PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Species identification”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
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↗
PubMed2026

Benchmarking Assembly-Free K-mer Methods for Species Identification in Complex Plant Groups: A Case Study in Populus.

Species identification in taxonomically complex plant groups is frequently limited by the inadequacy of organellar markers, whose phylogenetic signal is disrupted by cytonuclear discordance and chloroplast capture. Using the taxonomically complex genus Populus as a model, we evaluated an assembly-free k-mer workflow against a curated SNP reference benchmark. Whole-genome resequencing data from 235 Populus individuals were curated to a 202-individual, 34-species reference dataset in which all retained species are strictly monophyletic in a genome-wide SNP analysis. Independent maximum likelihood analyses further confirmed that the 31 non-hybrid backbone species each maintained high-support monophyly, while taxa of documented reticulate origin showed placement patterns consistent with their reticulate histories. ABBA-BABA D-statistics detected widespread residual allele sharing within the backbone, though the strongest signals did not correspond to the species pairs responsible for the few k-mer identification failures. Against this benchmark, complete plastomes showed limited resolution, recovering only 3.0% species monophyly and 71.1% nearest-neighbor assignment. The optimized k-mer workflow, operating directly on raw reads without assembly or alignment, recovered 91.2% species monophyly, 99.0% nearest-neighbor assignment, and 98.0% group-average assignment. K-mer length was the primary accuracy-controlling parameter, with k = 31 falling within a stable accuracy plateau. Distance-based metrics reached near-saturation at 0.2× sequencing depth, indicating that low-coverage genome skimming can support scalable nuclear genome-based identification with standard computational resources. K-mer distance heatmaps also flagged unusual genomic affinities in hybrid-origin and outlier samples, providing a rapid screen for subsequent population genomic analyses. These results support assembly-free k-mer distances as an efficient tool for reference-based species identification and sample screening in complex plant groups, with residual limitations concentrated near recently diverged species boundaries. Model-based phylogenomic, coalescent, and network analyses remain necessary for resolving deeper species relationships and detailed introgression histories.

Populus↗
PubMed1979

Fish species identification by thin layer isoelectric focusing.

Conventional electrophoretic techniques generally lack the resolution and reproducibility needed for the reliable identification of fish species. Variations in stabilizing media composition, sample application technique, separation time, applied voltage or current, and the analyst's skill all affect the protein pattern. Thin layer polyacrylamide gel isoelectric focusing (TLIEF), a high resolution protein separation technique, has been applied to the identification of fish species. Sarcoplasmic proteins are separated according to their isoelectric points in a stable, reproducible pH gradient. Protein patterns for 12 species of fish are compared in 4.0% polyacrylamide gels with pH 4.0--6.0 and pH 3.5--10 gradients. Similar patterns are shown in commercially prepared 5.0% polyacrylamide gels with pH 4.0--6.5 and pH 3.5--9.5 gradients (LKB PAG plates). The protein patterns are reproducible in each pH gradient and also correlate well between user-prepared and commercially prepared gels. The inherent high resolution and excellent reproducibility of TLIEF should allow the positive identification of fish species without the costly procedure of using known species as standards.

Animals↗
PubMed2026

Species identification, discovery, and biomonitoring: Strategic priorities for DNA barcoding in Europe, set in a global context.

The International Barcode of Life (iBOL) initiative is building a globally accessible DNA-based system for species identification and discovery. This paper outlines the mission and strategic priorities for the iBOL community in Europe (iBOL Europe), set in a global context. The mission of iBOL Europe is to produce, curate, and provide access to a complete DNA barcode reference library of European eukaryotic biodiversity, catalyzing species discovery and enabling comprehensive, harmonized species identification and biomonitoring, and supporting the global iBOL program. Immediate objectives include completing reference libraries for priority taxa, democratizing access to sequencing technologies, and strengthening a distributed community of practice. Key actions identified span five thematic areas: community building, sample collection and taxonomic verification, sequencing infrastructure, data management, and mainstreaming DNA-based approaches to meet societal needs. The strategy emphasizes integration with European research infrastructures to ensure long-term sustainability and resilience for biodiversity genomics in Europe.

DNA barcoding↗
PubMed2026

Plant species identification by genome skimming across the vascular plant tree of life.

Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution. We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL, matK, trnH-psbA and ITS resolved about half of species (49.3%), with six genera showing <&#x2009;25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k-mer analysis, achieving 66.8% species discrimination - an average gain of 17.5% over standard barcodes - while eliminating cases of extreme failure (<&#x2009;25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.

DNA Barcoding, Taxonomic↗
PubMed2026

PCR-based species identification tools for wireworms (Coleoptera: Elateridae) of economic importance in Canada.

