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At least 19 recordsLinked to original sources

PubMed2025

Extensive Introgression Failed to Erode Species Boundaries Among Multiple Sympatric Closely Related Species of Roscoea.

How species boundaries are maintained among sympatric closely related species experiencing gene flow is a puzzling question in evolutionary biology. Although introgression is commonly documented, the dynamics and gene function of introgression have rarely been explored to probe why frequent introgression does not necessarily destroy species boundaries in sympatry. In this study, we employ whole-genome resequencing data to examine introgression among five closely related species of Roscoea that coexist in a 'sky island' with seventeen distinct morphological traits. Our findings reveal that introgression has led to the phylogenomic discordance between nuclear and chloroplast genomes among these morphologically distinct species. Additionally, introgression is predominantly asymmetrical in both intensity and gene function, particularly concerning recombination. Notably, the majority of gene functions associated with introgressed loci are unrelated to reproductive processes. Our results suggest that closely related species with incomplete allele assortment can coexist despite theoretical predictions, highlighting the semipermeable nature of species boundaries as reproductive isolation develops. This provides a critical conceptual framework for understanding the interplay between introgression and species persistence. Our finding offers insights into how related sympatric species boundaries can be maintained in the face of frequent asymmetrical gene introgression.

Sympatry↗

PubMed2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings.

SUMMARY: 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 28 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. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Sequence Analysis, DNA↗

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↗

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↗

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 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↗

PubMed2026

RNA Virus Diversity, Cross-Species Transmission, and Molecular Constraints in Two Closely Related Rat Species.

Viral infection involves co-evolution with hosts, yet the molecular determinants that constrain viral cross-species transmission remain poorly understood. Here, we established conspecific and heterospecific co-housing models for two closely related rat species, Rattus norvegicus (RN) and Rattus tanezumi (RT), both maintained in laboratory settings for over 10 generations, together with wild-caught RT individuals. Using meta-transcriptomic sequencing and population genomic analyses, we compared their RNA virus profiles and investigated the potential molecular constraints on cross-species viral transmission. From 63 rats, we characterized an extensive RNA virome comprising more than 600 viruses, including 7 zoonotic viruses, 29 viruses with cross-species transmission potential, and 335 novel viruses. Notably, the prevalence of Seoul orthohantavirus (SEOV) was significantly higher in RN than in RT. Population genomic analysis revealed that RN exhibited higher heterozygosity in Itgb3 (the gene encoding the SEOV receptor, β3-integrin) and Tlr7 (the gene encoding the receptor for viral ssRNA, Toll-like receptor 7) compared to RT. These genetic variations likely represent the molecular determinants responsible for the differential susceptibility to SEOV between the two species. Our findings clarify the diversity and prevalence of RNA viruses in closely related rodent species and highlight host genetic barriers that may influence zoonotic spillover risk.

Animals↗

PubMed1978

A survey of Anopheles gambiae (species A) and An. arabiensis (species B) of the An. gambiae Giles complex in the Kisumu area of Kenya following insecticidal spraying with OMS-43 (Fenitrothion).

After village huts in the Kisumu area of Kenya had been sprayed with a nominal 2 g/m2 of OMS-43 (fenitrothion) as part of an insecticidal evaluation programme 964 adults of the Anopheles gambiae complex collected from huts were identified cytogenetically as either An. gambiae (species A) or An. arabiensis (species B). Similarly, cytogenetic methods were used to identify 349 adults collected from granaries and artificial pit-shelters. In addition, 2203 larvae of the gambiae complex collected from different types of habitats were specifically identified cytogenetically. As in a previous survey made prior to insecticidal spraying, adults of An. arabiensis predominated in outdoor collections while An. gambiae was highly endophilic. However, it appeared that spraying with fenitrothion had resulted in an increase in both the degree of exophily in An. arabiensis and also its relative numbers in respect to An. gambiae, although the overall pooulation of both species was greatly reduced by spraying. Insecticidal spraying may have diverted both species from feeding on man to cattle. Except for one village, where larvae of An. arabiensis were commoner than expected in cattle hoof-prints, there was little difference between the selection of different types of larval habitats by the two sibling species. Chromosomal inversions were more common in adults of An. arabiensis than in An. gambiae.

Animals↗

PubMed1979

Aspects of species recognition by sound in four species of damselfishes, genus Eupomacentrus (Pisces: Pomacentridae).

Members of four sympatric species of Eupomacentrus carry out reproductive activities at the same time of the year and produce similar pulsed courtship sounds. Such sounds are known to facilitate courtship among conspecifics. Consequently, members of the four species in the field and in the laboratory were tested with the various sounds to determine if they could distinguish their own species sounds from those produced by congeners. The differential responses clearly demonstrate species specific recognition by sound and indicate that the pulse interval and the number of pulses per sound are the important parameters for this recognition.

