was found to be 0.0002. This value appeared to be relatively much lower than expected at the interspecific level, even lower than that reported between two subspecies of Drosophila despite both being good species. This extreme closeness of their mtDNAs is discussed in the light of recent findings.

Animals↗
PubMed2001

Patterns of inversion polymorphism in three species of the Drosophila melanogaster species group.

In Drosophila, chromosomal polymorphism due to paracentric inversions is very common and constitutes an adaptive character. The degree of chromosomal variability varies in different species and also in different populations of the same species. Chromosomal polymorphism in Indian natural populations of three species, D. melaonogaster, D. ananassae and D. bipectinata which belong to the melanogaster species group has been studied and the quantitative data on frequency of inversions have been reported. Behaviour of chromosome inversions has also been studied in laboratory conditions. The present review summarises the work done on inversion polymorphism in Indian populations of three species which clearly demonstrates that these three species vary in their patterns of inversion polymorphism and have evolved different mechanisms for adjustment to their environments although they belong to the same species group.

Animals↗
PubMed2001

Quantitative analysis and molecular species fingerprinting of triacylglyceride molecular species directly from lipid extracts of biological samples by electrospray ionization tandem mass spectrometry.

Herein we describe a rapid, simple, and reliable method for the quantitative analysis and molecular species fingerprinting of triacylglycerides (TAG) directly from chloroform extracts of biological samples. Previous attempts at direct TAG quantitation by positive-ion electrospray ionization mass spectrometry (ESI/MS) were confounded by the presence of overlapping peaks from choline glycerophospholipids requiring chromatographic separation of lipid extracts prior to ESI/MS analyses. By exploiting the rapid loss of phosphocholine from choline glycerophospholipids, in conjunction with neutral-loss scanning for individual fatty acids, overlapping peaks in the ESI mass spectrum were deconvoluted generating a detailed molecular species fingerprint of individual TAG molecular species directly from chloroform extracts of biological samples. This method readily detects as little as 0.1 pmol of each TAG molecular species from chloroform extracts and is linear over a 1000-fold dynamic range. The sensitivity of individual TAG molecular species to ESI/MS/MS analyses correlated with the unsaturation index and inversely correlated with total aliphatic chain length of TAG. An algorithm was developed which identifies sensitivity factors, thereby allowing the rapid quantitation and molecular species fingerprinting of TAG molecular species directly from chloroform extracts of biological samples.

Animals↗