BACKGROUND: Coexistence of pest and non-pest wireworms (Coleoptera: Elateridae) in agricultural fields makes species-level identification critical to determine when pest management measures are required. However, morphological identification of wireworms (larval stage of click beetles) is challenging, as larvae are difficult to distinguish based on morphological features and misidentifications are common. Here, we developed species-specific primers for 15 click beetle species to be used in PCR-based species-level identification for agricultural fields across Canada. RESULTS: Partial sequences of the gene regions cytochrome c oxidase I (COXI), 16S, 12S, 28S, 18S, internal transcribed spacer 2 (ITS2), cytochrome-b (CYTB), elongation factor 1 (EF1), ATP6/8, NADH dehydrogenase 1 (ND1), NADH dehydrogenase 2 (ND2), NADH dehydrogenase 3 (ND3), NADH dehydrogenase 4 (ND4), NADH dehydrogenase 5 (ND5) and NADH dehydrogenase 6 (ND6) were generated for elaterid species of interest. Of these gene regions, primers were designed on the mitochondrial gene regions COXI, CYTB and ND1 that had sufficient variation to discriminate among species and tested for species specificity using additional pest and non-pest species from the families Elateridae, Carabidae, Scarabidae and Silphidae. Specificity testing confirmed that all primer sets were species-specific. CONCLUSION: The novel primers designed in this study allow for PCR-based species identification of 15 economically important click beetle pest species in Canada. Further testing is needed to validate the assay for use outside of Canada. Accurate species-level identification will benefit pest management professionals by informing management decisions and reducing the use of insurance insecticide applications due to difficulties with identifications of wireworm pest species. &#xa9; 2026 His Majesty the King in Right of Canada and The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. Reproduced with the permission of the Minister of Agriculture and Agri-Food.

Animals↗
PubMed1977

Species identification in the North American cowbird: appropriate responses to abnormal song.

Female cowbirds raised in auditory isolated from males responded to the songs of male cowbirds with copulatory postures. The songs of males reared in isolated were more effective in eliciting the posture than the songs of normally reared males. The females did not respond to the songs of other species. These results indicate one mechanism of species identification for this parasitic species.

Animals↗
PubMed1978

Species identification in protozoa: glucosephosphate isomerase variation in the Paramecium aurelia group.

Results are presented for intra- and interspecies variation in electrophoretic mobility of the enzyme glucosephosphate isomerase in the Paramecium aurelia species complex. Three new observations have been made: (1) the hitherto indistinguishable species 1 and 5 can be distinguished on the basis of GPI electrophoretic mobility, (2) the degree of intraspecies variation is much higher for GPI than for the previously studied mitochondrial dehydrogenases and esterases, and (3) several of the enzymatic variants observed in one species are apparently indistinguishable from some found in other species. The intraspecies variants found have been shown to be allelic, and, on the basis of the enzyme patterns of the heterozygotes, it is proposed that GPI is a dimeric enzyme determined by two loci. In view of the use of enzyme variation as a means of species identification in protozoa, these results suggest that the use of such methods can lead to underestimating the number of species and possibly to misclassification. The implications of these findings together with the results obtained with Tetrahymena are discussed.

Animals↗
PubMedDate not supplied

The species identification of very old human blood-stains.

The efficiency of 5% ammonia as an extractant of proteins from human bloodstains has been compared with that of water. Ammonia was shown to be a better extractant of protein than water and this allows the species identification of human bloodstains up to four years' old using conventional electrophoretic techniques.

Ammonia↗
PubMed1976

Species identification of blood meals from Culex tarsalis that had fed on passeriform birds.

Blood-engorged Culex tarsalis (4,209) collected during 1960 to 1965 in Kern County, California and previously shown to have fed on passeriform birds by the precipitin test were further tested by the more sensitive passive hemagglutination inhibition test (PHI). It was shown that these mosquitoes fed principally on House Finches and House Sparrows, the most common passeriform birds found in the collection areas. These data demonstrate the usefulness of the PHI test for the identification of arthropod blood meals from closely related species.

Animals↗
PubMed1978

Species identification of coagulase-negative staphylococci from urinary tract isolates.

A new scheme for identification of coagulase-negative staphylococci was applied to 138 consecutive urinary isolates of coagulase-negative staphylococci. The most common species were Staphylococcus epidermidis (53%), S. hominis (12%), and S. haemolyticus (10%). S. saprophyticus comprised only 5%. The disk method for antibiotic susceptibility for all species grouped together disclosed resistance most commonly to penicillin (35%), tetracycline (33%), methicillin (27%), and sulfonamide (24%). This pattern was also seen specifically with S. epidermidis. Further studies are needed to determine the incidence of species-specific antibiotic resistance and species-specific infection by site. This may be of particular interest in those patients with nosocomial infections due to coagulase-negative staphylococci.

Anti-Bacterial Agents↗
PubMed1977

Species identification and genome mapping of cytoplasmic adenovirus type 2 RNAs synthesized late in infection.