Animals↗

PubMed1978

Comparative analysis of karyotypes in European shrew species. I. The sibling species Sorex araneus and S. gemellus: Q-bands, G-bands, and position of NORs.

The karyotypes of two closely related species of the genus Sorex (Mammalia, Insectivora) were compared with each other by G- and Q-banding techniques and by Ag-AS staining (GOODPASTURE and BLOOM, 1975). By comparing the G-banded karyotypes, it could be ascertained that the basic differences in karyotype between the two species lie in three pericentric inversions, three paracentric inversions, and one reciprocal translocation. This is in near agreement with FORD and HAMERTON (1970), who assumed that both species differ by three pericentric inversions and one tandem translocation. Furthermore, the karyotype of S. araneus (race C) presented by HALKKA et al. (1974) has been compared with the S. araneus of the present report. Considering the species with respect to karyotypic evolution, it is supposed that S. araneus and S. gemellus derive from a common ancestor.

Animals↗

PubMed1978

Development of species identification in ducklings: IV. Change in species-specific perception caused by auditory deprivation.

The purpose of the present experiments was to identify the change in species-specific perception that underlies the aurally deprived ducklings' lack pf preference or discrimination in the mallard versus chicken call test. Among other acoustic differences, the mallard and chicken maternal calls differ in repetition rate (3.7 and 2.3 notes/sec, respectively). The present experiments showed the dimension of repetition rate to be uppermost in the perceptual hierarchy underlying the auditory aspect of species identification in Peking ducklings. The relatively narrow species-typical repetition-rate preferences of normal Peking ducklings (about 4--6 notes/sec) is lacking in the aurally deprived ducklings, and they respond to lower rates than usual (2.3 notes/sec). This broadening of the range of responsiveness on a perceptual dimension (repetition rate) that is basic to species identification accounts for the devocal ducklings' lack of discrimination in the mallard versus chicken call test.

Age Factors↗

PubMed1979

Species restriction of the mitogenicity induced by lanatoside C. Lymphocyte activation by digitalis glycosides is confined to cells from digitalis resistant species.

Activation of Na+, K+-ATPase has previously been suggested to be the triggering signal in mitogen-induced cell activation. Using a digitalis glycoside known to be a potent polyclonal B-cell activator, this hypothesis could be tested since digitalis activates ATPase at different concentrations in various species, depending on the degree of sensitivity to the toxic effects of glycosides. Lanatoside C was found to stimulate lymphocytes from glycoside resistant species such as rat, mouse and hamster. The possible involvement of Na+, K+-ATPase was made less likely by the similarity in dose--response profile in these cells although they have been reported to display varying degrees of glycoside resistance. Furthermore, using lymphocytes from digitalis-sensitive species such as man, guinea-pig or rabbit, no mitogenicity could be recorded, strongly suggesting a lack of correlation between glycoside-induced effects on Na+, K+-ATPase and cell activation.

Adenosine Triphosphatases↗

PubMed1977

Production of specific antibodies to contractile proteins, and their use in immunofluorescence microscopy. II. Species-specific and species-non-specific antibodies to smooth and striated chicken muscle actin.

The injection of rabbits with insoluble or soluble G-actin from chicken smooth or striated muscle will produce antibodies that are equally reactive, and species and tissue non-specific in immunoprecipitation, immunofluorescence and actin-activated Mg2+-ATPase inhibition tests. These antibodies have been used for the identification of actin-containing fibrils in a variety of tissues. When G-actins from chicken smooth or striated muscle are immobilized by chemical linkage to Affi-Gel 702 microbeads, their immunogenicity is increased, but the antibodies obtained against them are species-specific and will only react with actin and actin-containing structures from chicken and are therefore limited in use. It is concluded from this work that insoluble G-actin is the preferable immunogen to obtain precipitating antibodies for wide use.

Actins↗

PubMed1978

Species specificity of cholecystokinin in gut and brain of several mammalian species.

Immunoreactive intact cholecystokinin and its COOH-terminal octapeptide are found in brain as well as in extracts of gut of the monkey, dog, and pig, by using an antiserum with equivalent sensitivities for detecting the octapeptide in free form or incorporated in the intact molecule. The failure to detect intact cholecystokinin in extracts from monkey or dog by using an antiserum developed by immunization with porcine cholecystokinin is presumed to be due to marked species differences in the NH2-terminal portion of the molecule. Tryptic digestion converted the intact cholecystokinin from all species to a peptide resembling the COOH-terminal octapeptide. The amount of cholecystokinin in the brain is comparable to that found in the gastrointestinal tract, the traditional site for this peptide.

Animals↗

PubMed1979

Species specific grass pollen sensitivity: diagnosis and treatment with single grass species Allpyral vaccines.