Adenovirus type 2 cytoplasmic RNAs synthesized late in productive infection were resolved by electrophoresis on formamide gels. Regions of the adenovirus 2 genome specifying RNAs of distinct size were determined by hybridization to specific DNA fragments generated by cleavage with endo R.EcoRI and endo R.SmaI. From these studies 13 distinct viral RNA species were identified. A 26S to 28S size class and a 21S to 23S size class were each found to consist of four distinct RNA species. Three RNA species were identified in a 16S to 18S size class, and a fourth size class, 11S to 13S, was resolved into two components. The SmaI-D region (0.38 to 0.51 on the unit genome) and the EcoRI-F, D region (0.70 to 0.83) of the genome were found to code for multiple transcripts. Three RNAs (28S, 22S, and 18S) are specified by SmaI-D, and four components, 28S, 22S, 18S, and 16S, are encoded by EcoRI-F,D. The RNA represented by each set of multiple transcripts exceeds the coding capacity of the respective region, and the species within each set of RNAs appear to contain common sequences. The relationship between the cytoplasmic RNA species synthesized at late times and early cytoplasmic RNAs was determined by hybridization-inhibition experiments. The multiple transcripts encoded by the EcoRI-D fragment were found to contain sequences that are present in early cytoplasmic RNA. These studies enabled preparation of a map which accounts for transcription of approximately 67% of the r strand of the adenovirus 2 genome.

Adenoviruses, Human↗
PubMed1977

[Experiences with the API 20A system in routine species identification of anaerobes (author's transl)].

The API 20A System was tested in three modifications: a) The microtubes were inoculated with the API anaerobe basal medium, filled up completely with sterile mineral oil and incubated aerobically. b) The test strips were inoculated with the basal medium and incubated in an anaerobic chamber. c) The strips were inoculated with a modified Viande-Levure medium containing Tween 80, vitamin K3 and hemin. The microtubes were covered with sterile mineral oil and incubated in an anaerobic chamber. Each procedure was compared with the conventional method (PRAS) of the Virginia Polytechnic Institute. The overall agreement between the three modifications of the API System and the conventional method was 83.2, 91.7, and 98.5% related to the number of tests performed. The advantage of the modified medium was also demonstrated by measuring the growth rate of some anaerobes in thioglycolate broth, API basal medium and VL-medium, modified as mentioned above, nephelometrically. So the micromethod is more accurate and reliable when inoculated with an improved medium.

Anaerobiosis↗
PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗
PubMed2026

Comparative evaluation of molecular technologies for the identification of prevalent non-tuberculous mycobacteria in pulmonary infections: a systematic review and meta-analysis.

BACKGROUND: The increasing prevalence of non-tuberculous mycobacteria pulmonary disease (NTM PD) is a burden to public health. Successful management of NTM PD critically depends on accurate species identification and reliable drug susceptibility testing to guide appropriate antibiotic therapy. Emerging molecular technologies offer rapid diagnostic solutions compared to conventional methods, but their performance varies. This study aims to provide a comprehensive evaluation of current molecular techniques for NTM identification and to present a global antibiotic resistance profile. METHODS: A systematic literature search was conducted in PubMed and Web of Science for studies published between 2005 and 2024. Studies applying molecular methods for NTM identification and resistance detection in humans were included. Data on study characteristics, diagnostic methods, sample types, sample sizes, identification sensitivity, and drug susceptibility results were extracted. Meta-analysis was performed using R with the meta4diag package. The quality of included studies was assessed using the QUADAS-2 tool. RESULTS: The analysis included 49 studies on NTM identification and 33 studies on antibiotic resistance. For species identification, all evaluated molecular technologies (MALDI-TOF MS, PCR-based methods, Sequencing, DNA chip, and DNA strip) demonstrated high pooled sensitivities (>0.92). Subgroup analysis revealed that sample type significantly affected performance for MALDI-TOF MS. Preliminary analysis of antibiotic resistance rates revealed varying patterns. For slowly growing mycobacteria, a significantly high Ethambutol resistance rate was observed in M. avium (69.20%). Among rapidly growing mycobacteria, resistance to Imipenem was notable (54.22%), and Clarithromycin resistance varied significantly within the Mycobacterium abscessus complex. CONCLUSION: Emerging molecular technologies have revolutionized the methodology for NTM identification with excellent performance. However, their performance can be influenced by sample type, particularly for MALDI-TOF MS. The alarming and heterogeneous antibiotic resistance patterns also highlight the critical need for rapid and accurate species identification and drug susceptibility testing to inform effective therapeutic strategies. Key messagesMolecular technologies demonstrate high accuracy for NTM identification.Antibiotic resistance is a serious concern with variations among NTM species and subspecies.Rapid and accurate species identification and drug susceptibility testing are crucial for guiding effective clinical management of NTM PD.

Humans↗