Skin test titrations and nasal provocation tests in sixty patients with hay fever showed specific reactions to extracts of individual grass species. There was, however, no correlation between skin and nasal sensitivity. Repeat testing after treatment with Allpyral vaccines consisting of only the grass species to which the nasal reaction was most severe, or only one of several pollens to which reactions were equally severe, showed marked diminution of skin and nasal sensitivity not only to the single pollen used for immuno-therapy but to all five common pollens used in the Allpyral grass mix. Clinical results seemed much improved as compared with results in the same year for Allpyral five grass mix vaccines, especially in the case of patients treated with Timothy, rye, or cocksfoot. It was concluded that these three grassees were to be preferred for treatment in England, and that these grasses contain common allergens.

Dose-Response Relationship, Immunologic↗

PubMed2025

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.

The Klebsiella pneumoniae species complex inhabits a wide variety of hosts and environments, and is a major cause of antimicrobial resistant infections. Genomics has revealed the population comprises multiple species/sub-species and hundreds of distinct co-circulating sub-lineage (SLs) that are associated with distinct gene complements. A substantial fraction of the pan-genome is predicted to be involved in metabolic functions and hence these data are consistent with metabolic differentiation at the SL level. However, this has so far remained unsubstantiated because in the past it was not possible to explore metabolic variation at scale. Here, we used a combination of comparative genomics and high-throughput genome-scale metabolic modeling to systematically explore metabolic diversity across the K. pneumoniae species complex (n = 7,835 genomes). We simulated growth outcomes for each isolate using carbon, nitrogen, phosphorus, and sulfur sources under aerobic and anaerobic conditions (n = 1,278 conditions per isolate). We showed that the distributions of metabolic genes and growth capabilities are structured in the population, and confirmed that SLs exhibit unique metabolic profiles. In vitro co-culture experiments demonstrated reciprocal commensalistic cross-feeding between SLs, effectively extending the range of conditions supporting individual growth. We propose that these substrate specializations may promote the existence and persistence of co-circulating SLs by reducing nutrient competition and facilitating commensal interactions. Our findings have implications for understanding the eco-evolutionary dynamics of K. pneumoniae and for the design of novel strategies to prevent opportunistic infections caused by this World Health Organization priority antimicrobial resistant pathogen.

Klebsiella pneumoniae↗

PubMed1977

Serological cross-reactivity between group B Streptococcus and Sporothrix schenckii, Ceratocystis species, and Graphium species.

Serological cross-reactivity of a group B Streptococcus (H36B) with Sporothrix schenckii and 39 different Ceratocystis and Graphium species was investigated by double immunodiffusion. Rabbit anti-H36B serum reacted with antigens from S. schenckii and from 36 of 39 Ceratocystis and Graphium species. It is speculated that low-titer agglutinins to S. schenckii in normal sera are due to antibodies raised against various bacteria which share common antigens with S. schenckii.

Animals↗

PubMed1979

[Cytogenetic study of six species or sub-species of mangabeys monkeys (Papiinae, Cercopithecidae) (author's transl)].

Chromosome banding patterns of six Mangabey species or sub-species are studied and compared. By comparison with the other Papiinae previously studied (Papio and Macaca) Lophocebus albigena and L. aterrimus possess very similar karyotypes, differing a most by a pericentric inversion of the Y chromosome. The other four, Cercocebus torquatus torquatus, C. t. fuliginosus, C. galeritus galeritus and C. g. chrysogaster differ by a complex rearrangement of chromosome no. 10 and by acquisition of heterochromatin on chromosome no 12. No difference was detected nor between the two Lophocebus nor between the four Cercocebus. Cytogenetic criteria age thus in agreement with the morphological, immunological and hematological data, separating the two genuses, and placing Lophocebus closer to the Papio and Macaca than to Cercocebus.

Animals↗

PubMed1977

Restriction and modification in Bacillus species: genetic transformation of bacteria with DNA from different species, part I.

Host specific restriction was detected in 13 Bacillus strains, when 63 strains of Bacillus subtilis and 15 other Bacillus strains were tested with phage phi 105C. These 13 strains were classified into 8 groups (M,H,C,N,E,F,G,P) by the type of restriction. M-type strains (B. subtilis Marburg 168, its derivatives, and two other strains) showed relatively weak restriction, restricting phi 105C from other groups of Bacillus by ratios of 10(-1) to 10(-3). Strains of groups H,C,N,E,F,G, and P restricted phi 105C from other groups by ratios of 10(-2) to 10(-8). It was confirmed with some of the strains that type-specific modification was endowed only by the last host. Furthermore, we isolated one restriction deficient mutant of B. subtilis Marburg 168-YS11, which had also lost its modification phenotype.

Bacillus↗